Daily Papers

Developing robust representations of chemical structures that enable models to learn topological inductive biases is challenging. In this manuscript, we present a representation of atomistic systems. We begin by proving that our representation satisfies all structural, geometric, efficiency, and generalizability constraints. Afterward, we provide a general algorithm to encode any atomistic system. Finally, we report performance comparable to state-of-the-art methods on numerous tasks. We open-source all code and datasets. The code and data are available at https://github.com/rahulkhorana/PolyatomicComplexes.

Understanding and mapping a new environment are core abilities of any autonomously navigating agent. While classical robotics usually estimates maps in a stand-alone manner with SLAM variants, which maintain a topological or metric representation, end-to-end learning of navigation keeps some form of memory in a neural network. Networks are typically imbued with inductive biases, which can range from vectorial representations to birds-eye metric tensors or topological structures. In this work, we propose to structure neural networks with two neural implicit representations, which are learned dynamically during each episode and map the content of the scene: (i) the Semantic Finder predicts the position of a previously seen queried object; (ii) the Occupancy and Exploration Implicit Representation encapsulates information about explored area and obstacles, and is queried with a novel global read mechanism which directly maps from function space to a usable embedding space. Both representations are leveraged by an agent trained with Reinforcement Learning (RL) and learned online during each episode. We evaluate the agent on Multi-Object Navigation and show the high impact of using neural implicit representations as a memory source.

Much research in machine learning involves finding appropriate inductive biases (e.g. convolutional neural networks, momentum-based optimizers, transformers) to promote generalization on tasks. However, quantification of the amount of inductive bias associated with these architectures and hyperparameters has been limited. We propose a novel method for efficiently computing the inductive bias required for generalization on a task with a fixed training data budget; formally, this corresponds to the amount of information required to specify well-generalizing models within a specific hypothesis space of models. Our approach involves modeling the loss distribution of random hypotheses drawn from a hypothesis space to estimate the required inductive bias for a task relative to these hypotheses. Unlike prior work, our method provides a direct estimate of inductive bias without using bounds and is applicable to diverse hypothesis spaces. Moreover, we derive approximation error bounds for our estimation approach in terms of the number of sampled hypotheses. Consistent with prior results, our empirical results demonstrate that higher dimensional tasks require greater inductive bias. We show that relative to other expressive model classes, neural networks as a model class encode large amounts of inductive bias. Furthermore, our measure quantifies the relative difference in inductive bias between different neural network architectures. Our proposed inductive bias metric provides an information-theoretic interpretation of the benefits of specific model architectures for certain tasks and provides a quantitative guide to developing tasks requiring greater inductive bias, thereby encouraging the development of more powerful inductive biases.

Autoencoders have been proposed as a powerful tool for model-independent anomaly detection in high-energy physics. The operating principle is that events which do not belong to the space of training data will be reconstructed poorly, thus flagging them as anomalies. We point out that in a variety of examples of interest, the connection between large reconstruction error and anomalies is not so clear. In particular, for data sets with nontrivial topology, there will always be points that erroneously seem anomalous due to global issues. Conversely, neural networks typically have an inductive bias or prior to locally interpolate such that undersampled or rare events may be reconstructed with small error, despite actually being the desired anomalies. Taken together, these facts are in tension with the simple picture of the autoencoder as an anomaly detector. Using a series of illustrative low-dimensional examples, we show explicitly how the intrinsic and extrinsic topology of the dataset affects the behavior of an autoencoder and how this topology is manifested in the latent space representation during training. We ground this analysis in the discussion of a mock "bump hunt" in which the autoencoder fails to identify an anomalous "signal" for reasons tied to the intrinsic topology of n-particle phase space.

Our understanding of the generalization capabilities of neural networks (NNs) is still incomplete. Prevailing explanations are based on implicit biases of gradient descent (GD) but they cannot account for the capabilities of models from gradient-free methods nor the simplicity bias recently observed in untrained networks. This paper seeks other sources of generalization in NNs. Findings. To understand the inductive biases provided by architectures independently from GD, we examine untrained, random-weight networks. Even simple MLPs show strong inductive biases: uniform sampling in weight space yields a very biased distribution of functions in terms of complexity. But unlike common wisdom, NNs do not have an inherent "simplicity bias". This property depends on components such as ReLUs, residual connections, and layer normalizations. Alternative architectures can be built with a bias for any level of complexity. Transformers also inherit all these properties from their building blocks. Implications. We provide a fresh explanation for the success of deep learning independent from gradient-based training. It points at promising avenues for controlling the solutions implemented by trained models.

Representation learning, and interpreting learned representations, are key areas of focus in machine learning and neuroscience. Both fields generally use representations as a means to understand or improve a system's computations. In this work, however, we explore surprising dissociations between representation and computation that may pose challenges for such efforts. We create datasets in which we attempt to match the computational role that different features play, while manipulating other properties of the features or the data. We train various deep learning architectures to compute these multiple abstract features about their inputs. We find that their learned feature representations are systematically biased towards representing some features more strongly than others, depending upon extraneous properties such as feature complexity, the order in which features are learned, and the distribution of features over the inputs. For example, features that are simpler to compute or learned first tend to be represented more strongly and densely than features that are more complex or learned later, even if all features are learned equally well. We also explore how these biases are affected by architectures, optimizers, and training regimes (e.g., in transformers, features decoded earlier in the output sequence also tend to be represented more strongly). Our results help to characterize the inductive biases of gradient-based representation learning. These results also highlight a key challenge for interpretability - or for comparing the representations of models and brains - disentangling extraneous biases from the computationally important aspects of a system's internal representations.

The learnability of different neural architectures can be characterized directly by computable measures of data complexity. In this paper, we reframe the problem of architecture selection as understanding how data determines the most expressive and generalizable architectures suited to that data, beyond inductive bias. After suggesting algebraic topology as a measure for data complexity, we show that the power of a network to express the topological complexity of a dataset in its decision region is a strictly limiting factor in its ability to generalize. We then provide the first empirical characterization of the topological capacity of neural networks. Our empirical analysis shows that at every level of dataset complexity, neural networks exhibit topological phase transitions. This observation allowed us to connect existing theory to empirically driven conjectures on the choice of architectures for fully-connected neural networks.

Message Passing Neural Networks (MPNNs) are instances of Graph Neural Networks that leverage the graph to send messages over the edges. This inductive bias leads to a phenomenon known as over-squashing, where a node feature is insensitive to information contained at distant nodes. Despite recent methods introduced to mitigate this issue, an understanding of the causes for over-squashing and of possible solutions are lacking. In this theoretical work, we prove that: (i) Neural network width can mitigate over-squashing, but at the cost of making the whole network more sensitive; (ii) Conversely, depth cannot help mitigate over-squashing: increasing the number of layers leads to over-squashing being dominated by vanishing gradients; (iii) The graph topology plays the greatest role, since over-squashing occurs between nodes at high commute (access) time. Our analysis provides a unified framework to study different recent methods introduced to cope with over-squashing and serves as a justification for a class of methods that fall under graph rewiring.

Foundation models are premised on the idea that sequence prediction can uncover deeper domain understanding, much like how Kepler's predictions of planetary motion later led to the discovery of Newtonian mechanics. However, evaluating whether these models truly capture deeper structure remains a challenge. We develop a technique for evaluating foundation models that examines how they adapt to synthetic datasets generated from some postulated world model. Our technique measures whether the foundation model's inductive bias aligns with the world model, and so we refer to it as an inductive bias probe. Across multiple domains, we find that foundation models can excel at their training tasks yet fail to develop inductive biases towards the underlying world model when adapted to new tasks. We particularly find that foundation models trained on orbital trajectories consistently fail to apply Newtonian mechanics when adapted to new physics tasks. Further analysis reveals that these models behave as if they develop task-specific heuristics that fail to generalize.

Strong inductive biases enable learning from little data and help generalization outside of the training distribution. Popular neural architectures such as Transformers lack strong structural inductive biases for seq2seq NLP tasks on their own. Consequently, they struggle with systematic generalization beyond the training distribution, e.g. with extrapolating to longer inputs, even when pre-trained on large amounts of text. We show how a structural inductive bias can be efficiently injected into a seq2seq model by pre-training it to simulate structural transformations on synthetic data. Specifically, we inject an inductive bias towards Finite State Transducers (FSTs) into a Transformer by pre-training it to simulate FSTs given their descriptions. Our experiments show that our method imparts the desired inductive bias, resulting in improved systematic generalization and better few-shot learning for FST-like tasks. Our analysis shows that fine-tuned models accurately capture the state dynamics of the unseen underlying FSTs, suggesting that the simulation process is internalized by the fine-tuned model.

Graph-based deep learning methods have become popular tools to process collections of correlated time series. Differently from traditional multivariate forecasting methods, neural graph-based predictors take advantage of pairwise relationships by conditioning forecasts on a (possibly dynamic) graph spanning the time series collection. The conditioning can take the form of an architectural inductive bias on the neural forecasting architecture, resulting in a family of deep learning models called spatiotemporal graph neural networks. Such relational inductive biases enable the training of global forecasting models on large time-series collections, while at the same time localizing predictions w.r.t. each element in the set (i.e., graph nodes) by accounting for local correlations among them (i.e., graph edges). Indeed, recent theoretical and practical advances in graph neural networks and deep learning for time series forecasting make the adoption of such processing frameworks appealing and timely. However, most of the studies in the literature focus on proposing variations of existing neural architectures by taking advantage of modern deep learning practices, while foundational and methodological aspects have not been subject to systematic investigation. To fill the gap, this paper aims to introduce a comprehensive methodological framework that formalizes the forecasting problem and provides design principles for graph-based predictive models and methods to assess their performance. At the same time, together with an overview of the field, we provide design guidelines, recommendations, and best practices, as well as an in-depth discussion of open challenges and future research directions.

In Decentralized Multi-Agent Reinforcement Learning (MARL), the development of Emergent Communication has long been constrained by the ``Joint Exploration Dilemma'', leading agents to fall into a ``Communication Vacuum Equilibrium'' . Traditional methods address this by introducing inductive biases to facilitate communication emergence . This study fundamentally questions whether such artificial inductive biases are, in fact, over-engineering. Through experiments with the ``AI Mother Tongue'' (AIM) framework, based on a Vector Quantized Variational Autoencoder (VQ-VAE), we demonstrate that when agents possess an endogenous symbol system, their neural representations naturally exhibit spontaneous semantic compression and Nash equilibrium-driven semantic convergence, achieving effective symbolic communication without external inductive biases. This aligns with recent neuroscience findings suggesting that the human brain does not directly use human language for internal thought , and resonates with research on ``soft thinking'' capabilities in Large Language Models (LLMs) . Compared to traditional explicit communication methods, AIM demonstrates stronger generality and efficiency. The interpretable analysis toolkit developed in this study confirms that symbol usage exhibits a significant power-law distribution, leading to three major theoretical insights: the ``Neural Communication Hypothesis'', the ``Tool-First Principle'', and the ``Semantic Interpretability Paradigm''. Future research will explore the integration of Hierarchical Quantized Variational Autoencoders (HQ-VAE) to enhance AIM's complex expressive capabilities and investigate the potential for ``Reinforcement Learning (RL) Low-Level Pre-training''. This discovery offers new avenues for bridging symbolism and connectionism.

The topology of the hyperlink graph among pages expressing different opinions may influence the exposure of readers to diverse content. Structural bias may trap a reader in a polarized bubble with no access to other opinions. We model readers' behavior as random walks. A node is in a polarized bubble if the expected length of a random walk from it to a page of different opinion is large. The structural bias of a graph is the sum of the radii of highly-polarized bubbles. We study the problem of decreasing the structural bias through edge insertions. Healing all nodes with high polarized bubble radius is hard to approximate within a logarithmic factor, so we focus on finding the best k edges to insert to maximally reduce the structural bias. We present RePBubLik, an algorithm that leverages a variant of the random walk closeness centrality to select the edges to insert. RePBubLik obtains, under mild conditions, a constant-factor approximation. It reduces the structural bias faster than existing edge-recommendation methods, including some designed to reduce the polarization of a graph.

The inductive bias of a graph neural network (GNN) is largely encoded in its specified graph. Latent graph inference relies on latent geometric representations to dynamically rewire or infer a GNN's graph to maximize the GNN's predictive downstream performance, but it lacks solid theoretical foundations in terms of embedding-based representation guarantees. This paper addresses this issue by introducing a trainable deep learning architecture, coined neural snowflake, that can adaptively implement fractal-like metrics on R^d. We prove that any given finite weights graph can be isometrically embedded by a standard MLP encoder. Furthermore, when the latent graph can be represented in the feature space of a sufficiently regular kernel, we show that the combined neural snowflake and MLP encoder do not succumb to the curse of dimensionality by using only a low-degree polynomial number of parameters in the number of nodes. This implementation enables a low-dimensional isometric embedding of the latent graph. We conduct synthetic experiments to demonstrate the superior metric learning capabilities of neural snowflakes when compared to more familiar spaces like Euclidean space. Additionally, we carry out latent graph inference experiments on graph benchmarks. Consistently, the neural snowflake model achieves predictive performance that either matches or surpasses that of the state-of-the-art latent graph inference models. Importantly, this performance improvement is achieved without requiring random search for optimal latent geometry. Instead, the neural snowflake model achieves this enhancement in a differentiable manner.

The initial state of neural networks plays a central role in conditioning the subsequent training dynamics. In the context of classification problems, we provide a theoretical analysis demonstrating that the structure of a neural network can condition the model to assign all predictions to the same class, even before the beginning of training, and in the absence of explicit biases. We show that the presence of this phenomenon, which we call "Initial Guessing Bias" (IGB), depends on architectural choices such as activation functions, max-pooling layers, and network depth. Our analysis of IGB has practical consequences, in that it guides architecture selection and initialization. We also highlight theoretical consequences, such as the breakdown of node-permutation symmetry, the violation of self-averaging, the validity of some mean-field approximations, and the non-trivial differences arising with depth.

We explore the use of topological data analysis (TDA) combined with machine learning for discriminating standard model backgrounds from the invisible decay of the Z^prime boson associated with monophoton emission at a 3 TeV muon collider. Reconstructed events are mapped into a six-dimensional kinematic space and aggregated into bags of events, from which persistent homology is used to extract Betti number distributions. Within the Multiple Instance Learning paradigm, classifiers trained on these topological descriptors demonstrate significantly improved classification accuracy compared to the conventional ML approaches based on event-wise kinematic inputs. We also draw exclusion contours at 95\% CL in the (m_{Z^prime}, m_chi) parameter space, highlighting the potential of topological features to extend the discovery reach of future collider experiments.

The measure of a machine learning algorithm is the difficulty of the tasks it can perform, and sufficiently difficult tasks are critical drivers of strong machine learning models. However, quantifying the generalization difficulty of machine learning benchmarks has remained challenging. We propose what is to our knowledge the first model-agnostic measure of the inherent generalization difficulty of tasks. Our inductive bias complexity measure quantifies the total information required to generalize well on a task minus the information provided by the data. It does so by measuring the fractional volume occupied by hypotheses that generalize on a task given that they fit the training data. It scales exponentially with the intrinsic dimensionality of the space over which the model must generalize but only polynomially in resolution per dimension, showing that tasks which require generalizing over many dimensions are drastically more difficult than tasks involving more detail in fewer dimensions. Our measure can be applied to compute and compare supervised learning, reinforcement learning and meta-learning generalization difficulties against each other. We show that applied empirically, it formally quantifies intuitively expected trends, e.g. that in terms of required inductive bias, MNIST < CIFAR10 < Imagenet and fully observable Markov decision processes (MDPs) < partially observable MDPs. Further, we show that classification of complex images < few-shot meta-learning with simple images. Our measure provides a quantitative metric to guide the construction of more complex tasks requiring greater inductive bias, and thereby encourages the development of more sophisticated architectures and learning algorithms with more powerful generalization capabilities.

The inference of topological principles is a key problem in structured reconstruction. We observe that wrongly predicted topological relationships are often incurred by the lack of holistic geometry clues in low-level features. Inspired by the fact that massive signals can be compactly described with frequency analysis, we experimentally explore the efficiency and tendency of learning structure geometry in the frequency domain. Accordingly, we propose a frequency-domain feature learning strategy (F-Learn) to fuse scattered geometric fragments holistically for topology-intact structure reasoning. Benefiting from the parsimonious design, the F-Learn strategy can be easily deployed into a deep reconstructor with a lightweight model modification. Experiments demonstrate that the F-Learn strategy can effectively introduce structure awareness into geometric primitive detection and topology inference, bringing significant performance improvement to final structured reconstruction. Code and pre-trained models are available at https://github.com/Geo-Tell/F-Learn.

No free lunch theorems for supervised learning state that no learner can solve all problems or that all learners achieve exactly the same accuracy on average over a uniform distribution on learning problems. Accordingly, these theorems are often referenced in support of the notion that individual problems require specially tailored inductive biases. While virtually all uniformly sampled datasets have high complexity, real-world problems disproportionately generate low-complexity data, and we argue that neural network models share this same preference, formalized using Kolmogorov complexity. Notably, we show that architectures designed for a particular domain, such as computer vision, can compress datasets on a variety of seemingly unrelated domains. Our experiments show that pre-trained and even randomly initialized language models prefer to generate low-complexity sequences. Whereas no free lunch theorems seemingly indicate that individual problems require specialized learners, we explain how tasks that often require human intervention such as picking an appropriately sized model when labeled data is scarce or plentiful can be automated into a single learning algorithm. These observations justify the trend in deep learning of unifying seemingly disparate problems with an increasingly small set of machine learning models.

This paper considers the learning of logical (Boolean) functions with focus on the generalization on the unseen (GOTU) setting, a strong case of out-of-distribution generalization. This is motivated by the fact that the rich combinatorial nature of data in certain reasoning tasks (e.g., arithmetic/logic) makes representative data sampling challenging, and learning successfully under GOTU gives a first vignette of an 'extrapolating' or 'reasoning' learner. We then study how different network architectures trained by (S)GD perform under GOTU and provide both theoretical and experimental evidence that for a class of network models including instances of Transformers, random features models, and diagonal linear networks, a min-degree-interpolator (MDI) is learned on the unseen. We also provide evidence that other instances with larger learning rates or mean-field networks reach leaky MDIs. These findings lead to two implications: (1) we provide an explanation to the length generalization problem (e.g., Anil et al. 2022); (2) we introduce a curriculum learning algorithm called Degree-Curriculum that learns monomials more efficiently by incrementing supports.

Neural networks transform high-dimensional data into compact, structured representations, often modeled as elements of a lower dimensional latent space. In this paper, we present an alternative interpretation of neural models as dynamical systems acting on the latent manifold. Specifically, we show that autoencoder models implicitly define a latent vector field on the manifold, derived by iteratively applying the encoding-decoding map, without any additional training. We observe that standard training procedures introduce inductive biases that lead to the emergence of attractor points within this vector field. Drawing on this insight, we propose to leverage the vector field as a representation for the network, providing a novel tool to analyze the properties of the model and the data. This representation enables to: (i) analyze the generalization and memorization regimes of neural models, even throughout training; (ii) extract prior knowledge encoded in the network's parameters from the attractors, without requiring any input data; (iii) identify out-of-distribution samples from their trajectories in the vector field. We further validate our approach on vision foundation models, showcasing the applicability and effectiveness of our method in real-world scenarios.

In this work we revisit the most fundamental building block in deep learning, the multi-layer perceptron (MLP), and study the limits of its performance on vision tasks. Empirical insights into MLPs are important for multiple reasons. (1) Given the recent narrative "less inductive bias is better", popularized due to transformers eclipsing convolutional models, it is natural to explore the limits of this hypothesis. To that end, MLPs offer an ideal test bed, being completely free of any inductive bias. (2) MLPs have almost exclusively been the main protagonist in the deep learning theory literature due to their mathematical simplicity, serving as a proxy to explain empirical phenomena observed for more complex architectures. Surprisingly, experimental datapoints for MLPs are very difficult to find in the literature, especially when coupled with large pre-training protocols. This discrepancy between practice and theory is worrying: Do MLPs reflect the empirical advances exhibited by practical models? Or do theorists need to rethink the role of MLPs as a proxy? We provide insights into both these aspects. We show that the performance of MLPs drastically improves with scale (93% on CIFAR10, 79% on CIFAR100, 69% on TinyImageNet), highlighting that lack of inductive bias can indeed be compensated. We observe that MLPs mimic the behaviour of their modern counterparts faithfully, with some components in the learning setting however surprisingly exhibiting stronger or unexpected behaviours. Due to their inherent computational efficiency, large pre-training experiments become more accessible for academic researchers. All of our experiments were run on a single GPU.

This book develops an effective theory approach to understanding deep neural networks of practical relevance. Beginning from a first-principles component-level picture of networks, we explain how to determine an accurate description of the output of trained networks by solving layer-to-layer iteration equations and nonlinear learning dynamics. A main result is that the predictions of networks are described by nearly-Gaussian distributions, with the depth-to-width aspect ratio of the network controlling the deviations from the infinite-width Gaussian description. We explain how these effectively-deep networks learn nontrivial representations from training and more broadly analyze the mechanism of representation learning for nonlinear models. From a nearly-kernel-methods perspective, we find that the dependence of such models' predictions on the underlying learning algorithm can be expressed in a simple and universal way. To obtain these results, we develop the notion of representation group flow (RG flow) to characterize the propagation of signals through the network. By tuning networks to criticality, we give a practical solution to the exploding and vanishing gradient problem. We further explain how RG flow leads to near-universal behavior and lets us categorize networks built from different activation functions into universality classes. Altogether, we show that the depth-to-width ratio governs the effective model complexity of the ensemble of trained networks. By using information-theoretic techniques, we estimate the optimal aspect ratio at which we expect the network to be practically most useful and show how residual connections can be used to push this scale to arbitrary depths. With these tools, we can learn in detail about the inductive bias of architectures, hyperparameters, and optimizers.

Transformers for graph data are increasingly widely studied and successful in numerous learning tasks. Graph inductive biases are crucial for Graph Transformers, and previous works incorporate them using message-passing modules and/or positional encodings. However, Graph Transformers that use message-passing inherit known issues of message-passing, and differ significantly from Transformers used in other domains, thus making transfer of research advances more difficult. On the other hand, Graph Transformers without message-passing often perform poorly on smaller datasets, where inductive biases are more crucial. To bridge this gap, we propose the Graph Inductive bias Transformer (GRIT) -- a new Graph Transformer that incorporates graph inductive biases without using message passing. GRIT is based on several architectural changes that are each theoretically and empirically justified, including: learned relative positional encodings initialized with random walk probabilities, a flexible attention mechanism that updates node and node-pair representations, and injection of degree information in each layer. We prove that GRIT is expressive -- it can express shortest path distances and various graph propagation matrices. GRIT achieves state-of-the-art empirical performance across a variety of graph datasets, thus showing the power that Graph Transformers without message-passing can deliver.

Is the lottery ticket phenomenon an idiosyncrasy of gradient-based training or does it generalize to evolutionary optimization? In this paper we establish the existence of highly sparse trainable initializations for evolution strategies (ES) and characterize qualitative differences compared to gradient descent (GD)-based sparse training. We introduce a novel signal-to-noise iterative pruning procedure, which incorporates loss curvature information into the network pruning step. This can enable the discovery of even sparser trainable network initializations when using black-box evolution as compared to GD-based optimization. Furthermore, we find that these initializations encode an inductive bias, which transfers across different ES, related tasks and even to GD-based training. Finally, we compare the local optima resulting from the different optimization paradigms and sparsity levels. In contrast to GD, ES explore diverse and flat local optima and do not preserve linear mode connectivity across sparsity levels and independent runs. The results highlight qualitative differences between evolution and gradient-based learning dynamics, which can be uncovered by the study of iterative pruning procedures.

Network embedding, which maps graphs to distributed representations, is a unified framework for various graph inference tasks. According to the topology properties (e.g., structural roles and community memberships of nodes) to be preserved, it can be categorized into the identity and position embedding. However, existing methods can only capture one type of property. Some approaches can support the inductive inference that generalizes the embedding model to new nodes or graphs but relies on the availability of attributes. Due to the complicated correlations between topology and attributes, it is unclear for some inductive methods which type of property they can capture. In this study, we explore a unified framework for the joint inductive inference of identity and position embeddings without attributes. An inductive random walk embedding (IRWE) method is proposed, which combines multiple attention units to handle the random walk on graph topology and simultaneously derives identity and position embeddings that are jointly optimized. In particular, we demonstrate that some random walk statistics can be informative features to characterize node identities and positions while supporting the inductive embedding inference. Experiments validate the superior performance of IRWE beyond various baselines for the transductive and inductive inference of identity and position embeddings.

Graph Neural Networks (GNNs) have shown great promise in learning node embeddings for link prediction (LP). While numerous studies aim to improve the overall LP performance of GNNs, none have explored its varying performance across different nodes and its underlying reasons. To this end, we aim to demystify which nodes will perform better from the perspective of their local topology. Despite the widespread belief that low-degree nodes exhibit poorer LP performance, our empirical findings provide nuances to this viewpoint and prompt us to propose a better metric, Topological Concentration (TC), based on the intersection of the local subgraph of each node with the ones of its neighbors. We empirically demonstrate that TC has a higher correlation with LP performance than other node-level topological metrics like degree and subgraph density, offering a better way to identify low-performing nodes than using cold-start. With TC, we discover a novel topological distribution shift issue in which newly joined neighbors of a node tend to become less interactive with that node's existing neighbors, compromising the generalizability of node embeddings for LP at testing time. To make the computation of TC scalable, We further propose Approximated Topological Concentration (ATC) and theoretically/empirically justify its efficacy in approximating TC and reducing the computation complexity. Given the positive correlation between node TC and its LP performance, we explore the potential of boosting LP performance via enhancing TC by re-weighting edges in the message-passing and discuss its effectiveness with limitations. Our code is publicly available at https://github.com/YuWVandy/Topo_LP_GNN.

A central question for neuroscience is how to characterize brain representations of perceptual and cognitive content. An ideal characterization should distinguish different functional regions with robustness to noise and idiosyncrasies of individual brains that do not correspond to computational differences. Previous studies have characterized brain representations by their representational geometry, which is defined by the representational dissimilarity matrix (RDM), a summary statistic that abstracts from the roles of individual neurons (or responses channels) and characterizes the discriminability of stimuli. Here we explore a further step of abstraction: from the geometry to the topology of brain representations. We propose topological representational similarity analysis (tRSA), an extension of representational similarity analysis (RSA) that uses a family of geo-topological summary statistics that generalizes the RDM to characterize the topology while de-emphasizing the geometry. We evaluate this new family of statistics in terms of the sensitivity and specificity for model selection using both simulations and functional MRI (fMRI) data. In the simulations, the ground truth is a data-generating layer representation in a neural network model and the models are the same and other layers in different model instances (trained from different random seeds). In fMRI, the ground truth is a visual area and the models are the same and other areas measured in different subjects. Results show that topology-sensitive characterizations of population codes are robust to noise and interindividual variability and maintain excellent sensitivity to the unique representational signatures of different neural network layers and brain regions.

We define the bicategory of Graph Convolutional Neural Networks GCNN_n for an arbitrary graph with n nodes. We show it can be factored through the already existing categorical constructions for deep learning called Para and Lens with the base category set to the CoKleisli category of the product comonad. We prove that there exists an injective-on-objects, faithful 2-functor GCNN_n to Para(CoKl(R^{n times n} times -)). We show that this construction allows us to treat the adjacency matrix of a GCNN as a global parameter instead of a a local, layer-wise one. This gives us a high-level categorical characterisation of a particular kind of inductive bias GCNNs possess. Lastly, we hypothesize about possible generalisations of GCNNs to general message-passing graph neural networks, connections to equivariant learning, and the (lack of) functoriality of activation functions.

In this paper we introduce a novel family of attributed graphs for the purpose of shape discrimination. Our graphs typically arise from variations on the Mapper graph construction, which is an approximation of the Reeb graph for point cloud data. Our attributions enrich these constructions with (persistent) homology in ways that are provably stable, thereby recording extra topological information that is typically lost in these graph constructions. We provide experiments which illustrate the use of these invariants for shape representation and classification. In particular, we obtain competitive shape classification results when using our topologically attributed graphs as inputs to a simple graph neural network classifier.

We propose a novel approach for preserving topological structures of the input space in latent representations of autoencoders. Using persistent homology, a technique from topological data analysis, we calculate topological signatures of both the input and latent space to derive a topological loss term. Under weak theoretical assumptions, we construct this loss in a differentiable manner, such that the encoding learns to retain multi-scale connectivity information. We show that our approach is theoretically well-founded and that it exhibits favourable latent representations on a synthetic manifold as well as on real-world image data sets, while preserving low reconstruction errors.

Geometric deep learning, i.e., designing neural networks to handle the ubiquitous geometric data such as point clouds and graphs, have achieved great successes in the last decade. One critical inductive bias is that the model can maintain invariance towards various transformations such as translation, rotation, and scaling. The existing graph neural network (GNN) approaches can only maintain permutation-invariance, failing to guarantee invariance with respect to other transformations. Besides GNNs, other works design sophisticated transformation-invariant layers, which are computationally expensive and difficult to be extended. To solve this problem, we revisit why the existing neural networks cannot maintain transformation invariance when handling geometric data. Our findings show that transformation-invariant and distance-preserving initial representations are sufficient to achieve transformation invariance rather than needing sophisticated neural layer designs. Motivated by these findings, we propose Transformation Invariant Neural Networks (TinvNN), a straightforward and general framework for geometric data. Specifically, we realize transformation-invariant and distance-preserving initial point representations by modifying multi-dimensional scaling before feeding the representations into neural networks. We prove that TinvNN can strictly guarantee transformation invariance, being general and flexible enough to be combined with the existing neural networks. Extensive experimental results on point cloud analysis and combinatorial optimization demonstrate the effectiveness and general applicability of our proposed method. Based on the experimental results, we advocate that TinvNN should be considered a new starting point and an essential baseline for further studies of transformation-invariant geometric deep learning.

How to interact with LLMs through instructions has been widely studied by researchers. However, previous studies have treated the emergence of instructions and the training of LLMs on task data as separate processes, overlooking the inherent unity between the two. This paper proposes a neural network framework, VaiBot, that integrates VAE and VIB, designed to uniformly model, learn, and infer both deduction and induction tasks under LLMs. Through experiments, we demonstrate that VaiBot performs on par with existing baseline methods in terms of deductive capabilities while significantly surpassing them in inductive capabilities. We also find that VaiBot can scale up using general instruction-following data and exhibits excellent one-shot induction abilities. We finally synergistically integrate the deductive and inductive processes of VaiBot. Through T-SNE dimensionality reduction, we observe that its inductive-deductive process significantly improves the distribution of training parameters, enabling it to outperform baseline methods in inductive reasoning tasks. The code and data for this paper can be found at https://anonymous.4open.science/r/VaiBot-021F.

It stands to reason that the amount and the quality of data is of key importance for setting up accurate AI-driven models. Among others, a fundamental aspect to consider is the bias introduced during sample selection in database generation. This is particularly relevant when a model is trained on a specialized dataset to predict a property of interest, and then applied to forecast the same property over samples having a completely different genesis. Indeed, the resulting biased model will likely produce unreliable predictions for many of those out-of-the-box samples. Neglecting such an aspect may hinder the AI-based discovery process, even when high quality, sufficiently large and highly reputable data sources are available. In this regard, with superconducting and thermoelectric materials as two prototypical case studies in the field of energy material discovery, we present and validate a new method (based on a classification strategy) capable of detecting, quantifying and circumventing the presence of cross-domain data bias.

The natural world is full of complex systems characterized by intricate relations between their components: from social interactions between individuals in a social network to electrostatic interactions between atoms in a protein. Topological Deep Learning (TDL) provides a comprehensive framework to process and extract knowledge from data associated with these systems, such as predicting the social community to which an individual belongs or predicting whether a protein can be a reasonable target for drug development. TDL has demonstrated theoretical and practical advantages that hold the promise of breaking ground in the applied sciences and beyond. However, the rapid growth of the TDL literature has also led to a lack of unification in notation and language across Topological Neural Network (TNN) architectures. This presents a real obstacle for building upon existing works and for deploying TNNs to new real-world problems. To address this issue, we provide an accessible introduction to TDL, and compare the recently published TNNs using a unified mathematical and graphical notation. Through an intuitive and critical review of the emerging field of TDL, we extract valuable insights into current challenges and exciting opportunities for future development.

We develop a general approach to distill symbolic representations of a learned deep model by introducing strong inductive biases. We focus on Graph Neural Networks (GNNs). The technique works as follows: we first encourage sparse latent representations when we train a GNN in a supervised setting, then we apply symbolic regression to components of the learned model to extract explicit physical relations. We find the correct known equations, including force laws and Hamiltonians, can be extracted from the neural network. We then apply our method to a non-trivial cosmology example-a detailed dark matter simulation-and discover a new analytic formula which can predict the concentration of dark matter from the mass distribution of nearby cosmic structures. The symbolic expressions extracted from the GNN using our technique also generalized to out-of-distribution data better than the GNN itself. Our approach offers alternative directions for interpreting neural networks and discovering novel physical principles from the representations they learn.

There often is a dilemma between ease of optimization and robust out-of-distribution (OoD) generalization. For instance, many OoD methods rely on penalty terms whose optimization is challenging. They are either too strong to optimize reliably or too weak to achieve their goals. We propose to initialize the networks with a rich representation containing a palette of potentially useful features, ready to be used by even simple models. On the one hand, a rich representation provides a good initialization for the optimizer. On the other hand, it also provides an inductive bias that helps OoD generalization. Such a representation is constructed with the Rich Feature Construction (RFC) algorithm, also called the Bonsai algorithm, which consists of a succession of training episodes. During discovery episodes, we craft a multi-objective optimization criterion and its associated datasets in a manner that prevents the network from using the features constructed in the previous iterations. During synthesis episodes, we use knowledge distillation to force the network to simultaneously represent all the previously discovered features. Initializing the networks with Bonsai representations consistently helps six OoD methods achieve top performance on ColoredMNIST benchmark. The same technique substantially outperforms comparable results on the Wilds Camelyon17 task, eliminates the high result variance that plagues other methods, and makes hyperparameter tuning and model selection more reliable.

A directed acyclic graph (DAG) provides valuable prior knowledge that is often discarded in regression tasks in machine learning. We show that the independences arising from the presence of collider structures in DAGs provide meaningful inductive biases, which constrain the regression hypothesis space and improve predictive performance. We introduce collider regression, a framework to incorporate probabilistic causal knowledge from a collider in a regression problem. When the hypothesis space is a reproducing kernel Hilbert space, we prove a strictly positive generalisation benefit under mild assumptions and provide closed-form estimators of the empirical risk minimiser. Experiments on synthetic and climate model data demonstrate performance gains of the proposed methodology.

This paper aims to understand how neural networks learn algorithmic reasoning by addressing two questions: How faithful are learned algorithms when they are effective, and why do neural networks fail to learn effective algorithms otherwise? To answer these questions, we use neural compilation, a technique that directly encodes a source algorithm into neural network parameters, enabling the network to compute the algorithm exactly. This enables comparison between compiled and conventionally learned parameters, intermediate vectors, and behaviors. This investigation is crucial for developing neural networks that robustly learn complexalgorithms from data. Our analysis focuses on graph neural networks (GNNs), which are naturally aligned with algorithmic reasoning tasks, specifically our choices of BFS, DFS, and Bellman-Ford, which cover the spectrum of effective, faithful, and ineffective learned algorithms. Commonly, learning algorithmic reasoning is framed as induction over synthetic data, where a parameterized model is trained on inputs, traces, and outputs produced by an underlying ground truth algorithm. In contrast, we introduce a neural compilation method for GNNs, which sets network parameters analytically, bypassing training. Focusing on GNNs leverages their alignment with algorithmic reasoning, extensive algorithmic induction literature, and the novel application of neural compilation to GNNs. Overall, this paper aims to characterize expressability-trainability gaps - a fundamental shortcoming in learning algorithmic reasoning. We hypothesize that inductive learning is most effective for parallel algorithms contained within the computational class NC.

Characteristic classes, which are abstract topological invariants associated with vector bundles, have become an important notion in modern physics with surprising real-world consequences. As a representative example, the incredible properties of topological insulators, which are insulators in their bulk but conductors on their surface, can be completely characterized by a specific characteristic class associated with their electronic band structure, the first Chern class. Given their importance to next generation computing and the computational challenge of calculating them using first-principles approaches, there is a need to develop machine learning approaches to predict the characteristic classes associated with a material system. To aid in this program we introduce the {Haldane bundle dataset}, which consists of synthetically generated complex line bundles on the 2-torus. We envision this dataset, which is not as challenging as noisy and sparsely measured real-world datasets but (as we show) still difficult for off-the-shelf architectures, to be a testing ground for architectures that incorporate the rich topological and geometric priors underlying characteristic classes.

The manifold hypothesis, which assumes that data lies on or close to an unknown manifold of low intrinsic dimension, is a staple of modern machine learning research. However, recent work has shown that real-world data exhibits distinct non-manifold structures, i.e. singularities, that can lead to erroneous findings. Detecting such singularities is therefore crucial as a precursor to interpolation and inference tasks. We address this issue by developing a topological framework that (i) quantifies the local intrinsic dimension, and (ii) yields a Euclidicity score for assessing the 'manifoldness' of a point along multiple scales. Our approach identifies singularities of complex spaces, while also capturing singular structures and local geometric complexity in image data.

TabPFN [Hollmann et al., 2023], a Transformer model pretrained to perform in-context learning on fresh tabular classification problems, was presented at the last ICLR conference. To better understand its behavior, we treat it as a black-box function approximator generator and observe its generated function approximations on a varied selection of training datasets. Exploring its learned inductive biases in this manner, we observe behavior that is at turns either brilliant or baffling. We conclude this post with thoughts on how these results might inform the development, evaluation, and application of prior-data fitted networks (PFNs) in the future.

This paper considers the Pointer Value Retrieval (PVR) benchmark introduced in [ZRKB21], where a 'reasoning' function acts on a string of digits to produce the label. More generally, the paper considers the learning of logical functions with gradient descent (GD) on neural networks. It is first shown that in order to learn logical functions with gradient descent on symmetric neural networks, the generalization error can be lower-bounded in terms of the noise-stability of the target function, supporting a conjecture made in [ZRKB21]. It is then shown that in the distribution shift setting, when the data withholding corresponds to freezing a single feature (referred to as canonical holdout), the generalization error of gradient descent admits a tight characterization in terms of the Boolean influence for several relevant architectures. This is shown on linear models and supported experimentally on other models such as MLPs and Transformers. In particular, this puts forward the hypothesis that for such architectures and for learning logical functions such as PVR functions, GD tends to have an implicit bias towards low-degree representations, which in turn gives the Boolean influence for the generalization error under quadratic loss.

We present TopoMortar, a brick wall dataset that is the first dataset specifically designed to evaluate topology-focused image segmentation methods, such as topology loss functions. TopoMortar enables to investigate in two ways whether methods incorporate prior topological knowledge. First, by eliminating challenges seen in real-world data, such as small training set, noisy labels, and out-of-distribution test-set images, that, as we show, impact the effectiveness of topology losses. Second, by allowing to assess in the same dataset topology accuracy across dataset challenges, isolating dataset-related effects from the effect of incorporating prior topological knowledge. In these two experiments, it is deliberately difficult to improve topology accuracy without actually using topology information, thus, permitting to attribute an improvement in topology accuracy to the incorporation of prior topological knowledge. To this end, TopoMortar includes three types of labels (accurate, noisy, pseudo-labels), two fixed training sets (large and small), and in-distribution and out-of-distribution test-set images. We compared eight loss functions on TopoMortar, and we found that clDice achieved the most topologically accurate segmentations, Skeleton Recall loss performed best particularly with noisy labels, and the relative advantageousness of the other loss functions depended on the experimental setting. Additionally, we show that simple methods, such as data augmentation and self-distillation, can elevate Cross entropy Dice loss to surpass most topology loss functions, and that those simple methods can enhance topology loss functions as well. clDice and Skeleton Recall loss, both skeletonization-based loss functions, were also the fastest to train, making this type of loss function a promising research direction. TopoMortar and our code can be found at https://github.com/jmlipman/TopoMortar

Triggered by limitations of graph-based deep learning methods in terms of computational expressivity and model flexibility, recent years have seen a surge of interest in computational models that operate on higher-order topological domains such as hypergraphs and simplicial complexes. While the increased expressivity of these models can indeed lead to a better classification performance and a more faithful representation of the underlying system, the computational cost of these higher-order models can increase dramatically. To this end, we here explore a simplicial complex neural network learning architecture based on random walks and fast 1D convolutions (SCRaWl), in which we can adjust the increase in computational cost by varying the length and number of random walks considered while accounting for higher-order relationships. Importantly, due to the random walk-based design, the expressivity of the proposed architecture is provably incomparable to that of existing message-passing simplicial neural networks. We empirically evaluate SCRaWl on real-world datasets and show that it outperforms other simplicial neural networks.

Large language models (LLMs) exhibit cognitive biases -- systematic tendencies of irrational decision-making, similar to those seen in humans. Prior work has found that these biases vary across models and can be amplified by instruction tuning. However, it remains unclear if these differences in biases stem from pretraining, finetuning, or even random noise due to training stochasticity. We propose a two-step causal experimental approach to disentangle these factors. First, we finetune models multiple times using different random seeds to study how training randomness affects over 30 cognitive biases. Second, we introduce cross-tuning -- swapping instruction datasets between models to isolate bias sources. This swap uses datasets that led to different bias patterns, directly testing whether biases are dataset-dependent. Our findings reveal that while training randomness introduces some variability, biases are mainly shaped by pretraining: models with the same pretrained backbone exhibit more similar bias patterns than those sharing only finetuning data. These insights suggest that understanding biases in finetuned models requires considering their pretraining origins beyond finetuning effects. This perspective can guide future efforts to develop principled strategies for evaluating and mitigating bias in LLMs.

We study the implications of the modeling choice to use a graph, instead of a hypergraph, to represent real-world interconnected systems whose constituent relationships are of higher order by nature. Such a modeling choice typically involves an underlying projection process that maps the original hypergraph onto a graph, and is common in graph-based analysis. While hypergraph projection can potentially lead to loss of higher-order relations, there exists very limited studies on the consequences of doing so, as well as its remediation. This work fills this gap by doing two things: (1) we develop analysis based on graph and set theory, showing two ubiquitous patterns of hyperedges that are root to structural information loss in all hypergraph projections; we also quantify the combinatorial impossibility of recovering the lost higher-order structures if no extra help is provided; (2) we still seek to recover the lost higher-order structures in hypergraph projection, and in light of (1)'s findings we propose to relax the problem into a learning-based setting. Under this setting, we develop a learning-based hypergraph reconstruction method based on an important statistic of hyperedge distributions that we find. Our reconstruction method is evaluated on 8 real-world datasets under different settings, and exhibits consistently good performance. We also demonstrate benefits of the reconstructed hypergraphs via use cases of protein rankings and link predictions.

Model Predictive Controllers (MPC) require a good model for the controlled process. In this paper I infer inductive biases about a physical system. I use these biases to derive a new neural network architecture that can model this real system that has noise and inertia. The main inductive biases exploited here are: the delayed impact of some inputs on the system and the separability between the temporal component and how the inputs interact to produce the output of a system. The inputs are independently delayed using shifted convolutional kernels. Feature interactions are modelled using a fully connected network that does not have access to temporal information. The available data and the problem setup allow the usage of Self Supervised Learning in order to train the models. The baseline architecture is an Attention based Reccurent network adapted to work with MPC like inputs. The proposed networks are faster, better at exploiting larger data volumes and are almost as good as baseline networks in terms of prediction performance. The proposed architecture family called Delay can be used in a real scenario to control systems with delayed responses with respect to its controls or inputs. Ablation studies show that the presence of delay kernels are vital to obtain any learning in proposed architecture. Code and some experimental data are available online.

Topological Neural Networks (TNNs) incorporate higher-order relational information beyond pairwise interactions, enabling richer representations than Graph Neural Networks (GNNs). Concurrently, topological descriptors based on persistent homology (PH) are being increasingly employed to augment the GNNs. We investigate the benefits of integrating these two paradigms. Specifically, we introduce TopNets as a broad framework that subsumes and unifies various methods in the intersection of GNNs/TNNs and PH such as (generalizations of) RePHINE and TOGL. TopNets can also be readily adapted to handle (symmetries in) geometric complexes, extending the scope of TNNs and PH to spatial settings. Theoretically, we show that PH descriptors can provably enhance the expressivity of simplicial message-passing networks. Empirically, (continuous and E(n)-equivariant extensions of) TopNets achieve strong performance across diverse tasks, including antibody design, molecular dynamics simulation, and drug property prediction.

Random walks are widely used for mining networks due to the computational efficiency of computing them. For instance, graph representation learning learns a d-dimensional embedding space, so that the nodes that tend to co-occur on random walks (a proxy of being in the same network neighborhood) are close in the embedding space. Specific local network topology (i.e., structure) influences the co-occurrence of nodes on random walks, so random walks of limited length capture only partial topological information, hence diminishing the performance of downstream methods. We explicitly capture all topological neighborhood information and improve performance by introducing orbit adjacencies that quantify the adjacencies of two nodes as co-occurring on a given pair of graphlet orbits, which are symmetric positions on graphlets (small, connected, non-isomorphic, induced subgraphs of a large network). Importantly, we mathematically prove that random walks on up to k nodes capture only a subset of all the possible orbit adjacencies for up to k-node graphlets. Furthermore, we enable orbit adjacency-based analysis of networks by developing an efficient GRaphlet-orbit ADjacency COunter (GRADCO), which exhaustively computes all 28 orbit adjacency matrices for up to four-node graphlets. Note that four-node graphlets suffice, because real networks are usually small-world. In large networks on around 20,000 nodes, GRADCOcomputesthe28matricesinminutes. Onsixrealnetworksfromvarious domains, we compare the performance of node-label predictors obtained by using the network embeddings based on our orbit adjacencies to those based on random walks. We find that orbit adjacencies, which include those unseen by random walks, outperform random walk-based adjacencies, demonstrating the importance of the inclusion of the topological neighborhood information that is unseen by random walks.

Attention-based architectures have become ubiquitous in machine learning, yet our understanding of the reasons for their effectiveness remains limited. This work proposes a new way to understand self-attention networks: we show that their output can be decomposed into a sum of smaller terms, each involving the operation of a sequence of attention heads across layers. Using this decomposition, we prove that self-attention possesses a strong inductive bias towards "token uniformity". Specifically, without skip connections or multi-layer perceptrons (MLPs), the output converges doubly exponentially to a rank-1 matrix. On the other hand, skip connections and MLPs stop the output from degeneration. Our experiments verify the identified convergence phenomena on different variants of standard transformer architectures.

The goal of few-shot learning is to generalize and achieve high performance on new unseen learning tasks, where each task has only a limited number of examples available. Gradient-based meta-learning attempts to address this challenging task by learning how to learn new tasks by embedding inductive biases informed by prior learning experiences into the components of the learning algorithm. In this work, we build upon prior research and propose Neural Procedural Bias Meta-Learning (NPBML), a novel framework designed to meta-learn task-adaptive procedural biases. Our approach aims to consolidate recent advancements in meta-learned initializations, optimizers, and loss functions by learning them simultaneously and making them adapt to each individual task to maximize the strength of the learned inductive biases. This imbues each learning task with a unique set of procedural biases which is specifically designed and selected to attain strong learning performance in only a few gradient steps. The experimental results show that by meta-learning the procedural biases of a neural network, we can induce strong inductive biases towards a distribution of learning tasks, enabling robust learning performance across many well-established few-shot learning benchmarks.

The ability of deep neural networks to generalise well even when they interpolate their training data has been explained using various "simplicity biases". These theories postulate that neural networks avoid overfitting by first learning simple functions, say a linear classifier, before learning more complex, non-linear functions. Meanwhile, data structure is also recognised as a key ingredient for good generalisation, yet its role in simplicity biases is not yet understood. Here, we show that neural networks trained using stochastic gradient descent initially classify their inputs using lower-order input statistics, like mean and covariance, and exploit higher-order statistics only later during training. We first demonstrate this distributional simplicity bias (DSB) in a solvable model of a neural network trained on synthetic data. We empirically demonstrate DSB in a range of deep convolutional networks and visual transformers trained on CIFAR10, and show that it even holds in networks pre-trained on ImageNet. We discuss the relation of DSB to other simplicity biases and consider its implications for the principle of Gaussian universality in learning.

In theoretical neuroscience, recent work leverages deep learning tools to explore how some network attributes critically influence its learning dynamics. Notably, initial weight distributions with small (resp. large) variance may yield a rich (resp. lazy) regime, where significant (resp. minor) changes to network states and representation are observed over the course of learning. However, in biology, neural circuit connectivity could exhibit a low-rank structure and therefore differs markedly from the random initializations generally used for these studies. As such, here we investigate how the structure of the initial weights -- in particular their effective rank -- influences the network learning regime. Through both empirical and theoretical analyses, we discover that high-rank initializations typically yield smaller network changes indicative of lazier learning, a finding we also confirm with experimentally-driven initial connectivity in recurrent neural networks. Conversely, low-rank initialization biases learning towards richer learning. Importantly, however, as an exception to this rule, we find lazier learning can still occur with a low-rank initialization that aligns with task and data statistics. Our research highlights the pivotal role of initial weight structures in shaping learning regimes, with implications for metabolic costs of plasticity and risks of catastrophic forgetting.

This paper studies how to keep a vision backbone effective while removing token mixers in its basic building blocks. Token mixers, as self-attention for vision transformers (ViTs), are intended to perform information communication between different spatial tokens but suffer from considerable computational cost and latency. However, directly removing them will lead to an incomplete model structure prior, and thus brings a significant accuracy drop. To this end, we first develop an RepIdentityFormer base on the re-parameterizing idea, to study the token mixer free model architecture. And we then explore the improved learning paradigm to break the limitation of simple token mixer free backbone, and summarize the empirical practice into 5 guidelines. Equipped with the proposed optimization strategy, we are able to build an extremely simple vision backbone with encouraging performance, while enjoying the high efficiency during inference. Extensive experiments and ablative analysis also demonstrate that the inductive bias of network architecture, can be incorporated into simple network structure with appropriate optimization strategy. We hope this work can serve as a starting point for the exploration of optimization-driven efficient network design. Project page: https://techmonsterwang.github.io/RIFormer/.

Why do brains have inhibitory connections? Why do deep networks have negative weights? We propose an answer from the perspective of representation capacity. We believe representing functions is the primary role of both (i) the brain in natural intelligence, and (ii) deep networks in artificial intelligence. Our answer to why there are inhibitory/negative weights is: to learn more functions. We prove that, in the absence of negative weights, neural networks with non-decreasing activation functions are not universal approximators. While this may be an intuitive result to some, to the best of our knowledge, there is no formal theory, in either machine learning or neuroscience, that demonstrates why negative weights are crucial in the context of representation capacity. Further, we provide insights on the geometric properties of the representation space that non-negative deep networks cannot represent. We expect these insights will yield a deeper understanding of more sophisticated inductive priors imposed on the distribution of weights that lead to more efficient biological and machine learning.

We introduce a theoretical framework for differentiable surface evolution that allows discrete topology changes through the use of topological derivatives for variational optimization of image functionals. While prior methods for inverse rendering of geometry rely on silhouette gradients for topology changes, such signals are sparse. In contrast, our theory derives topological derivatives that relate the introduction of vanishing holes and phases to changes in image intensity. As a result, we enable differentiable shape perturbations in the form of hole or phase nucleation. We validate the proposed theory with optimization of closed curves in 2D and surfaces in 3D to lend insights into limitations of current methods and enable improved applications such as image vectorization, vector-graphics generation from text prompts, single-image reconstruction of shape ambigrams and multi-view 3D reconstruction.

Large language models (LLMs) have shown remarkable improvements in reasoning and many existing benchmarks have been addressed by models such as o1 and o3 either fully or partially. However, a majority of these benchmarks emphasize deductive reasoning, including mathematical and coding tasks in which rules such as mathematical axioms or programming syntax are clearly defined, based on which LLMs can plan and apply these rules to arrive at a solution. In contrast, inductive reasoning, where one infers the underlying rules from observed data, remains less explored. Such inductive processes lie at the heart of scientific discovery, as they enable researchers to extract general principles from empirical observations. To assess whether LLMs possess this capacity, we introduce InductionBench, a new benchmark designed to evaluate the inductive reasoning ability of LLMs. Our experimental findings reveal that even the most advanced models available struggle to master the simplest complexity classes within the subregular hierarchy of functions, highlighting a notable deficiency in current LLMs' inductive reasoning capabilities. Coda and data are available https://github.com/Wenyueh/inductive_reasoning_benchmark.

Modern large language models (LLMs) are inherently auto-regressive, requiring input to be serialized into flat sequences regardless of their structural dependencies. This serialization hinders the model's ability to leverage structural inductive biases, especially in tasks such as retrieval-augmented generation (RAG) and reasoning on data with native graph structures, where inter-segment dependencies are crucial. We introduce Graph-KV with the potential to overcome this limitation. Graph-KV leverages the KV-cache of text segments as condensed representations and governs their interaction through structural inductive biases. In this framework, 'target' segments selectively attend only to the KV-caches of their designated 'source' segments, rather than all preceding segments in a serialized sequence. This approach induces a graph-structured block mask, sparsifying attention and enabling a message-passing-like step within the LLM. Furthermore, strategically allocated positional encodings for source and target segments reduce positional bias and context window consumption. We evaluate Graph-KV across three scenarios: (1) seven RAG benchmarks spanning direct inference, multi-hop reasoning, and long-document understanding; (2) Arxiv-QA, a novel academic paper QA task with full-text scientific papers structured as citation ego-graphs; and (3) paper topic classification within a citation network. By effectively reducing positional bias and harnessing structural inductive biases, Graph-KV substantially outperforms baselines, including standard costly sequential encoding, across various settings. Code and the Graph-KV data are publicly available.

Several works have proposed Simplicity Bias (SB)---the tendency of standard training procedures such as Stochastic Gradient Descent (SGD) to find simple models---to justify why neural networks generalize well [Arpit et al. 2017, Nakkiran et al. 2019, Soudry et al. 2018]. However, the precise notion of simplicity remains vague. Furthermore, previous settings that use SB to theoretically justify why neural networks generalize well do not simultaneously capture the non-robustness of neural networks---a widely observed phenomenon in practice [Goodfellow et al. 2014, Jo and Bengio 2017]. We attempt to reconcile SB and the superior standard generalization of neural networks with the non-robustness observed in practice by designing datasets that (a) incorporate a precise notion of simplicity, (b) comprise multiple predictive features with varying levels of simplicity, and (c) capture the non-robustness of neural networks trained on real data. Through theory and empirics on these datasets, we make four observations: (i) SB of SGD and variants can be extreme: neural networks can exclusively rely on the simplest feature and remain invariant to all predictive complex features. (ii) The extreme aspect of SB could explain why seemingly benign distribution shifts and small adversarial perturbations significantly degrade model performance. (iii) Contrary to conventional wisdom, SB can also hurt generalization on the same data distribution, as SB persists even when the simplest feature has less predictive power than the more complex features. (iv) Common approaches to improve generalization and robustness---ensembles and adversarial training---can fail in mitigating SB and its pitfalls. Given the role of SB in training neural networks, we hope that the proposed datasets and methods serve as an effective testbed to evaluate novel algorithmic approaches aimed at avoiding the pitfalls of SB.

Previous literature offers limited clues on how to learn a periodic function using modern neural networks. We start with a study of the extrapolation properties of neural networks; we prove and demonstrate experimentally that the standard activations functions, such as ReLU, tanh, sigmoid, along with their variants, all fail to learn to extrapolate simple periodic functions. We hypothesize that this is due to their lack of a "periodic" inductive bias. As a fix of this problem, we propose a new activation, namely, x + sin^2(x), which achieves the desired periodic inductive bias to learn a periodic function while maintaining a favorable optimization property of the ReLU-based activations. Experimentally, we apply the proposed method to temperature and financial data prediction.

In disentangled representation learning, a model is asked to tease apart a dataset's underlying sources of variation and represent them independently of one another. Since the model is provided with no ground truth information about these sources, inductive biases take a paramount role in enabling disentanglement. In this work, we construct an inductive bias towards encoding to and decoding from an organized latent space. Concretely, we do this by (i) quantizing the latent space into discrete code vectors with a separate learnable scalar codebook per dimension and (ii) applying strong model regularization via an unusually high weight decay. Intuitively, the latent space design forces the encoder to combinatorially construct codes from a small number of distinct scalar values, which in turn enables the decoder to assign a consistent meaning to each value. Regularization then serves to drive the model towards this parsimonious strategy. We demonstrate the broad applicability of this approach by adding it to both basic data-reconstructing (vanilla autoencoder) and latent-reconstructing (InfoGAN) generative models. For reliable evaluation, we also propose InfoMEC, a new set of metrics for disentanglement that is cohesively grounded in information theory and fixes well-established shortcomings in previous metrics. Together with regularization, latent quantization dramatically improves the modularity and explicitness of learned representations on a representative suite of benchmark datasets. In particular, our quantized-latent autoencoder (QLAE) consistently outperforms strong methods from prior work in these key disentanglement properties without compromising data reconstruction.

In recent years, Graph Neural Networks (GNNs) have made significant advances in processing structured data. However, most of them primarily adopted a model-centric approach, which simplifies graphs by converting them into undirected formats and emphasizes model designs. This approach is inherently limited in real-world applications due to the unavoidable information loss in simple undirected graphs and the model optimization challenges that arise when exceeding the upper bounds of this sub-optimal data representational capacity. As a result, there has been a shift toward data-centric methods that prioritize improving graph quality and representation. Specifically, various types of graphs can be derived from naturally structured data, including heterogeneous graphs, hypergraphs, and directed graphs. Among these, directed graphs offer distinct advantages in topological systems by modeling causal relationships, and directed GNNs have been extensively studied in recent years. However, a comprehensive survey of this emerging topic is still lacking. Therefore, we aim to provide a comprehensive review of directed graph learning, with a particular focus on a data-centric perspective. Specifically, we first introduce a novel taxonomy for existing studies. Subsequently, we re-examine these methods from the data-centric perspective, with an emphasis on understanding and improving data representation. It demonstrates that a deep understanding of directed graphs and their quality plays a crucial role in model performance. Additionally, we explore the diverse applications of directed GNNs across 10+ domains, highlighting their broad applicability. Finally, we identify key opportunities and challenges within the field, offering insights that can guide future research and development in directed graph learning.

Pairwise clustering, in general, partitions a set of items via a known similarity function. In our treatment, clustering is modeled as a transductive prediction problem. Thus rather than beginning with a known similarity function, the function instead is hidden and the learner only receives a random sample consisting of a subset of the pairwise similarities. An additional set of pairwise side-information may be given to the learner, which then determines the inductive bias of our algorithms. We measure performance not based on the recovery of the hidden similarity function, but instead on how well we classify each item. We give tight bounds on the number of misclassifications. We provide two algorithms. The first algorithm SACA is a simple agglomerative clustering algorithm which runs in near linear time, and which serves as a baseline for our analyses. Whereas the second algorithm, RGCA, enables the incorporation of side-information which may lead to improved bounds at the cost of a longer running time.

A recent study has shown that large-scale visual datasets are very biased: they can be easily classified by modern neural networks. However, the concrete forms of bias among these datasets remain unclear. In this study, we propose a framework to identify the unique visual attributes distinguishing these datasets. Our approach applies various transformations to extract semantic, structural, boundary, color, and frequency information from datasets, and assess how much each type of information reflects their bias. We further decompose their semantic bias with object-level analysis, and leverage natural language methods to generate detailed, open-ended descriptions of each dataset's characteristics. Our work aims to help researchers understand the bias in existing large-scale pre-training datasets, and build more diverse and representative ones in the future. Our project page and code are available at http://boyazeng.github.io/understand_bias .

Complex prediction models such as deep learning are the output from fitting machine learning, neural networks, or AI models to a set of training data. These are now standard tools in science. A key challenge with the current generation of models is that they are highly parameterized, which makes describing and interpreting the prediction strategies difficult. We use topological data analysis to transform these complex prediction models into pictures representing a topological view. The result is a map of the predictions that enables inspection. The methods scale up to large datasets across different domains and enable us to detect labeling errors in training data, understand generalization in image classification, and inspect predictions of likely pathogenic mutations in the BRCA1 gene.

Deep neural networks (DNNs) trained for image denoising are able to generate high-quality samples with score-based reverse diffusion algorithms. These impressive capabilities seem to imply an escape from the curse of dimensionality, but recent reports of memorization of the training set raise the question of whether these networks are learning the "true" continuous density of the data. Here, we show that two DNNs trained on non-overlapping subsets of a dataset learn nearly the same score function, and thus the same density, when the number of training images is large enough. In this regime of strong generalization, diffusion-generated images are distinct from the training set, and are of high visual quality, suggesting that the inductive biases of the DNNs are well-aligned with the data density. We analyze the learned denoising functions and show that the inductive biases give rise to a shrinkage operation in a basis adapted to the underlying image. Examination of these bases reveals oscillating harmonic structures along contours and in homogeneous regions. We demonstrate that trained denoisers are inductively biased towards these geometry-adaptive harmonic bases since they arise not only when the network is trained on photographic images, but also when it is trained on image classes supported on low-dimensional manifolds for which the harmonic basis is suboptimal. Finally, we show that when trained on regular image classes for which the optimal basis is known to be geometry-adaptive and harmonic, the denoising performance of the networks is near-optimal.

A central objective in computer vision is to design models with appropriate 2-D inductive bias. Desiderata for 2D inductive bias include two-dimensional position awareness, dynamic spatial locality, and translation and permutation invariance. To address these goals, we leverage an expressive variation of the multidimensional State Space Model (SSM). Our approach introduces efficient parameterization, accelerated computation, and a suitable normalization scheme. Empirically, we observe that incorporating our layer at the beginning of each transformer block of Vision Transformers (ViT) significantly enhances performance for multiple ViT backbones and across datasets. The new layer is effective even with a negligible amount of additional parameters and inference time. Ablation studies and visualizations demonstrate that the layer has a strong 2-D inductive bias. For example, vision transformers equipped with our layer exhibit effective performance even without positional encoding

Inferring causal structure poses a combinatorial search problem that typically involves evaluating structures with a score or independence test. The resulting search is costly, and designing suitable scores or tests that capture prior knowledge is difficult. In this work, we propose to amortize causal structure learning. Rather than searching over structures, we train a variational inference model to directly predict the causal structure from observational or interventional data. This allows our inference model to acquire domain-specific inductive biases for causal discovery solely from data generated by a simulator, bypassing both the hand-engineering of suitable score functions and the search over graphs. The architecture of our inference model emulates permutation invariances that are crucial for statistical efficiency in structure learning, which facilitates generalization to significantly larger problem instances than seen during training. On synthetic data and semisynthetic gene expression data, our models exhibit robust generalization capabilities when subject to substantial distribution shifts and significantly outperform existing algorithms, especially in the challenging genomics domain. Our code and models are publicly available at: https://github.com/larslorch/avici.

We use tools from geometric statistics to analyze the usual estimation procedure of a template shape. This applies to shapes from landmarks, curves, surfaces, images etc. We demonstrate the asymptotic bias of the template shape estimation using the stratified geometry of the shape space. We give a Taylor expansion of the bias with respect to a parameter sigma describing the measurement error on the data. We propose two bootstrap procedures that quantify the bias and correct it, if needed. They are applicable for any type of shape data. We give a rule of thumb to provide intuition on whether the bias has to be corrected. This exhibits the parameters that control the bias' magnitude. We illustrate our results on simulated and real shape data.

Many recent methods for unsupervised or self-supervised representation learning train feature extractors by maximizing an estimate of the mutual information (MI) between different views of the data. This comes with several immediate problems: For example, MI is notoriously hard to estimate, and using it as an objective for representation learning may lead to highly entangled representations due to its invariance under arbitrary invertible transformations. Nevertheless, these methods have been repeatedly shown to excel in practice. In this paper we argue, and provide empirical evidence, that the success of these methods cannot be attributed to the properties of MI alone, and that they strongly depend on the inductive bias in both the choice of feature extractor architectures and the parametrization of the employed MI estimators. Finally, we establish a connection to deep metric learning and argue that this interpretation may be a plausible explanation for the success of the recently introduced methods.

The ability to derive underlying principles from a handful of observations and then generalize to novel situations -- known as inductive reasoning -- is central to human intelligence. Prior work suggests that language models (LMs) often fall short on inductive reasoning, despite achieving impressive success on research benchmarks. In this work, we conduct a systematic study of the inductive reasoning capabilities of LMs through iterative hypothesis refinement, a technique that more closely mirrors the human inductive process than standard input-output prompting. Iterative hypothesis refinement employs a three-step process: proposing, selecting, and refining hypotheses in the form of textual rules. By examining the intermediate rules, we observe that LMs are phenomenal hypothesis proposers (i.e., generating candidate rules), and when coupled with a (task-specific) symbolic interpreter that is able to systematically filter the proposed set of rules, this hybrid approach achieves strong results across inductive reasoning benchmarks that require inducing causal relations, language-like instructions, and symbolic concepts. However, they also behave as puzzling inductive reasoners, showing notable performance gaps between rule induction (i.e., identifying plausible rules) and rule application (i.e., applying proposed rules to instances), suggesting that LMs are proposing hypotheses without being able to actually apply the rules. Through empirical and human analyses, we further reveal several discrepancies between the inductive reasoning processes of LMs and humans, shedding light on both the potentials and limitations of using LMs in inductive reasoning tasks.

Graph Neural Networks (GNNs) with equivariant properties have emerged as powerful tools for modeling complex dynamics of multi-object physical systems. However, their generalization ability is limited by the inadequate consideration of physical inductive biases: (1) Existing studies overlook the continuity of transitions among system states, opting to employ several discrete transformation layers to learn the direct mapping between two adjacent states; (2) Most models only account for first-order velocity information, despite the fact that many physical systems are governed by second-order motion laws. To incorporate these inductive biases, we propose the Second-order Equivariant Graph Neural Ordinary Differential Equation (SEGNO). Specifically, we show how the second-order continuity can be incorporated into GNNs while maintaining the equivariant property. Furthermore, we offer theoretical insights into SEGNO, highlighting that it can learn a unique trajectory between adjacent states, which is crucial for model generalization. Additionally, we prove that the discrepancy between this learned trajectory of SEGNO and the true trajectory is bounded. Extensive experiments on complex dynamical systems including molecular dynamics and motion capture demonstrate that our model yields a significant improvement over the state-of-the-art baselines.

Dataset bias, where data points are skewed to certain concepts, is ubiquitous in machine learning datasets. Yet, systematically identifying these biases is challenging without costly, fine-grained attribute annotations. We present ConceptScope, a scalable and automated framework for analyzing visual datasets by discovering and quantifying human-interpretable concepts using Sparse Autoencoders trained on representations from vision foundation models. ConceptScope categorizes concepts into target, context, and bias types based on their semantic relevance and statistical correlation to class labels, enabling class-level dataset characterization, bias identification, and robustness evaluation through concept-based subgrouping. We validate that ConceptScope captures a wide range of visual concepts, including objects, textures, backgrounds, facial attributes, emotions, and actions, through comparisons with annotated datasets. Furthermore, we show that concept activations produce spatial attributions that align with semantically meaningful image regions. ConceptScope reliably detects known biases (e.g., background bias in Waterbirds) and uncovers previously unannotated ones (e.g, co-occurring objects in ImageNet), offering a practical tool for dataset auditing and model diagnostics.

The proliferation of machine learning models in critical decision making processes has underscored the need for bias discovery and mitigation strategies. Identifying the reasons behind a biased system is not straightforward, since in many occasions they are associated with hidden spurious correlations which are not easy to spot. Standard approaches rely on bias audits performed by analyzing model performance in pre-defined subgroups of data samples, usually characterized by common attributes like gender or ethnicity when it comes to people, or other specific attributes defining semantically coherent groups of images. However, it is not always possible to know a-priori the specific attributes defining the failure modes of visual recognition systems. Recent approaches propose to discover these groups by leveraging large vision language models, which enable the extraction of cross-modal embeddings and the generation of textual descriptions to characterize the subgroups where a certain model is underperforming. In this work, we argue that incorporating visual explanations (e.g. heatmaps generated via GradCAM or other approaches) can boost the performance of such bias discovery and mitigation frameworks. To this end, we introduce Visually Grounded Bias Discovery and Mitigation (ViG-Bias), a simple yet effective technique which can be integrated to a variety of existing frameworks to improve both, discovery and mitigation performance. Our comprehensive evaluation shows that incorporating visual explanations enhances existing techniques like DOMINO, FACTS and Bias-to-Text, across several challenging datasets, including CelebA, Waterbirds, and NICO++.

Implicit Neural Representations (INRs), as a versatile representation paradigm, have achieved success in various computer vision tasks. Due to the spectral bias of the vanilla multi-layer perceptrons (MLPs), existing methods focus on designing MLPs with sophisticated architectures or repurposing training techniques for highly accurate INRs. In this paper, we delve into the linear dynamics model of MLPs and theoretically identify the empirical Neural Tangent Kernel (eNTK) matrix as a reliable link between spectral bias and training dynamics. Based on this insight, we propose a practical Inductive Gradient Adjustment (IGA) method, which could purposefully improve the spectral bias via inductive generalization of eNTK-based gradient transformation matrix. Theoretical and empirical analyses validate impacts of IGA on spectral bias. Further, we evaluate our method on different INRs tasks with various INR architectures and compare to existing training techniques. The superior and consistent improvements clearly validate the advantage of our IGA. Armed with our gradient adjustment method, better INRs with more enhanced texture details and sharpened edges can be learned from data by tailored impacts on spectral bias.

Vision Transformers (ViT), when paired with large-scale pretraining, have shown remarkable performance across various computer vision tasks, primarily due to their weak inductive bias. However, while such weak inductive bias aids in pretraining scalability, this may hinder the effective adaptation of ViTs for visuo-motor control tasks as a result of the absence of control-centric inductive biases. Such absent inductive biases include spatial locality and translation equivariance bias which convolutions naturally offer. To this end, we introduce Convolution Injector (CoIn), an add-on module that injects convolutions which are rich in locality and equivariance biases into a pretrained ViT for effective adaptation in visuo-motor control. We evaluate CoIn with three distinct types of pretrained ViTs (CLIP, MVP, VC-1) across 12 varied control tasks within three separate domains (Adroit, MetaWorld, DMC), and demonstrate that CoIn consistently enhances control task performance across all experimented environments and models, validating the effectiveness of providing pretrained ViTs with control-centric biases.

In this paper, we propose REASON, a novel framework that enables the automatic discovery of both intra-level (i.e., within-network) and inter-level (i.e., across-network) causal relationships for root cause localization. REASON consists of Topological Causal Discovery and Individual Causal Discovery. The Topological Causal Discovery component aims to model the fault propagation in order to trace back to the root causes. To achieve this, we propose novel hierarchical graph neural networks to construct interdependent causal networks by modeling both intra-level and inter-level non-linear causal relations. Based on the learned interdependent causal networks, we then leverage random walks with restarts to model the network propagation of a system fault. The Individual Causal Discovery component focuses on capturing abrupt change patterns of a single system entity. This component examines the temporal patterns of each entity's metric data (i.e., time series), and estimates its likelihood of being a root cause based on the Extreme Value theory. Combining the topological and individual causal scores, the top K system entities are identified as root causes. Extensive experiments on three real-world datasets with case studies demonstrate the effectiveness and superiority of the proposed framework.

Graph neural networks (GNNs), in general, are built on the assumption of a static set of features characterizing each node in a graph. This assumption is often violated in practice. Existing methods partly address this issue through feature imputation. However, these techniques (i) assume uniformity of feature set across nodes, (ii) are transductive by nature, and (iii) fail to work when features are added or removed over time. In this work, we address these limitations through a novel GNN framework called GRAFENNE. GRAFENNE performs a novel allotropic transformation on the original graph, wherein the nodes and features are decoupled through a bipartite encoding. Through a carefully chosen message passing framework on the allotropic transformation, we make the model parameter size independent of the number of features and thereby inductive to both unseen nodes and features. We prove that GRAFENNE is at least as expressive as any of the existing message-passing GNNs in terms of Weisfeiler-Leman tests, and therefore, the additional inductivity to unseen features does not come at the cost of expressivity. In addition, as demonstrated over four real-world graphs, GRAFENNE empowers the underlying GNN with high empirical efficacy and the ability to learn in continual fashion over streaming feature sets.

We study the realizability of simplicial complexes with a given pair of integer sequences, representing the node degree distribution and the facet size distribution, respectively. While the s-uniform variant of the problem is NP-complete when s geq 3, we identify two populations of input sequences, most of which can be solved in polynomial time using a recursive algorithm that we contribute. Combining with a sampler for the simplicial configuration model [J.-G. Young et al., Phys. Rev. E 96, 032312 (2017)], we facilitate the efficient sampling of simplicial ensembles from arbitrary degree and size distributions. We find that, contrary to expectations based on dyadic networks, increasing the nodes' degrees reduces the number of loops in simplicial complexes. Our work unveils a fundamental constraint on the degree-size sequences and sheds light on further analysis of higher-order phenomena based on local structures.

Latent Graph Inference (LGI) relaxed the reliance of Graph Neural Networks (GNNs) on a given graph topology by dynamically learning it. However, most of LGI methods assume to have a (noisy, incomplete, improvable, ...) input graph to rewire and can solely learn regular graph topologies. In the wake of the success of Topological Deep Learning (TDL), we study Latent Topology Inference (LTI) for learning higher-order cell complexes (with sparse and not regular topology) describing multi-way interactions between data points. To this aim, we introduce the Differentiable Cell Complex Module (DCM), a novel learnable function that computes cell probabilities in the complex to improve the downstream task. We show how to integrate DCM with cell complex message passing networks layers and train it in a end-to-end fashion, thanks to a two-step inference procedure that avoids an exhaustive search across all possible cells in the input, thus maintaining scalability. Our model is tested on several homophilic and heterophilic graph datasets and it is shown to outperform other state-of-the-art techniques, offering significant improvements especially in cases where an input graph is not provided.

Deep graph learning has gained grand popularity over the past years due to its versatility and success in representing graph data across a wide range of domains. However, the pervasive issue of imbalanced graph data distributions, where certain parts exhibit disproportionally abundant data while others remain sparse, undermines the efficacy of conventional graph learning algorithms, leading to biased outcomes. To address this challenge, Imbalanced Graph Learning (IGL) has garnered substantial attention, enabling more balanced data distributions and better task performance. Despite the proliferation of IGL algorithms, the absence of consistent experimental protocols and fair performance comparisons pose a significant barrier to comprehending advancements in this field. To bridge this gap, we introduce IGL-Bench, a foundational comprehensive benchmark for imbalanced graph learning, embarking on 16 diverse graph datasets and 24 distinct IGL algorithms with uniform data processing and splitting strategies. Specifically, IGL-Bench systematically investigates state-of-the-art IGL algorithms in terms of effectiveness, robustness, and efficiency on node-level and graph-level tasks, with the scope of class-imbalance and topology-imbalance. Extensive experiments demonstrate the potential benefits of IGL algorithms on various imbalanced conditions, offering insights and opportunities in the IGL field. Further, we have developed an open-sourced and unified package to facilitate reproducible evaluation and inspire further innovative research, which is available at https://github.com/RingBDStack/IGL-Bench.

Language models are increasingly capable, yet still fail at a seemingly simple task of multi-digit multiplication. In this work, we study why, by reverse-engineering a model that successfully learns multiplication via implicit chain-of-thought, and report three findings: (1) Evidence of long-range structure: Logit attributions and linear probes indicate that the model encodes the necessary long-range dependencies for multi-digit multiplication. (2) Mechanism: the model encodes long-range dependencies using attention to construct a directed acyclic graph to ``cache'' and ``retrieve'' pairwise partial products. (3) Geometry: the model implements partial products in attention heads by forming Minkowski sums between pairs of digits, and digits are represented using a Fourier basis, both of which are intuitive and efficient representations that the standard fine-tuning model lacks. With these insights, we revisit the learning dynamics of standard fine-tuning and find that the model converges to a local optimum that lacks the required long-range dependencies. We further validate this understanding by introducing an auxiliary loss that predicts the ``running sum'' via a linear regression probe, which provides an inductive bias that enables the model to successfully learn multi-digit multiplication. In summary, by reverse-engineering the mechanisms of an implicit chain-of-thought model we uncover a pitfall for learning long-range dependencies in Transformers and provide an example of how the correct inductive bias can address this issue.

Bias in Large Language Models (LLMs) significantly undermines their reliability and fairness. We focus on a common form of bias: when two reference concepts in the model's concept space, such as sentiment polarities (e.g., "positive" and "negative"), are asymmetrically correlated with a third, target concept, such as a reviewing aspect, the model exhibits unintended bias. For instance, the understanding of "food" should not skew toward any particular sentiment. Existing bias evaluation methods assess behavioral differences of LLMs by constructing labeled data for different social groups and measuring model responses across them, a process that requires substantial human effort and captures only a limited set of social concepts. To overcome these limitations, we propose BiasLens, a test-set-free bias analysis framework based on the structure of the model's vector space. BiasLens combines Concept Activation Vectors (CAVs) with Sparse Autoencoders (SAEs) to extract interpretable concept representations, and quantifies bias by measuring the variation in representational similarity between the target concept and each of the reference concepts. Even without labeled data, BiasLens shows strong agreement with traditional bias evaluation metrics (Spearman correlation r > 0.85). Moreover, BiasLens reveals forms of bias that are difficult to detect using existing methods. For example, in simulated clinical scenarios, a patient's insurance status can cause the LLM to produce biased diagnostic assessments. Overall, BiasLens offers a scalable, interpretable, and efficient paradigm for bias discovery, paving the way for improving fairness and transparency in LLMs.

Many machine learning algorithms are trained and evaluated by splitting data from a single source into training and test sets. While such focus on in-distribution learning scenarios has led to interesting advancement, it has not been able to tell if models are relying on dataset biases as shortcuts for successful prediction (e.g., using snow cues for recognising snowmobiles), resulting in biased models that fail to generalise when the bias shifts to a different class. The cross-bias generalisation problem has been addressed by de-biasing training data through augmentation or re-sampling, which are often prohibitive due to the data collection cost (e.g., collecting images of a snowmobile on a desert) and the difficulty of quantifying or expressing biases in the first place. In this work, we propose a novel framework to train a de-biased representation by encouraging it to be different from a set of representations that are biased by design. This tactic is feasible in many scenarios where it is much easier to define a set of biased representations than to define and quantify bias. We demonstrate the efficacy of our method across a variety of synthetic and real-world biases; our experiments show that the method discourages models from taking bias shortcuts, resulting in improved generalisation. Source code is available at https://github.com/clovaai/rebias.

Despite the tremendous success, existing machine learning models still fall short of human-like systematic generalization -- learning compositional rules from limited data and applying them to unseen combinations in various domains. We propose Neural-Symbolic Recursive Machine (NSR) to tackle this deficiency. The core representation of NSR is a Grounded Symbol System (GSS) with combinatorial syntax and semantics, which entirely emerges from training data. Akin to the neuroscience studies suggesting separate brain systems for perceptual, syntactic, and semantic processing, NSR implements analogous separate modules of neural perception, syntactic parsing, and semantic reasoning, which are jointly learned by a deduction-abduction algorithm. We prove that NSR is expressive enough to model various sequence-to-sequence tasks. Superior systematic generalization is achieved via the inductive biases of equivariance and recursiveness embedded in NSR. In experiments, NSR achieves state-of-the-art performance in three benchmarks from different domains: SCAN for semantic parsing, PCFG for string manipulation, and HINT for arithmetic reasoning. Specifically, NSR achieves 100% generalization accuracy on SCAN and PCFG and outperforms state-of-the-art models on HINT by about 23%. Our NSR demonstrates stronger generalization than pure neural networks due to its symbolic representation and inductive biases. NSR also demonstrates better transferability than existing neural-symbolic approaches due to less domain-specific knowledge required.

Medical image classification requires not only high predictive performance but also interpretability to ensure clinical trust and adoption. Graph Neural Networks (GNNs) offer a powerful framework for modeling relational structures within datasets; however, standard GNNs often operate as black boxes, limiting transparency and usability, particularly in clinical settings. In this work, we present an interpretable graph-based learning framework named FireGNN that integrates trainable fuzzy rules into GNNs for medical image classification. These rules embed topological descriptors - node degree, clustering coefficient, and label agreement - using learnable thresholds and sharpness parameters to enable intrinsic symbolic reasoning. Additionally, we explore auxiliary self-supervised tasks (e.g., homophily prediction, similarity entropy) as a benchmark to evaluate the contribution of topological learning. Our fuzzy-rule-enhanced model achieves strong performance across five MedMNIST benchmarks and the synthetic dataset MorphoMNIST, while also generating interpretable rule-based explanations. To our knowledge, this is the first integration of trainable fuzzy rules within a GNN. Source Code: https://github.com/basiralab/FireGNN

Neural networks can approximate complex functions, but they struggle to perform exact arithmetic operations over real numbers. The lack of inductive bias for arithmetic operations leaves neural networks without the underlying logic necessary to extrapolate on tasks such as addition, subtraction, and multiplication. We present two new neural network components: the Neural Addition Unit (NAU), which can learn exact addition and subtraction; and the Neural Multiplication Unit (NMU) that can multiply subsets of a vector. The NMU is, to our knowledge, the first arithmetic neural network component that can learn to multiply elements from a vector, when the hidden size is large. The two new components draw inspiration from a theoretical analysis of recently proposed arithmetic components. We find that careful initialization, restricting parameter space, and regularizing for sparsity is important when optimizing the NAU and NMU. Our proposed units NAU and NMU, compared with previous neural units, converge more consistently, have fewer parameters, learn faster, can converge for larger hidden sizes, obtain sparse and meaningful weights, and can extrapolate to negative and small values.

Most positive and unlabeled data is subject to selection biases. The labeled examples can, for example, be selected from the positive set because they are easier to obtain or more obviously positive. This paper investigates how learning can be ena BHbled in this setting. We propose and theoretically analyze an empirical-risk-based method for incorporating the labeling mechanism. Additionally, we investigate under which assumptions learning is possible when the labeling mechanism is not fully understood and propose a practical method to enable this. Our empirical analysis supports the theoretical results and shows that taking into account the possibility of a selection bias, even when the labeling mechanism is unknown, improves the trained classifiers.

Simplicity bias is the concerning tendency of deep networks to over-depend on simple, weakly predictive features, to the exclusion of stronger, more complex features. This is exacerbated in real-world applications by limited training data and spurious feature-label correlations, leading to biased, incorrect predictions. We propose a direct, interventional method for addressing simplicity bias in DNNs, which we call the feature sieve. We aim to automatically identify and suppress easily-computable spurious features in lower layers of the network, thereby allowing the higher network levels to extract and utilize richer, more meaningful representations. We provide concrete evidence of this differential suppression & enhancement of relevant features on both controlled datasets and real-world images, and report substantial gains on many real-world debiasing benchmarks (11.4% relative gain on Imagenet-A; 3.2% on BAR, etc). Crucially, we do not depend on prior knowledge of spurious attributes or features, and in fact outperform many baselines that explicitly incorporate such information. We believe that our feature sieve work opens up exciting new research directions in automated adversarial feature extraction and representation learning for deep networks.

This paper considers the problem of undersampled MRI reconstruction. We propose a novel Transformer-based framework for directly processing signal in k-space, going beyond the limitation of regular grids as ConvNets do. We adopt an implicit representation of k-space spectrogram, treating spatial coordinates as inputs, and dynamically query the sparsely sampled points to reconstruct the spectrogram, i.e. learning the inductive bias in k-space. To strike a balance between computational cost and reconstruction quality, we build the decoder with hierarchical structure to generate low-resolution and high-resolution outputs respectively. To validate the effectiveness of our proposed method, we have conducted extensive experiments on two public datasets, and demonstrate superior or comparable performance to state-of-the-art approaches.

The role of hidden units in recurrent neural networks is typically seen as modeling memory, with research focusing on enhancing information retention through gating mechanisms. A less explored perspective views hidden units as active participants in the computation performed by the network, rather than passive memory stores. In this work, we revisit bi-linear operations, which involve multiplicative interactions between hidden units and input embeddings. We demonstrate theoretically and empirically that they constitute a natural inductive bias for representing the evolution of hidden states in state tracking tasks. These are the simplest type of task that require hidden units to actively contribute to the behavior of the network. We also show that bi-linear state updates form a natural hierarchy corresponding to state tracking tasks of increasing complexity, with popular linear recurrent networks such as Mamba residing at the lowest-complexity center of that hierarchy.

Persistent homology, a technique from computational topology, has recently shown strong empirical performance in the context of graph classification. Being able to capture long range graph properties via higher-order topological features, such as cycles of arbitrary length, in combination with multi-scale topological descriptors, has improved predictive performance for data sets with prominent topological structures, such as molecules. At the same time, the theoretical properties of persistent homology have not been formally assessed in this context. This paper intends to bridge the gap between computational topology and graph machine learning by providing a brief introduction to persistent homology in the context of graphs, as well as a theoretical discussion and empirical analysis of its expressivity for graph learning tasks.

Equilibrium propagation (EP) is a compelling alternative to the backpropagation of error algorithm (BP) for computing gradients of neural networks on biological or analog neuromorphic substrates. Still, the algorithm requires weight symmetry and infinitesimal equilibrium perturbations, i.e., nudges, to estimate unbiased gradients efficiently. Both requirements are challenging to implement in physical systems. Yet, whether and how weight asymmetry affects its applicability is unknown because, in practice, it may be masked by biases introduced through the finite nudge. To address this question, we study generalized EP, which can be formulated without weight symmetry, and analytically isolate the two sources of bias. For complex-differentiable non-symmetric networks, we show that the finite nudge does not pose a problem, as exact derivatives can still be estimated via a Cauchy integral. In contrast, weight asymmetry introduces bias resulting in low task performance due to poor alignment of EP's neuronal error vectors compared to BP. To mitigate this issue, we present a new homeostatic objective that directly penalizes functional asymmetries of the Jacobian at the network's fixed point. This homeostatic objective dramatically improves the network's ability to solve complex tasks such as ImageNet 32x32. Our results lay the theoretical groundwork for studying and mitigating the adverse effects of imperfections of physical networks on learning algorithms that rely on the substrate's relaxation dynamics.

We propose prototypical networks for the problem of few-shot classification, where a classifier must generalize to new classes not seen in the training set, given only a small number of examples of each new class. Prototypical networks learn a metric space in which classification can be performed by computing distances to prototype representations of each class. Compared to recent approaches for few-shot learning, they reflect a simpler inductive bias that is beneficial in this limited-data regime, and achieve excellent results. We provide an analysis showing that some simple design decisions can yield substantial improvements over recent approaches involving complicated architectural choices and meta-learning. We further extend prototypical networks to zero-shot learning and achieve state-of-the-art results on the CU-Birds dataset.

Machine learning frameworks such as graph neural networks typically rely on a given, fixed graph to exploit relational inductive biases and thus effectively learn from network data. However, when said graphs are (partially) unobserved, noisy, or dynamic, the problem of inferring graph structure from data becomes relevant. In this paper, we postulate a graph convolutional relationship between the observed and latent graphs, and formulate the graph learning task as a network inverse (deconvolution) problem. In lieu of eigendecomposition-based spectral methods or iterative optimization solutions, we unroll and truncate proximal gradient iterations to arrive at a parameterized neural network architecture that we call a Graph Deconvolution Network (GDN). GDNs can learn a distribution of graphs in a supervised fashion, perform link prediction or edge-weight regression tasks by adapting the loss function, and they are inherently inductive. We corroborate GDN's superior graph recovery performance and its generalization to larger graphs using synthetic data in supervised settings. Furthermore, we demonstrate the robustness and representation power of GDNs on real world neuroimaging and social network datasets.

In-context learning (ICL) is a type of prompting where a transformer model operates on a sequence of (input, output) examples and performs inference on-the-fly. In this work, we formalize in-context learning as an algorithm learning problem where a transformer model implicitly constructs a hypothesis function at inference-time. We first explore the statistical aspects of this abstraction through the lens of multitask learning: We obtain generalization bounds for ICL when the input prompt is (1) a sequence of i.i.d. (input, label) pairs or (2) a trajectory arising from a dynamical system. The crux of our analysis is relating the excess risk to the stability of the algorithm implemented by the transformer. We characterize when transformer/attention architecture provably obeys the stability condition and also provide empirical verification. For generalization on unseen tasks, we identify an inductive bias phenomenon in which the transfer learning risk is governed by the task complexity and the number of MTL tasks in a highly predictable manner. Finally, we provide numerical evaluations that (1) demonstrate transformers can indeed implement near-optimal algorithms on classical regression problems with i.i.d. and dynamic data, (2) provide insights on stability, and (3) verify our theoretical predictions.

Invariance and equivariance to geometrical transformations have proven to be very useful inductive biases when training (convolutional) neural network models, especially in the low-data regime. Much work has focused on the case where the symmetry group employed is compact or abelian, or both. Recent work has explored enlarging the class of transformations used to the case of Lie groups, principally through the use of their Lie algebra, as well as the group exponential and logarithm maps. The applicability of such methods to larger transformation groups is limited by the fact that depending on the group of interest G, the exponential map may not be surjective. Further limitations are encountered when G is neither compact nor abelian. Using the structure and geometry of Lie groups and their homogeneous spaces, we present a framework by which it is possible to work with such groups primarily focusing on the Lie groups G = GL^{+}(n, R) and G = SL(n, R), as well as their representation as affine transformations R^{n} rtimes G. Invariant integration as well as a global parametrization is realized by decomposing the `larger` groups into subgroups and submanifolds which can be handled individually. Under this framework, we show how convolution kernels can be parametrized to build models equivariant with respect to affine transformations. We evaluate the robustness and out-of-distribution generalisation capability of our model on the standard affine-invariant benchmark classification task, where we outperform all previous equivariant models as well as all Capsule Network proposals.

Machine learning is becoming an increasingly valuable tool in mathematics, enabling one to identify subtle patterns across collections of examples so vast that they would be impossible for a single researcher to feasibly review and analyze. In this work, we use graph neural networks to investigate quiver mutation -- an operation that transforms one quiver (or directed multigraph) into another -- which is central to the theory of cluster algebras with deep connections to geometry, topology, and physics. In the study of cluster algebras, the question of mutation equivalence is of fundamental concern: given two quivers, can one efficiently determine if one quiver can be transformed into the other through a sequence of mutations? In this paper, we use graph neural networks and AI explainability techniques to independently discover mutation equivalence criteria for quivers of type D. Along the way, we also show that even without explicit training to do so, our model captures structure within its hidden representation that allows us to reconstruct known criteria from type D, adding to the growing evidence that modern machine learning models are capable of learning abstract and parsimonious rules from mathematical data.

Bias in training datasets must be managed for various groups in classification tasks to ensure parity or equal treatment. With the recent growth in artificial intelligence models and their expanding role in automated decision-making, ensuring that these models are not biased is vital. There is an abundance of evidence suggesting that these models could contain or even amplify the bias present in the data on which they are trained, inherent to their objective function and learning algorithms; Many researchers direct their attention to this issue in different directions, namely, changing data to be statistically independent, adversarial training for restricting the capabilities of a particular competitor who aims to maximize parity, etc. These methods result in information loss and do not provide a suitable balance between accuracy and fairness or do not ensure limiting the biases in training. To this end, we propose a powerful strategy for training deep learning models called the Distraction module, which can be theoretically proven effective in controlling bias from affecting the classification results. This method can be utilized with different data types (e.g., Tabular, images, graphs, etc.). We demonstrate the potency of the proposed method by testing it on UCI Adult and Heritage Health datasets (tabular), POKEC-Z, POKEC-N and NBA datasets (graph), and CelebA dataset (vision). Using state-of-the-art methods proposed in the fairness literature for each dataset, we exhibit our model is superior to these proposed methods in minimizing bias and maintaining accuracy.

According to the principle of compositional generalization, the meaning of a complex expression can be understood as a function of the meaning of its parts and of how they are combined. This principle is crucial for human language processing and also, arguably, for NLP models in the face of out-of-distribution data. However, many neural network models, including Transformers, have been shown to struggle with compositional generalization. In this paper, we hypothesize that forcing models to in-context learn can provide an inductive bias to promote compositional generalization. To test this hypothesis, we train a causal Transformer in a setting that renders ordinary learning very difficult: we present it with different orderings of the training instance and shuffle instance labels. This corresponds to training the model on all possible few-shot learning problems attainable from the dataset. The model can solve the task, however, by utilizing earlier examples to generalize to later ones (i.e. in-context learning). In evaluations on the datasets, SCAN, COGS, and GeoQuery, models trained in this manner indeed show improved compositional generalization. This indicates the usefulness of in-context learning problems as an inductive bias for generalization.

As machine learning models become increasingly larger, trained weakly supervised on large, possibly uncurated data sets, it becomes increasingly important to establish mechanisms for inspecting, interacting, and revising models to mitigate learning shortcuts and guarantee their learned knowledge is aligned with human knowledge. The recently proposed XIL framework was developed for this purpose, and several such methods have been introduced, each with individual motivations and methodological details. In this work, we provide a unification of various XIL methods into a single typology by establishing a common set of basic modules. In doing so, we pave the way for a principled comparison of existing, but, importantly, also future XIL approaches. In addition, we discuss existing and introduce novel measures and benchmarks for evaluating the overall abilities of a XIL method. Given this extensive toolbox, including our typology, measures, and benchmarks, we finally compare several recent XIL methods methodologically and quantitatively. In our evaluations, all methods prove to revise a model successfully. However, we found remarkable differences in individual benchmark tasks, revealing valuable application-relevant aspects for integrating these benchmarks in developing future methods.

We generalize the notion of social biases from language embeddings to grounded vision and language embeddings. Biases are present in grounded embeddings, and indeed seem to be equally or more significant than for ungrounded embeddings. This is despite the fact that vision and language can suffer from different biases, which one might hope could attenuate the biases in both. Multiple ways exist to generalize metrics measuring bias in word embeddings to this new setting. We introduce the space of generalizations (Grounded-WEAT and Grounded-SEAT) and demonstrate that three generalizations answer different yet important questions about how biases, language, and vision interact. These metrics are used on a new dataset, the first for grounded bias, created by augmenting extending standard linguistic bias benchmarks with 10,228 images from COCO, Conceptual Captions, and Google Images. Dataset construction is challenging because vision datasets are themselves very biased. The presence of these biases in systems will begin to have real-world consequences as they are deployed, making carefully measuring bias and then mitigating it critical to building a fair society.

Chain-of-Thought (CoT) prompting has been shown to improve Large Language Model (LLM) performance on various tasks. With this approach, LLMs appear to produce human-like reasoning steps before providing answers (a.k.a., CoT reasoning), which often leads to the perception that they engage in deliberate inferential processes. However, some initial findings suggest that CoT reasoning may be more superficial than it appears, motivating us to explore further. In this paper, we study CoT reasoning via a data distribution lens and investigate if CoT reasoning reflects a structured inductive bias learned from in-distribution data, allowing the model to conditionally generate reasoning paths that approximate those seen during training. Thus, its effectiveness is fundamentally bounded by the degree of distribution discrepancy between the training data and the test queries. With this lens, we dissect CoT reasoning via three dimensions: task, length, and format. To investigate each dimension, we design DataAlchemy, an isolated and controlled environment to train LLMs from scratch and systematically probe them under various distribution conditions. Our results reveal that CoT reasoning is a brittle mirage that vanishes when it is pushed beyond training distributions. This work offers a deeper understanding of why and when CoT reasoning fails, emphasizing the ongoing challenge of achieving genuine and generalizable reasoning.

Many problems in machine learning involve bilevel optimization (BLO), including hyperparameter optimization, meta-learning, and dataset distillation. Bilevel problems consist of two nested sub-problems, called the outer and inner problems, respectively. In practice, often at least one of these sub-problems is overparameterized. In this case, there are many ways to choose among optima that achieve equivalent objective values. Inspired by recent studies of the implicit bias induced by optimization algorithms in single-level optimization, we investigate the implicit bias of gradient-based algorithms for bilevel optimization. We delineate two standard BLO methods -- cold-start and warm-start -- and show that the converged solution or long-run behavior depends to a large degree on these and other algorithmic choices, such as the hypergradient approximation. We also show that the inner solutions obtained by warm-start BLO can encode a surprising amount of information about the outer objective, even when the outer parameters are low-dimensional. We believe that implicit bias deserves as central a role in the study of bilevel optimization as it has attained in the study of single-level neural net optimization.

Recent advances in large language models (LLMs) have enabled automatic generation of chain-of-thought (CoT) reasoning, leading to strong performance on tasks such as math and code. However, when reasoning steps reflect social stereotypes (e.g., those related to gender, race or age), they can reinforce harmful associations and lead to misleading conclusions. We present the first systematic evaluation of social bias within LLM-generated reasoning, using the BBQ dataset to analyze both prediction accuracy and bias. Our study spans a wide range of mainstream reasoning models, including instruction-tuned and CoT-augmented variants of DeepSeek-R1 (8B/32B), ChatGPT, and other open-source LLMs. We quantify how biased reasoning steps correlate with incorrect predictions and often lead to stereotype expression. To mitigate reasoning-induced bias, we propose Answer Distribution as Bias Proxy (ADBP), a lightweight mitigation method that detects bias by tracking how model predictions change across incremental reasoning steps. ADBP outperforms a stereotype-free baseline in most cases, mitigating bias and improving the accuracy of LLM outputs. Code will be released upon paper acceptance.

Recent studies suggest that deep learning models inductive bias towards favoring simpler features may be one of the sources of shortcut learning. Yet, there has been limited focus on understanding the complexity of the myriad features that models learn. In this work, we introduce a new metric for quantifying feature complexity, based on V-information and capturing whether a feature requires complex computational transformations to be extracted. Using this V-information metric, we analyze the complexities of 10,000 features, represented as directions in the penultimate layer, that were extracted from a standard ImageNet-trained vision model. Our study addresses four key questions: First, we ask what features look like as a function of complexity and find a spectrum of simple to complex features present within the model. Second, we ask when features are learned during training. We find that simpler features dominate early in training, and more complex features emerge gradually. Third, we investigate where within the network simple and complex features flow, and find that simpler features tend to bypass the visual hierarchy via residual connections. Fourth, we explore the connection between features complexity and their importance in driving the networks decision. We find that complex features tend to be less important. Surprisingly, important features become accessible at earlier layers during training, like a sedimentation process, allowing the model to build upon these foundational elements.

This paper introduces a novel approach to evaluating deep learning models' capacity for in-diagram logic interpretation. Leveraging the intriguing realm of visual illusions, we establish a unique dataset, InDL, designed to rigorously test and benchmark these models. Deep learning has witnessed remarkable progress in domains such as computer vision and natural language processing. However, models often stumble in tasks requiring logical reasoning due to their inherent 'black box' characteristics, which obscure the decision-making process. Our work presents a new lens to understand these models better by focusing on their handling of visual illusions -- a complex interplay of perception and logic. We utilize six classic geometric optical illusions to create a comparative framework between human and machine visual perception. This methodology offers a quantifiable measure to rank models, elucidating potential weaknesses and providing actionable insights for model improvements. Our experimental results affirm the efficacy of our benchmarking strategy, demonstrating its ability to effectively rank models based on their logic interpretation ability. As part of our commitment to reproducible research, the source code and datasets will be made publicly available at https://github.com/rabbit-magic-wh/InDL

Error slice discovery is crucial to diagnose and mitigate model errors. Current clustering or discrete attribute-based slice discovery methods face key limitations: 1) clustering results in incoherent slices, while assigning discrete attributes to slices leads to incomplete coverage of error patterns due to missing or insufficient attributes; 2) these methods lack complex reasoning, preventing them from fully explaining model biases; 3) they fail to integrate domain knowledge, limiting their usage in specialized fields \eg radiology. We propose\ladder (Language-Driven Discovery and Error Rectification), to address the limitations by: (1) leveraging the flexibility of natural language to address incompleteness, (2) employing LLM's latent domain knowledge and advanced reasoning to analyze sentences and derive testable hypotheses directly, identifying biased attributes, and form coherent error slices without clustering. Existing mitigation methods typically address only the worst-performing group, often amplifying errors in other subgroups. In contrast,\ladder generates pseudo attributes from the discovered hypotheses to mitigate errors across all biases without explicit attribute annotations or prior knowledge of bias. Rigorous evaluations on 6 datasets spanning natural and medical images -- comparing 200+ classifiers with diverse architectures, pretraining strategies, and LLMs -- show that\ladder consistently outperforms existing baselines in discovering and mitigating biases.

The growing importance of understanding and addressing algorithmic bias in artificial intelligence (AI) has led to a surge in research on AI fairness, which often assumes that the underlying data is independent and identically distributed (IID). However, real-world data frequently exists in non-IID graph structures that capture connections among individual units. To effectively mitigate bias in AI systems, it is essential to bridge the gap between traditional fairness literature, designed for IID data, and the prevalence of non-IID graph data. This survey reviews recent advancements in fairness amidst non-IID graph data, including the newly introduced fair graph generation and the commonly studied fair graph classification. In addition, available datasets and evaluation metrics for future research are identified, the limitations of existing work are highlighted, and promising future directions are proposed.

Transformers achieve state-of-the-art accuracy and robustness across many tasks, but an understanding of the inductive biases that they have and how those biases are different from other neural network architectures remains elusive. Various neural network architectures such as fully connected networks have been found to have a simplicity bias towards simple functions of the data; one version of this simplicity bias is a spectral bias to learn simple functions in the Fourier space. In this work, we identify the notion of sensitivity of the model to random changes in the input as a notion of simplicity bias which provides a unified metric to explain the simplicity and spectral bias of transformers across different data modalities. We show that transformers have lower sensitivity than alternative architectures, such as LSTMs, MLPs and CNNs, across both vision and language tasks. We also show that low-sensitivity bias correlates with improved robustness; furthermore, it can also be used as an efficient intervention to further improve the robustness of transformers.

Large Reasoning Models (LRMs) like DeepSeek-R1 and OpenAI-o1 have demonstrated remarkable reasoning capabilities, raising important questions about their biases in LLM-as-a-judge settings. We present a comprehensive benchmark comparing judging biases between LLMs and LRMs across both subjective preference-alignment datasets and objective fact-based datasets. Through investigation of bandwagon, authority, position, and distraction biases, we uncover four key findings: (1) despite their advanced reasoning capabilities, LRMs remain susceptible to the above biases; (2) LRMs demonstrate better robustness than LLMs specifically on fact-related datasets; (3) LRMs exhibit notable position bias, preferring options in later positions; and (4) we identify a novel "superficial reflection bias" where phrases mimicking reasoning (e.g., "wait, let me think...") significantly influence model judgments. To address these biases, we design and evaluate three mitigation strategies: specialized system prompts that reduce judging biases by up to 19\% in preference alignment datasets and 14\% in fact-related datasets, in-context learning that provides up to 27\% improvement on preference tasks but shows inconsistent results on factual tasks, and a self-reflection mechanism that reduces biases by up to 10\% in preference datasets and 16\% in fact-related datasets, with self-reflection proving particularly effective for LRMs. Our work provides crucial insights for developing more reliable LLM-as-a-Judge frameworks, especially as LRMs become increasingly deployed as automated judges.

We propose a new method for generating realistic datasets with distribution shifts using any decoder-based generative model. Our approach systematically creates datasets with varying intensities of distribution shifts, facilitating a comprehensive analysis of model performance degradation. We then use these generated datasets to evaluate the performance of various commonly used networks and observe a consistent decline in performance with increasing shift intensity, even when the effect is almost perceptually unnoticeable to the human eye. We see this degradation even when using data augmentations. We also find that enlarging the training dataset beyond a certain point has no effect on the robustness and that stronger inductive biases increase robustness.

Neural architectures that learn potential energy surfaces from molecular data have undergone fast improvement in recent years. A key driver of this success is the Message Passing Neural Network (MPNN) paradigm. Its favorable scaling with system size partly relies upon a spatial distance limit on messages. While this focus on locality is a useful inductive bias, it also impedes the learning of long-range interactions such as electrostatics and van der Waals forces. To address this drawback, we propose Ewald message passing: a nonlocal Fourier space scheme which limits interactions via a cutoff on frequency instead of distance, and is theoretically well-founded in the Ewald summation method. It can serve as an augmentation on top of existing MPNN architectures as it is computationally inexpensive and agnostic to architectural details. We test the approach with four baseline models and two datasets containing diverse periodic (OC20) and aperiodic structures (OE62). We observe robust improvements in energy mean absolute errors across all models and datasets, averaging 10% on OC20 and 16% on OE62. Our analysis shows an outsize impact of these improvements on structures with high long-range contributions to the ground truth energy.

Answering counterfactual queries has many important applications such as knowledge discovery and explainability, but is challenging when causal variables are unobserved and we only see a projection onto an observation space, for instance, image pixels. One approach is to recover the latent Structural Causal Model (SCM), but this typically needs unrealistic assumptions, such as linearity of the causal mechanisms. Another approach is to use na\"ive ML approximations, such as generative models, to generate counterfactual samples; however, these lack guarantees of accuracy. In this work, we strive to strike a balance between practicality and theoretical guarantees by focusing on a specific type of causal query called domain counterfactuals, which hypothesizes what a sample would have looked like if it had been generated in a different domain (or environment). Concretely, by only assuming invertibility, sparse domain interventions and access to observational data from different domains, we aim to improve domain counterfactual estimation both theoretically and practically with less restrictive assumptions. We define domain counterfactually equivalent models and prove necessary and sufficient properties for equivalent models that provide a tight characterization of the domain counterfactual equivalence classes. Building upon this result, we prove that every equivalence class contains a model where all intervened variables are at the end when topologically sorted by the causal DAG. This surprising result suggests that a model design that only allows intervention in the last k latent variables may improve model estimation for counterfactuals. We then test this model design on extensive simulated and image-based experiments which show the sparse canonical model indeed improves counterfactual estimation over baseline non-sparse models.

Despite tremendous success in many application scenarios, the training and inference costs of using deep learning are also rapidly increasing over time. The lottery ticket hypothesis (LTH) emerges as a promising framework to leverage a special sparse subnetwork (i.e., winning ticket) instead of a full model for both training and inference, that can lower both costs without sacrificing the performance. The main resource bottleneck of LTH is however the extraordinary cost to find the sparse mask of the winning ticket. That makes the found winning ticket become a valuable asset to the owners, highlighting the necessity of protecting its copyright. Our setting adds a new dimension to the recently soaring interest in protecting against the intellectual property (IP) infringement of deep models and verifying their ownerships, since they take owners' massive/unique resources to develop or train. While existing methods explored encrypted weights or predictions, we investigate a unique way to leverage sparse topological information to perform lottery verification, by developing several graph-based signatures that can be embedded as credentials. By further combining trigger set-based methods, our proposal can work in both white-box and black-box verification scenarios. Through extensive experiments, we demonstrate the effectiveness of lottery verification in diverse models (ResNet-20, ResNet-18, ResNet-50) on CIFAR-10 and CIFAR-100. Specifically, our verification is shown to be robust to removal attacks such as model fine-tuning and pruning, as well as several ambiguity attacks. Our codes are available at https://github.com/VITA-Group/NO-stealing-LTH.

The enduring legacy of Euclidean geometry underpins classical machine learning, which, for decades, has been primarily developed for data lying in Euclidean space. Yet, modern machine learning increasingly encounters richly structured data that is inherently nonEuclidean. This data can exhibit intricate geometric, topological and algebraic structure: from the geometry of the curvature of space-time, to topologically complex interactions between neurons in the brain, to the algebraic transformations describing symmetries of physical systems. Extracting knowledge from such non-Euclidean data necessitates a broader mathematical perspective. Echoing the 19th-century revolutions that gave rise to non-Euclidean geometry, an emerging line of research is redefining modern machine learning with non-Euclidean structures. Its goal: generalizing classical methods to unconventional data types with geometry, topology, and algebra. In this review, we provide an accessible gateway to this fast-growing field and propose a graphical taxonomy that integrates recent advances into an intuitive unified framework. We subsequently extract insights into current challenges and highlight exciting opportunities for future development in this field.

Do large language models (LLMs) exhibit sociodemographic biases, even when they decline to respond? To bypass their refusal to "speak," we study this research question by probing contextualized embeddings and exploring whether this bias is encoded in its latent representations. We propose a logistic Bradley-Terry probe which predicts word pair preferences of LLMs from the words' hidden vectors. We first validate our probe on three pair preference tasks and thirteen LLMs, where we outperform the word embedding association test (WEAT), a standard approach in testing for implicit association, by a relative 27% in error rate. We also find that word pair preferences are best represented in the middle layers. Next, we transfer probes trained on harmless tasks (e.g., pick the larger number) to controversial ones (compare ethnicities) to examine biases in nationality, politics, religion, and gender. We observe substantial bias for all target classes: for instance, the Mistral model implicitly prefers Europe to Africa, Christianity to Judaism, and left-wing to right-wing politics, despite declining to answer. This suggests that instruction fine-tuning does not necessarily debias contextualized embeddings. Our codebase is at https://github.com/castorini/biasprobe.

Accurately predicting road networks from satellite images requires a global understanding of the network topology. We propose to capture such high-level information by introducing a graph-based framework that simulates the addition of sequences of graph edges using a reinforcement learning (RL) approach. In particular, given a partially generated graph associated with a satellite image, an RL agent nominates modifications that maximize a cumulative reward. As opposed to standard supervised techniques that tend to be more restricted to commonly used surrogate losses, these rewards can be based on various complex, potentially non-continuous, metrics of interest. This yields more power and flexibility to encode problem-dependent knowledge. Empirical results on several benchmark datasets demonstrate enhanced performance and increased high-level reasoning about the graph topology when using a tree-based search. We further highlight the superiority of our approach under substantial occlusions by introducing a new synthetic benchmark dataset for this task.

We introduce a new generative model that combines latent diffusion with persistent homology to create 3D shapes with high diversity, with a special emphasis on their topological characteristics. Our method involves representing 3D shapes as implicit fields, then employing persistent homology to extract topological features, including Betti numbers and persistence diagrams. The shape generation process consists of two steps. Initially, we employ a transformer-based autoencoding module to embed the implicit representation of each 3D shape into a set of latent vectors. Subsequently, we navigate through the learned latent space via a diffusion model. By strategically incorporating topological features into the diffusion process, our generative module is able to produce a richer variety of 3D shapes with different topological structures. Furthermore, our framework is flexible, supporting generation tasks constrained by a variety of inputs, including sparse and partial point clouds, as well as sketches. By modifying the persistence diagrams, we can alter the topology of the shapes generated from these input modalities.

Time series reasoning treats time as a first-class axis and incorporates intermediate evidence directly into the answer. This survey defines the problem and organizes the literature by reasoning topology with three families: direct reasoning in one step, linear chain reasoning with explicit intermediates, and branch-structured reasoning that explores, revises, and aggregates. The topology is crossed with the main objectives of the field, including traditional time series analysis, explanation and understanding, causal inference and decision making, and time series generation, while a compact tag set spans these axes and captures decomposition and verification, ensembling, tool use, knowledge access, multimodality, agent loops, and LLM alignment regimes. Methods and systems are reviewed across domains, showing what each topology enables and where it breaks down in faithfulness or robustness, along with curated datasets, benchmarks, and resources that support study and deployment (https://github.com/blacksnail789521/Time-Series-Reasoning-Survey). Evaluation practices that keep evidence visible and temporally aligned are highlighted, and guidance is distilled on matching topology to uncertainty, grounding with observable artifacts, planning for shift and streaming, and treating cost and latency as design budgets. We emphasize that reasoning structures must balance capacity for grounding and self-correction against computational cost and reproducibility, while future progress will likely depend on benchmarks that tie reasoning quality to utility and on closed-loop testbeds that trade off cost and risk under shift-aware, streaming, and long-horizon settings. Taken together, these directions mark a shift from narrow accuracy toward reliability at scale, enabling systems that not only analyze but also understand, explain, and act on dynamic worlds with traceable evidence and credible outcomes.

We carry out an information-theoretical analysis of a two-layer neural network trained from input-output pairs generated by a teacher network with matching architecture, in overparametrized regimes. Our results come in the form of bounds relating i) the mutual information between training data and network weights, or ii) the Bayes-optimal generalization error, to the same quantities but for a simpler (generalized) linear model for which explicit expressions are rigorously known. Our bounds, which are expressed in terms of the number of training samples, input dimension and number of hidden units, thus yield fundamental performance limits for any neural network (and actually any learning procedure) trained from limited data generated according to our two-layer teacher neural network model. The proof relies on rigorous tools from spin glasses and is guided by ``Gaussian equivalence principles'' lying at the core of numerous recent analyses of neural networks. With respect to the existing literature, which is either non-rigorous or restricted to the case of the learning of the readout weights only, our results are information-theoretic (i.e. are not specific to any learning algorithm) and, importantly, cover a setting where all the network parameters are trained.

Machine learning for point clouds has been attracting much attention, with many applications in various fields, such as shape recognition and material science. For enhancing the accuracy of such machine learning methods, it is often effective to incorporate global topological features, which are typically extracted by persistent homology. In the calculation of persistent homology for a point cloud, we choose a filtration for the point cloud, an increasing sequence of spaces. Since the performance of machine learning methods combined with persistent homology is highly affected by the choice of a filtration, we need to tune it depending on data and tasks. In this paper, we propose a framework that learns a filtration adaptively with the use of neural networks. In order to make the resulting persistent homology isometry-invariant, we develop a neural network architecture with such invariance. Additionally, we show a theoretical result on a finite-dimensional approximation of filtration functions, which justifies the proposed network architecture. Experimental results demonstrated the efficacy of our framework in several classification tasks.

The use of graph neural networks has produced significant advances in point cloud problems, such as those found in high energy physics. The question of how to produce a graph structure in these problems is usually treated as a matter of heuristics, employing fully connected graphs or K-nearest neighbors. In this work, we elevate this question to utmost importance as the Topology Problem. We propose an attention mechanism that allows a graph to be constructed in a learned space that handles geometrically the flow of relevance, providing one solution to the Topology Problem. We test this architecture, called GravNetNorm, on the task of top jet tagging, and show that it is competitive in tagging accuracy, and uses far fewer computational resources than all other comparable models.

Understanding the internal representations learned by neural networks is a cornerstone challenge in the science of machine learning. While there have been significant recent strides in some cases towards understanding how neural networks implement specific target functions, this paper explores a complementary question -- why do networks arrive at particular computational strategies? Our inquiry focuses on the algebraic learning tasks of modular addition, sparse parities, and finite group operations. Our primary theoretical findings analytically characterize the features learned by stylized neural networks for these algebraic tasks. Notably, our main technique demonstrates how the principle of margin maximization alone can be used to fully specify the features learned by the network. Specifically, we prove that the trained networks utilize Fourier features to perform modular addition and employ features corresponding to irreducible group-theoretic representations to perform compositions in general groups, aligning closely with the empirical observations of Nanda et al. and Chughtai et al. More generally, we hope our techniques can help to foster a deeper understanding of why neural networks adopt specific computational strategies.

The parameter space for any fixed architecture of feedforward ReLU neural networks serves as a proxy during training for the associated class of functions - but how faithful is this representation? It is known that many different parameter settings can determine the same function. Moreover, the degree of this redundancy is inhomogeneous: for some networks, the only symmetries are permutation of neurons in a layer and positive scaling of parameters at a neuron, while other networks admit additional hidden symmetries. In this work, we prove that, for any network architecture where no layer is narrower than the input, there exist parameter settings with no hidden symmetries. We also describe a number of mechanisms through which hidden symmetries can arise, and empirically approximate the functional dimension of different network architectures at initialization. These experiments indicate that the probability that a network has no hidden symmetries decreases towards 0 as depth increases, while increasing towards 1 as width and input dimension increase.

We introduce LeapfrogLayers, an invertible neural network architecture that can be trained to efficiently sample the topology of a 2D U(1) lattice gauge theory. We show an improvement in the integrated autocorrelation time of the topological charge when compared with traditional HMC, and look at how different quantities transform under our model. Our implementation is open source, and is publicly available on github at https://github.com/saforem2/l2hmc-qcd.

Recent work by Power et al. (2022) highlighted a surprising "grokking" phenomenon in learning arithmetic tasks: a neural net first "memorizes" the training set, resulting in perfect training accuracy but near-random test accuracy, and after training for sufficiently longer, it suddenly transitions to perfect test accuracy. This paper studies the grokking phenomenon in theoretical setups and shows that it can be induced by a dichotomy of early and late phase implicit biases. Specifically, when training homogeneous neural nets with large initialization and small weight decay on both classification and regression tasks, we prove that the training process gets trapped at a solution corresponding to a kernel predictor for a long time, and then a very sharp transition to min-norm/max-margin predictors occurs, leading to a dramatic change in test accuracy.

"Induction heads" are attention heads that implement a simple algorithm to complete token sequences like [A][B] ... [A] -> [B]. In this work, we present preliminary and indirect evidence for a hypothesis that induction heads might constitute the mechanism for the majority of all "in-context learning" in large transformer models (i.e. decreasing loss at increasing token indices). We find that induction heads develop at precisely the same point as a sudden sharp increase in in-context learning ability, visible as a bump in the training loss. We present six complementary lines of evidence, arguing that induction heads may be the mechanistic source of general in-context learning in transformer models of any size. For small attention-only models, we present strong, causal evidence; for larger models with MLPs, we present correlational evidence.

We demonstrate that architectures which traditionally are considered to be ill-suited for a task can be trained using inductive biases from another architecture. Networks are considered untrainable when they overfit, underfit, or converge to poor results even when tuning their hyperparameters. For example, plain fully connected networks overfit on object recognition while deep convolutional networks without residual connections underfit. The traditional answer is to change the architecture to impose some inductive bias, although what that bias is remains unknown. We introduce guidance, where a guide network guides a target network using a neural distance function. The target is optimized to perform well and to match its internal representations, layer-by-layer, to those of the guide; the guide is unchanged. If the guide is trained, this transfers over part of the architectural prior and knowledge of the guide to the target. If the guide is untrained, this transfers over only part of the architectural prior of the guide. In this manner, we can investigate what kinds of priors different architectures place on untrainable networks such as fully connected networks. We demonstrate that this method overcomes the immediate overfitting of fully connected networks on vision tasks, makes plain CNNs competitive to ResNets, closes much of the gap between plain vanilla RNNs and Transformers, and can even help Transformers learn tasks which RNNs can perform more easily. We also discover evidence that better initializations of fully connected networks likely exist to avoid overfitting. Our method provides a mathematical tool to investigate priors and architectures, and in the long term, may demystify the dark art of architecture creation, even perhaps turning architectures into a continuous optimizable parameter of the network.

In-context learning is one of the surprising and useful features of large language models. How it works is an active area of research. Recently, stylized meta-learning-like setups have been devised that train these models on a sequence of input-output pairs (x, f(x)) from a function class using the language modeling loss and observe generalization to unseen functions from the same class. One of the main discoveries in this line of research has been that for several problems such as linear regression, trained transformers learn algorithms for learning functions in context. However, the inductive biases of these models resulting in this behavior are not clearly understood. A model with unlimited training data and compute is a Bayesian predictor: it learns the pretraining distribution. It has been shown that high-capacity transformers mimic the Bayesian predictor for linear regression. In this paper, we show empirical evidence of transformers exhibiting the behavior of this ideal learner across different linear and non-linear function classes. We also extend the previous setups to work in the multitask setting and verify that transformers can do in-context learning in this setup as well and the Bayesian perspective sheds light on this setting also. Finally, via the example of learning Fourier series, we study the inductive bias for in-context learning. We find that in-context learning may or may not have simplicity bias depending on the pretraining data distribution.

Existing studies on fairness are largely Western-focused, making them inadequate for culturally diverse countries such as India. To address this gap, we introduce INDIC-BIAS, a comprehensive India-centric benchmark designed to evaluate fairness of LLMs across 85 identity groups encompassing diverse castes, religions, regions, and tribes. We first consult domain experts to curate over 1,800 socio-cultural topics spanning behaviors and situations, where biases and stereotypes are likely to emerge. Grounded in these topics, we generate and manually validate 20,000 real-world scenario templates to probe LLMs for fairness. We structure these templates into three evaluation tasks: plausibility, judgment, and generation. Our evaluation of 14 popular LLMs on these tasks reveals strong negative biases against marginalized identities, with models frequently reinforcing common stereotypes. Additionally, we find that models struggle to mitigate bias even when explicitly asked to rationalize their decision. Our evaluation provides evidence of both allocative and representational harms that current LLMs could cause towards Indian identities, calling for a more cautious usage in practical applications. We release INDIC-BIAS as an open-source benchmark to advance research on benchmarking and mitigating biases and stereotypes in the Indian context.

Diffusion models have demonstrated impressive capabilities in synthesizing diverse content. However, despite their high-quality outputs, these models often perpetuate social biases, including those related to gender and race. These biases can potentially contribute to harmful real-world consequences, reinforcing stereotypes and exacerbating inequalities in various social contexts. While existing research on diffusion bias mitigation has predominantly focused on guiding content generation, it often neglects the intrinsic mechanisms within diffusion models that causally drive biased outputs. In this paper, we investigate the internal processes of diffusion models, identifying specific decision-making mechanisms, termed bias features, embedded within the model architecture. By directly manipulating these features, our method precisely isolates and adjusts the elements responsible for bias generation, permitting granular control over the bias levels in the generated content. Through experiments on both unconditional and conditional diffusion models across various social bias attributes, we demonstrate our method's efficacy in managing generation distribution while preserving image quality. We also dissect the discovered model mechanism, revealing different intrinsic features controlling fine-grained aspects of generation, boosting further research on mechanistic interpretability of diffusion models.

Self-supervised learning excels at learning representations from large amounts of data. At the same time, generative models offer the complementary property of learning information about the underlying data generation process. In this study, we aim at establishing a principled connection between these two paradigms and highlight the benefits of their complementarity. In particular, we perform an analysis of self-supervised learning objectives, elucidating the underlying probabilistic graphical models and presenting a standardized methodology for their derivation from first principles. The analysis suggests a natural means of integrating self-supervised learning with likelihood-based generative models. We instantiate this concept within the realm of cluster-based self-supervised learning and energy models, introducing a lower bound proven to reliably penalize the most important failure modes and unlocking full unification. Our theoretical findings are substantiated through experiments on synthetic and real-world data, including SVHN, CIFAR10, and CIFAR100, demonstrating that our objective function allows to jointly train a backbone network in a discriminative and generative fashion, consequently outperforming existing self-supervised learning strategies in terms of clustering, generation and out-of-distribution detection performance by a wide margin. We also demonstrate that the solution can be integrated into a neuro-symbolic framework to tackle a simple yet non-trivial instantiation of the symbol grounding problem. The code is publicly available at https://github.com/emsansone/GEDI.

Transformer models can use two fundamentally different kinds of information: information stored in weights during training, and information provided ``in-context'' at inference time. In this work, we show that transformers exhibit different inductive biases in how they represent and generalize from the information in these two sources. In particular, we characterize whether they generalize via parsimonious rules (rule-based generalization) or via direct comparison with observed examples (exemplar-based generalization). This is of important practical consequence, as it informs whether to encode information in weights or in context, depending on how we want models to use that information. In transformers trained on controlled stimuli, we find that generalization from weights is more rule-based whereas generalization from context is largely exemplar-based. In contrast, we find that in transformers pre-trained on natural language, in-context learning is significantly rule-based, with larger models showing more rule-basedness. We hypothesise that rule-based generalization from in-context information might be an emergent consequence of large-scale training on language, which has sparse rule-like structure. Using controlled stimuli, we verify that transformers pretrained on data containing sparse rule-like structure exhibit more rule-based generalization.

We are born with the ability to learn concepts by comparing diverse observations. This helps us to understand the new world in a compositional manner and facilitates extrapolation, as objects naturally consist of multiple concepts. In this work, we argue that the cognitive mechanism of comparison, fundamental to human learning, is also vital for machines to recover true concepts underlying the data. This offers correctness guarantees for the field of concept learning, which, despite its impressive empirical successes, still lacks general theoretical support. Specifically, we aim to develop a theoretical framework for the identifiability of concepts with multiple classes of observations. We show that with sufficient diversity across classes, hidden concepts can be identified without assuming specific concept types, functional relations, or parametric generative models. Interestingly, even when conditions are not globally satisfied, we can still provide alternative guarantees for as many concepts as possible based on local comparisons, thereby extending the applicability of our theory to more flexible scenarios. Moreover, the hidden structure between classes and concepts can also be identified nonparametrically. We validate our theoretical results in both synthetic and real-world settings.

Polynomial neural networks (PNNs) have been recently shown to be particularly effective at image generation and face recognition, where high-frequency information is critical. Previous studies have revealed that neural networks demonstrate a spectral bias towards low-frequency functions, which yields faster learning of low-frequency components during training. Inspired by such studies, we conduct a spectral analysis of the Neural Tangent Kernel (NTK) of PNNs. We find that the Pi-Net family, i.e., a recently proposed parametrization of PNNs, speeds up the learning of the higher frequencies. We verify the theoretical bias through extensive experiments. We expect our analysis to provide novel insights into designing architectures and learning frameworks by incorporating multiplicative interactions via polynomials.

When learning an input-output mapping from very few examples, is it better to first infer a latent function that explains the examples, or is it better to directly predict new test outputs, e.g. using a neural network? We study this question on ARC by training neural models for induction (inferring latent functions) and transduction (directly predicting the test output for a given test input). We train on synthetically generated variations of Python programs that solve ARC training tasks. We find inductive and transductive models solve different kinds of test problems, despite having the same training problems and sharing the same neural architecture: Inductive program synthesis excels at precise computations, and at composing multiple concepts, while transduction succeeds on fuzzier perceptual concepts. Ensembling them approaches human-level performance on ARC.

Image segmentation is a largely researched field where neural networks find vast applications in many facets of technology. Some of the most popular approaches to train segmentation networks employ loss functions optimizing pixel-overlap, an objective that is insufficient for many segmentation tasks. In recent years, their limitations fueled a growing interest in topology-aware methods, which aim to recover the correct topology of the segmented structures. However, so far, none of the existing approaches achieve a spatially correct matching between the topological features of ground truth and prediction. In this work, we propose the first topologically and feature-wise accurate metric and loss function for supervised image segmentation, which we term Betti matching. We show how induced matchings guarantee the spatially correct matching between barcodes in a segmentation setting. Furthermore, we propose an efficient algorithm to compute the Betti matching of images. We show that the Betti matching error is an interpretable metric to evaluate the topological correctness of segmentations, which is more sensitive than the well-established Betti number error. Moreover, the differentiability of the Betti matching loss enables its use as a loss function. It improves the topological performance of segmentation networks across six diverse datasets while preserving the volumetric performance. Our code is available in https://github.com/nstucki/Betti-matching.

Neural networks trained with ERM (empirical risk minimization) sometimes learn unintended decision rules, in particular when their training data is biased, i.e., when training labels are strongly correlated with undesirable features. To prevent a network from learning such features, recent methods augment training data such that examples displaying spurious correlations (i.e., bias-aligned examples) become a minority, whereas the other, bias-conflicting examples become prevalent. However, these approaches are sometimes difficult to train and scale to real-world data because they rely on generative models or disentangled representations. We propose an alternative based on mixup, a popular augmentation that creates convex combinations of training examples. Our method, coined SelecMix, applies mixup to contradicting pairs of examples, defined as showing either (i) the same label but dissimilar biased features, or (ii) different labels but similar biased features. Identifying such pairs requires comparing examples with respect to unknown biased features. For this, we utilize an auxiliary contrastive model with the popular heuristic that biased features are learned preferentially during training. Experiments on standard benchmarks demonstrate the effectiveness of the method, in particular when label noise complicates the identification of bias-conflicting examples.

Can we modify the training data distribution to encourage the underlying optimization method toward finding solutions with superior generalization performance on in-distribution data? In this work, we approach this question for the first time by comparing the inductive bias of gradient descent (GD) with that of sharpness-aware minimization (SAM). By studying a two-layer CNN, we rigorously prove that SAM learns different features more uniformly, particularly in early epochs. That is, SAM is less susceptible to simplicity bias compared to GD. We also show that examples containing features that are learned early are separable from the rest based on the model's output. Based on this observation, we propose a method that (i) clusters examples based on the network output early in training, (ii) identifies a cluster of examples with similar network output, and (iii) upsamples the rest of examples only once to alleviate the simplicity bias. We show empirically that USEFUL effectively improves the generalization performance on the original data distribution when training with various gradient methods, including (S)GD and SAM. Notably, we demonstrate that our method can be combined with SAM variants and existing data augmentation strategies to achieve, to the best of our knowledge, state-of-the-art performance for training ResNet18 on CIFAR10, STL10, CINIC10, Tiny-ImageNet; ResNet34 on CIFAR100; and VGG19 and DenseNet121 on CIFAR10.

Spectral bias is an important observation of neural network training, stating that the network will learn a low frequency representation of the target function before converging to higher frequency components. This property is interesting due to its link to good generalization in over-parameterized networks. However, in low dimensional settings, a severe spectral bias occurs that obstructs convergence to high frequency components entirely. In order to overcome this limitation, one can encode the inputs using a high frequency sinusoidal encoding. Previous works attempted to explain this phenomenon using Neural Tangent Kernel (NTK) and Fourier analysis. However, NTK does not capture real network dynamics, and Fourier analysis only offers a global perspective on the network properties that induce this bias. In this paper, we provide a novel approach towards understanding spectral bias by directly studying ReLU MLP training dynamics. Specifically, we focus on the connection between the computations of ReLU networks (activation regions), and the speed of gradient descent convergence. We study these dynamics in relation to the spatial information of the signal to understand how they influence spectral bias. We then use this formulation to study the severity of spectral bias in low dimensional settings, and how positional encoding overcomes this.

We formalize constraint-based structure learning of the "true" causal graph from observed data when unobserved variables are also existent. We provide conditions for a "natural" family of constraint-based structure-learning algorithms that output graphs that are Markov equivalent to the causal graph. Under the faithfulness assumption, this natural family contains all exact structure-learning algorithms. We also provide a set of assumptions, under which any natural structure-learning algorithm outputs Markov equivalent graphs to the causal graph. These assumptions can be thought of as a relaxation of faithfulness, and most of them can be directly tested from (the underlying distribution) of the data, particularly when one focuses on structural causal models. We specialize the definitions and results for structural causal models.

We introduce a generalized attention mechanism for spherical domains, enabling Transformer architectures to natively process data defined on the two-dimensional sphere - a critical need in fields such as atmospheric physics, cosmology, and robotics, where preserving spherical symmetries and topology is essential for physical accuracy. By integrating numerical quadrature weights into the attention mechanism, we obtain a geometrically faithful spherical attention that is approximately rotationally equivariant, providing strong inductive biases and leading to better performance than Cartesian approaches. To further enhance both scalability and model performance, we propose neighborhood attention on the sphere, which confines interactions to geodesic neighborhoods. This approach reduces computational complexity and introduces the additional inductive bias for locality, while retaining the symmetry properties of our method. We provide optimized CUDA kernels and memory-efficient implementations to ensure practical applicability. The method is validated on three diverse tasks: simulating shallow water equations on the rotating sphere, spherical image segmentation, and spherical depth estimation. Across all tasks, our spherical Transformers consistently outperform their planar counterparts, highlighting the advantage of geometric priors for learning on spherical domains.

Masked graph autoencoders have emerged as a powerful graph self-supervised learning method that has yet to be fully explored. In this paper, we unveil that the existing discrete edge masking and binary link reconstruction strategies are insufficient to learn topologically informative representations, from the perspective of message propagation on graph neural networks. These limitations include blocking message flows, vulnerability to over-smoothness, and suboptimal neighborhood discriminability. Inspired by these understandings, we explore non-discrete edge masks, which are sampled from a continuous and dispersive probability distribution instead of the discrete Bernoulli distribution. These masks restrict the amount of output messages for each edge, referred to as "bandwidths". We propose a novel, informative, and effective topological masked graph autoencoder using bandwidth masking and a layer-wise bandwidth prediction objective. We demonstrate its powerful graph topological learning ability both theoretically and empirically. Our proposed framework outperforms representative baselines in both self-supervised link prediction (improving the discrete edge reconstructors by at most 20%) and node classification on numerous datasets, solely with a structure-learning pretext. Our implementation is available at https://github.com/Newiz430/Bandana.

Prediction tasks over nodes and edges in networks require careful effort in engineering features used by learning algorithms. Recent research in the broader field of representation learning has led to significant progress in automating prediction by learning the features themselves. However, present feature learning approaches are not expressive enough to capture the diversity of connectivity patterns observed in networks. Here we propose node2vec, an algorithmic framework for learning continuous feature representations for nodes in networks. In node2vec, we learn a mapping of nodes to a low-dimensional space of features that maximizes the likelihood of preserving network neighborhoods of nodes. We define a flexible notion of a node's network neighborhood and design a biased random walk procedure, which efficiently explores diverse neighborhoods. Our algorithm generalizes prior work which is based on rigid notions of network neighborhoods, and we argue that the added flexibility in exploring neighborhoods is the key to learning richer representations. We demonstrate the efficacy of node2vec over existing state-of-the-art techniques on multi-label classification and link prediction in several real-world networks from diverse domains. Taken together, our work represents a new way for efficiently learning state-of-the-art task-independent representations in complex networks.

We introduce the concept of programmable feature engineering for time series modeling and propose a feature programming framework. This framework generates large amounts of predictive features for noisy multivariate time series while allowing users to incorporate their inductive bias with minimal effort. The key motivation of our framework is to view any multivariate time series as a cumulative sum of fine-grained trajectory increments, with each increment governed by a novel spin-gas dynamical Ising model. This fine-grained perspective motivates the development of a parsimonious set of operators that summarize multivariate time series in an abstract fashion, serving as the foundation for large-scale automated feature engineering. Numerically, we validate the efficacy of our method on several synthetic and real-world noisy time series datasets.

Models need appropriate inductive biases to effectively learn from small amounts of data and generalize systematically outside of the training distribution. While Transformers are highly versatile and powerful, they can still benefit from enhanced structural inductive biases for seq2seq tasks, especially those involving syntactic transformations, such as converting active to passive voice or semantic parsing. In this paper, we propose to strengthen the structural inductive bias of a Transformer by intermediate pre-training to perform synthetically generated syntactic transformations of dependency trees given a description of the transformation. Our experiments confirm that this helps with few-shot learning of syntactic tasks such as chunking, and also improves structural generalization for semantic parsing. Our analysis shows that the intermediate pre-training leads to attention heads that keep track of which syntactic transformation needs to be applied to which token, and that the model can leverage these attention heads on downstream tasks.

Hypergraphs are marked by complex topology, expressing higher-order interactions among multiple nodes with hyperedges, and better capturing the topology is essential for effective representation learning. Recent advances in generative self-supervised learning (SSL) suggest that hypergraph neural networks learned from generative self supervision have the potential to effectively encode the complex hypergraph topology. Designing a generative SSL strategy for hypergraphs, however, is not straightforward. Questions remain with regard to its generative SSL task, connection to downstream tasks, and empirical properties of learned representations. In light of the promises and challenges, we propose a novel generative SSL strategy for hypergraphs. We first formulate a generative SSL task on hypergraphs, hyperedge filling, and highlight its theoretical connection to node classification. Based on the generative SSL task, we propose a hypergraph SSL method, HypeBoy. HypeBoy learns effective general-purpose hypergraph representations, outperforming 16 baseline methods across 11 benchmark datasets.

Concept-based interpretability methods aim to explain deep neural network model predictions using a predefined set of semantic concepts. These methods evaluate a trained model on a new, "probe" dataset and correlate model predictions with the visual concepts labeled in that dataset. Despite their popularity, they suffer from limitations that are not well-understood and articulated by the literature. In this work, we analyze three commonly overlooked factors in concept-based explanations. First, the choice of the probe dataset has a profound impact on the generated explanations. Our analysis reveals that different probe datasets may lead to very different explanations, and suggests that the explanations are not generalizable outside the probe dataset. Second, we find that concepts in the probe dataset are often less salient and harder to learn than the classes they claim to explain, calling into question the correctness of the explanations. We argue that only visually salient concepts should be used in concept-based explanations. Finally, while existing methods use hundreds or even thousands of concepts, our human studies reveal a much stricter upper bound of 32 concepts or less, beyond which the explanations are much less practically useful. We make suggestions for future development and analysis of concept-based interpretability methods. Code for our analysis and user interface can be found at https://github.com/princetonvisualai/OverlookedFactors

Convolutional Neural Networks (CNN) have been successful in processing data signals that are uniformly sampled in the spatial domain (e.g., images). However, most data signals do not natively exist on a grid, and in the process of being sampled onto a uniform physical grid suffer significant aliasing error and information loss. Moreover, signals can exist in different topological structures as, for example, points, lines, surfaces and volumes. It has been challenging to analyze signals with mixed topologies (for example, point cloud with surface mesh). To this end, we develop mathematical formulations for Non-Uniform Fourier Transforms (NUFT) to directly, and optimally, sample nonuniform data signals of different topologies defined on a simplex mesh into the spectral domain with no spatial sampling error. The spectral transform is performed in the Euclidean space, which removes the translation ambiguity from works on the graph spectrum. Our representation has four distinct advantages: (1) the process causes no spatial sampling error during the initial sampling, (2) the generality of this approach provides a unified framework for using CNNs to analyze signals of mixed topologies, (3) it allows us to leverage state-of-the-art backbone CNN architectures for effective learning without having to design a particular architecture for a particular data structure in an ad-hoc fashion, and (4) the representation allows weighted meshes where each element has a different weight (i.e., texture) indicating local properties. We achieve results on par with the state-of-the-art for the 3D shape retrieval task, and a new state-of-the-art for the point cloud to surface reconstruction task.

In this paper, we study the problem of unsupervised object segmentation from single images. We do not introduce a new algorithm, but systematically investigate the effectiveness of existing unsupervised models on challenging real-world images. We firstly introduce four complexity factors to quantitatively measure the distributions of object- and scene-level biases in appearance and geometry for datasets with human annotations. With the aid of these factors, we empirically find that, not surprisingly, existing unsupervised models catastrophically fail to segment generic objects in real-world images, although they can easily achieve excellent performance on numerous simple synthetic datasets, due to the vast gap in objectness biases between synthetic and real images. By conducting extensive experiments on multiple groups of ablated real-world datasets, we ultimately find that the key factors underlying the colossal failure of existing unsupervised models on real-world images are the challenging distributions of object- and scene-level biases in appearance and geometry. Because of this, the inductive biases introduced in existing unsupervised models can hardly capture the diverse object distributions. Our research results suggest that future work should exploit more explicit objectness biases in the network design.

Two different approaches exist to handle missing values for prediction: either imputation, prior to fitting any predictive algorithms, or dedicated methods able to natively incorporate missing values. While imputation is widely (and easily) use, it is unfortunately biased when low-capacity predictors (such as linear models) are applied afterward. However, in practice, naive imputation exhibits good predictive performance. In this paper, we study the impact of imputation in a high-dimensional linear model with MCAR missing data. We prove that zero imputation performs an implicit regularization closely related to the ridge method, often used in high-dimensional problems. Leveraging on this connection, we establish that the imputation bias is controlled by a ridge bias, which vanishes in high dimension. As a predictor, we argue in favor of the averaged SGD strategy, applied to zero-imputed data. We establish an upper bound on its generalization error, highlighting that imputation is benign in the d sqrt n regime. Experiments illustrate our findings.

Recent studies show that instruction tuning and learning from human feedback improve the abilities of large language models (LMs) dramatically. While these tuning methods can make models generate high-quality text, we conjecture that more implicit cognitive biases may arise in these fine-tuned models. Our work provides evidence that these fine-tuned models exhibit biases that were absent or less pronounced in their pretrained predecessors. We examine the extent of this phenomenon in three cognitive biases - the decoy effect, the certainty effect, and the belief bias - all of which are known to influence human decision-making and reasoning. Our findings highlight the presence of these biases in various models, especially those that have undergone instruction tuning, such as Flan-T5, GPT3.5, and GPT4. This research constitutes a step toward comprehending cognitive biases in instruction-tuned LMs, which is crucial for the development of more reliable and unbiased language models.

Wikipedia relies on an extensive review process to verify that the content of each individual page is unbiased and presents a neutral point of view. Less attention has been paid to possible biases in the hyperlink structure of Wikipedia, which has a significant influence on the user's exploration process when visiting more than one page. The evaluation of hyperlink bias is challenging because it depends on the global view rather than the text of individual pages. In this paper, we focus on the influence of the interconnect topology between articles describing complementary aspects of polarizing topics. We introduce a novel measure of exposure to diverse information to quantify users' exposure to different aspects of a topic throughout an entire surfing session, rather than just one click ahead. We apply this measure to six polarizing topics (e.g., gun control and gun right), and we identify cases in which the network topology significantly limits the exposure of users to diverse information on the topic, encouraging users to remain in a knowledge bubble. Our findings demonstrate the importance of evaluating Wikipedia's network structure in addition to the extensive review of individual articles.

Persistent homology (PH) provides topological descriptors for geometric data, such as weighted graphs, which are interpretable, stable to perturbations, and invariant under, e.g., relabeling. Most applications of PH focus on the one-parameter case -- where the descriptors summarize the changes in topology of data as it is filtered by a single quantity of interest -- and there is now a wide array of methods enabling the use of one-parameter PH descriptors in data science, which rely on the stable vectorization of these descriptors as elements of a Hilbert space. Although the multiparameter PH (MPH) of data that is filtered by several quantities of interest encodes much richer information than its one-parameter counterpart, the scarceness of stability results for MPH descriptors has so far limited the available options for the stable vectorization of MPH. In this paper, we aim to bring together the best of both worlds by showing how the interpretation of signed barcodes -- a recent family of MPH descriptors -- as signed measures leads to natural extensions of vectorization strategies from one parameter to multiple parameters. The resulting feature vectors are easy to define and to compute, and provably stable. While, as a proof of concept, we focus on simple choices of signed barcodes and vectorizations, we already see notable performance improvements when comparing our feature vectors to state-of-the-art topology-based methods on various types of data.

Learning representations that generalize under distribution shifts is critical for building robust machine learning models. However, despite significant efforts in recent years, algorithmic advances in this direction have been limited. In this work, we seek to understand the fundamental difficulty of out-of-distribution generalization with deep neural networks. We first empirically show that perhaps surprisingly, even allowing a neural network to explicitly fit the representations obtained from a teacher network that can generalize out-of-distribution is insufficient for the generalization of the student network. Then, by a theoretical study of two-layer ReLU networks optimized by stochastic gradient descent (SGD) under a structured feature model, we identify a fundamental yet unexplored feature learning proclivity of neural networks, feature contamination: neural networks can learn uncorrelated features together with predictive features, resulting in generalization failure under distribution shifts. Notably, this mechanism essentially differs from the prevailing narrative in the literature that attributes the generalization failure to spurious correlations. Overall, our results offer new insights into the non-linear feature learning dynamics of neural networks and highlight the necessity of considering inductive biases in out-of-distribution generalization.

Existing alignment methods share a common topology of information flow, where reward information is collected from humans, modeled with preference learning, and used to tune language models. However, this shared topology has not been systematically characterized, nor have its alternatives been thoroughly explored, leaving the problems of low data efficiency and unreliable generalization unaddressed. As a solution, we introduce a theoretical framework for investigating reward generalization in reinforcement learning from human feedback (RLHF), focusing on the topology of information flow at both macro and micro levels. At the macro level, we portray the RLHF information flow as an autoencoding process over behavior distributions, formalizing the RLHF objective of distributional consistency between human preference and model behavior. At the micro level, we present induced Bayesian networks as a theory of reward generalization in RLHF, introducing fine-grained dataset topologies into generalization bounds. Combining analysis on both levels, we propose reward modeling from tree-structured preference information. It is shown to reduce reward uncertainty by up to Theta(log n/loglog n) times compared to baselines, where n is the dataset size. Validation on three NLP tasks shows that our tree-based reward model achieves an average win rate of 65% against baseline methods, thus improving reward generalization for free via topology design.

Inductive reasoning is a core problem-solving capacity: humans can identify underlying principles from a few examples, which can then be robustly generalized to novel scenarios. Recent work has evaluated large language models (LLMs) on inductive reasoning tasks by directly prompting them yielding "in context learning." This can work well for straightforward inductive tasks, but performs very poorly on more complex tasks such as the Abstraction and Reasoning Corpus (ARC). In this work, we propose to improve the inductive reasoning ability of LLMs by generating explicit hypotheses at multiple levels of abstraction: we prompt the LLM to propose multiple abstract hypotheses about the problem, in natural language, then implement the natural language hypotheses as concrete Python programs. These programs can be directly verified by running on the observed examples and generalized to novel inputs. Because of the prohibitive cost of generation with state-of-the-art LLMs, we consider a middle step to filter the set of hypotheses that will be implemented into programs: we either ask the LLM to summarize into a smaller set of hypotheses, or ask human annotators to select a subset of the hypotheses. We verify our pipeline's effectiveness on the ARC visual inductive reasoning benchmark, its variant 1D-ARC, and string transformation dataset SyGuS. On a random 40-problem subset of ARC, our automated pipeline using LLM summaries achieves 27.5% accuracy, significantly outperforming the direct prompting baseline (accuracy of 12.5%). With the minimal human input of selecting from LLM-generated candidates, the performance is boosted to 37.5%. (And we argue this is a lower bound on the performance of our approach without filtering.) Our ablation studies show that abstract hypothesis generation and concrete program representations are both beneficial for LLMs to perform inductive reasoning tasks.

Despite their remarkable effectiveness and broad application, the drivers of success underlying ensembles of trees are still not fully understood. In this paper, we highlight how interpreting tree ensembles as adaptive and self-regularizing smoothers can provide new intuition and deeper insight to this topic. We use this perspective to show that, when studied as smoothers, randomized tree ensembles not only make predictions that are quantifiably more smooth than the predictions of the individual trees they consist of, but also further regulate their smoothness at test-time based on the dissimilarity between testing and training inputs. First, we use this insight to revisit, refine and reconcile two recent explanations of forest success by providing a new way of quantifying the conjectured behaviors of tree ensembles objectively by measuring the effective degree of smoothing they imply. Then, we move beyond existing explanations for the mechanisms by which tree ensembles improve upon individual trees and challenge the popular wisdom that the superior performance of forests should be understood as a consequence of variance reduction alone. We argue that the current high-level dichotomy into bias- and variance-reduction prevalent in statistics is insufficient to understand tree ensembles -- because the prevailing definition of bias does not capture differences in the expressivity of the hypothesis classes formed by trees and forests. Instead, we show that forests can improve upon trees by three distinct mechanisms that are usually implicitly entangled. In particular, we demonstrate that the smoothing effect of ensembling can reduce variance in predictions due to noise in outcome generation, reduce variability in the quality of the learned function given fixed input data and reduce potential bias in learnable functions by enriching the available hypothesis space.

Self-supervised learning holds promise to revolutionize molecule property prediction - a central task to drug discovery and many more industries - by enabling data efficient learning from scarce experimental data. Despite significant progress, non-pretrained methods can be still competitive in certain settings. We reason that architecture might be a key bottleneck. In particular, enriching the backbone architecture with domain-specific inductive biases has been key for the success of self-supervised learning in other domains. In this spirit, we methodologically explore the design space of the self-attention mechanism tailored to molecular data. We identify a novel variant of self-attention adapted to processing molecules, inspired by the relative self-attention layer, which involves fusing embedded graph and distance relationships between atoms. Our main contribution is Relative Molecule Attention Transformer (R-MAT): a novel Transformer-based model based on the developed self-attention layer that achieves state-of-the-art or very competitive results across a~wide range of molecule property prediction tasks.

In contrast to classical reinforcement learning, distributional reinforcement learning algorithms aim to learn the distribution of returns rather than their expected value. Since the nature of the return distribution is generally unknown a priori or arbitrarily complex, a common approach finds approximations within a set of representable, parametric distributions. Typically, this involves a projection of the unconstrained distribution onto the set of simplified distributions. We argue that this projection step entails a strong inductive bias when coupled with neural networks and gradient descent, thereby profoundly impacting the generalization behavior of learned models. In order to facilitate reliable uncertainty estimation through diversity, this work studies the combination of several different projections and representations in a distributional ensemble. We establish theoretical properties of such projection ensembles and derive an algorithm that uses ensemble disagreement, measured by the average 1-Wasserstein distance, as a bonus for deep exploration. We evaluate our algorithm on the behavior suite benchmark and find that diverse projection ensembles lead to significant performance improvements over existing methods on a wide variety of tasks with the most pronounced gains in directed exploration problems.

Graph Neural Networks (GNNs) are able to achieve high classification accuracy on many important real world datasets, but provide no rigorous notion of predictive uncertainty. Quantifying the confidence of GNN models is difficult due to the dependence between datapoints induced by the graph structure. We leverage recent advances in conformal prediction to construct prediction sets for node classification in inductive learning scenarios. We do this by taking an existing approach for conformal classification that relies on exchangeable data and modifying it by appropriately weighting the conformal scores to reflect the network structure. We show through experiments on standard benchmark datasets using popular GNN models that our approach provides tighter and better calibrated prediction sets than a naive application of conformal prediction.

Despite the significant recent progress in deep generative models, the underlying structure of their latent spaces is still poorly understood, thereby making the task of performing semantically meaningful latent traversals an open research challenge. Most prior work has aimed to solve this challenge by modeling latent structures linearly, and finding corresponding linear directions which result in `disentangled' generations. In this work, we instead propose to model latent structures with a learned dynamic potential landscape, thereby performing latent traversals as the flow of samples down the landscape's gradient. Inspired by physics, optimal transport, and neuroscience, these potential landscapes are learned as physically realistic partial differential equations, thereby allowing them to flexibly vary over both space and time. To achieve disentanglement, multiple potentials are learned simultaneously, and are constrained by a classifier to be distinct and semantically self-consistent. Experimentally, we demonstrate that our method achieves both more qualitatively and quantitatively disentangled trajectories than state-of-the-art baselines. Further, we demonstrate that our method can be integrated as a regularization term during training, thereby acting as an inductive bias towards the learning of structured representations, ultimately improving model likelihood on similarly structured data.

Recently, researchers have uncovered that neural retrieval models prefer AI-generated content (AIGC), called source bias. Compared to active search behavior, recommendation represents another important means of information acquisition, where users are more prone to source bias. Furthermore, delving into the recommendation scenario, as AIGC becomes integrated within the feedback loop involving users, data, and the recommender system, it progressively contaminates the candidate items, the user interaction history, and ultimately, the data used to train the recommendation models. How and to what extent the source bias affects the neural recommendation models within feedback loop remains unknown. In this study, we extend the investigation of source bias into the realm of recommender systems, specifically examining its impact across different phases of the feedback loop. We conceptualize the progression of AIGC integration into the recommendation content ecosystem in three distinct phases-HGC dominate, HGC-AIGC coexist, and AIGC dominance-each representing past, present, and future states, respectively. Through extensive experiments across three datasets from diverse domains, we demonstrate the prevalence of source bias and reveal a potential digital echo chamber with source bias amplification throughout the feedback loop. This trend risks creating a recommender ecosystem with limited information source, such as AIGC, being disproportionately recommended. To counteract this bias and prevent its escalation in the feedback loop, we introduce a black-box debiasing method that maintains model impartiality towards both HGC and AIGC. Our experimental results validate the effectiveness of the proposed debiasing method, confirming its potential to disrupt the feedback loop.

As LLMs are increasingly integrated into user-facing applications, addressing biases that perpetuate societal inequalities is crucial. While much work has gone into measuring or mitigating biases in these models, fewer studies have investigated their origins. Therefore, this study examines the correlation between gender-occupation bias in pre-training data and their manifestation in LLMs, focusing on the Dolma dataset and the OLMo model. Using zero-shot prompting and token co-occurrence analyses, we explore how biases in training data influence model outputs. Our findings reveal that biases present in pre-training data are amplified in model outputs. The study also examines the effects of prompt types, hyperparameters, and instruction-tuning on bias expression, finding instruction-tuning partially alleviating representational bias while still maintaining overall stereotypical gender associations, whereas hyperparameters and prompting variation have a lesser effect on bias expression. Our research traces bias throughout the LLM development pipeline and underscores the importance of mitigating bias at the pretraining stage.

We introduce a randomized topological augmentor based on Schur complements for Graph Contrastive Learning (GCL). Given a graph laplacian matrix, the technique generates unbiased approximations of its Schur complements and treats the corresponding graphs as augmented views. We discuss the benefits of our approach, provide theoretical justifications and present connections with graph diffusion. Unlike previous efforts, we study the empirical effectiveness of the augmentor in a controlled fashion by varying the design choices for subsequent GCL phases, such as encoding and contrasting. Extensive experiments on node and graph classification benchmarks demonstrate that our technique consistently outperforms pre-defined and adaptive augmentation approaches to achieve state-of-the-art results.

We study deceptive fairness attacks on graphs to answer the following question: How can we achieve poisoning attacks on a graph learning model to exacerbate the bias deceptively? We answer this question via a bi-level optimization problem and propose a meta learning-based framework named FATE. FATE is broadly applicable with respect to various fairness definitions and graph learning models, as well as arbitrary choices of manipulation operations. We further instantiate FATE to attack statistical parity and individual fairness on graph neural networks. We conduct extensive experimental evaluations on real-world datasets in the task of semi-supervised node classification. The experimental results demonstrate that FATE could amplify the bias of graph neural networks with or without fairness consideration while maintaining the utility on the downstream task. We hope this paper provides insights into the adversarial robustness of fair graph learning and can shed light on designing robust and fair graph learning in future studies.

Set representation has become ubiquitous in deep learning for modeling the inductive bias of neural networks that are insensitive to the input order. DeepSets is the most widely used neural network architecture for set representation. It involves embedding each set element into a latent space with dimension L, followed by a sum pooling to obtain a whole-set embedding, and finally mapping the whole-set embedding to the output. In this work, we investigate the impact of the dimension L on the expressive power of DeepSets. Previous analyses either oversimplified high-dimensional features to be one-dimensional features or were limited to analytic activations, thereby diverging from practical use or resulting in L that grows exponentially with the set size N and feature dimension D. To investigate the minimal value of L that achieves sufficient expressive power, we present two set-element embedding layers: (a) linear + power activation (LP) and (b) linear + exponential activations (LE). We demonstrate that L being poly(N, D) is sufficient for set representation using both embedding layers. We also provide a lower bound of L for the LP embedding layer. Furthermore, we extend our results to permutation-equivariant set functions and the complex field.

Despite the impressive advancements of Large Language Models (LLMs) in generating text, they are often limited by the knowledge contained in the input and prone to producing inaccurate or hallucinated content. To tackle these issues, Retrieval-augmented Generation (RAG) is employed as an effective strategy to enhance the available knowledge base and anchor the responses in reality by pulling additional texts from external databases. In real-world applications, texts are often linked through entities within a graph, such as citations in academic papers or comments in social networks. This paper exploits these topological relationships to guide the retrieval process in RAG. Specifically, we explore two kinds of topological connections: proximity-based, focusing on closely connected nodes, and role-based, which looks at nodes sharing similar subgraph structures. Our empirical research confirms their relevance to text relationships, leading us to develop a Topology-aware Retrieval-augmented Generation framework. This framework includes a retrieval module that selects texts based on their topological relationships and an aggregation module that integrates these texts into prompts to stimulate LLMs for text generation. We have curated established text-attributed networks and conducted comprehensive experiments to validate the effectiveness of this framework, demonstrating its potential to enhance RAG with topological awareness.

Graph Neural Networks (GNNs) are popular models for machine learning on graphs that typically follow the message-passing paradigm, whereby the feature of a node is updated recursively upon aggregating information over its neighbors. While exchanging messages over the input graph endows GNNs with a strong inductive bias, it can also make GNNs susceptible to over-squashing, thereby preventing them from capturing long-range interactions in the given graph. To rectify this issue, graph rewiring techniques have been proposed as a means of improving information flow by altering the graph connectivity. In this work, we identify three desiderata for graph-rewiring: (i) reduce over-squashing, (ii) respect the locality of the graph, and (iii) preserve the sparsity of the graph. We highlight fundamental trade-offs that occur between spatial and spectral rewiring techniques; while the former often satisfy (i) and (ii) but not (iii), the latter generally satisfy (i) and (iii) at the expense of (ii). We propose a novel rewiring framework that satisfies all of (i)--(iii) through a locality-aware sequence of rewiring operations. We then discuss a specific instance of such rewiring framework and validate its effectiveness on several real-world benchmarks, showing that it either matches or significantly outperforms existing rewiring approaches.

Long-range dependencies are critical for effective graph representation learning, yet most existing datasets focus on small graphs tailored to inductive tasks, offering limited insight into long-range interactions. Current evaluations primarily compare models employing global attention (e.g., graph transformers) with those using local neighborhood aggregation (e.g., message-passing neural networks) without a direct measurement of long-range dependency. In this work, we introduce City-Networks, a novel large-scale transductive learning dataset derived from real-world city roads. This dataset features graphs with over 10^5 nodes and significantly larger diameters than those in existing benchmarks, naturally embodying long-range information. We annotate the graphs using an eccentricity-based approach, ensuring that the classification task inherently requires information from distant nodes. Furthermore, we propose a model-agnostic measurement based on the Jacobians of neighbors from distant hops, offering a principled quantification of long-range dependencies. Finally, we provide theoretical justifications for both our dataset design and the proposed measurement - particularly by focusing on over-smoothing and influence score dilution - which establishes a robust foundation for further exploration of long-range interactions in graph neural networks.

To fully understand the behavior of a large language model (LLM) requires our understanding of its input space. If this input space differs from our assumption, our understanding of and conclusions about the LLM is likely flawed, regardless of its architecture. Here, we elucidate the structure of the token embeddings, the input domain for LLMs, both empirically and theoretically. We present a generalized and statistically testable model where the neighborhood of each token splits into well-defined signal and noise dimensions. This model is based on a generalization of a manifold called a fiber bundle, so we denote our hypothesis test as the ``fiber bundle null.'' Failing to reject the null is uninformative, but rejecting it at a specific token indicates that token has a statistically significant local structure, and so is of interest to us. By running our test over several open-source LLMs, each with unique token embeddings, we find that the null is frequently rejected, and so the token subspace is provably not a fiber bundle and hence also not a manifold. As a consequence of our findings, when an LLM is presented with two semantically equivalent prompts, and if one prompt contains a token implicated by our test, that prompt will likely exhibit more output variability proportional to the local signal dimension of the token.

Various design settings for in-context learning (ICL), such as the choice and order of the in-context examples, can bias a model toward a particular prediction without being reflective of an understanding of the task. While many studies discuss these design choices, there have been few systematic investigations into categorizing them and mitigating their impact. In this work, we define a typology for three types of label biases in ICL for text classification: vanilla-label bias, context-label bias, and domain-label bias (which we conceptualize and detect for the first time). Our analysis demonstrates that prior label bias calibration methods fall short of addressing all three types of biases. Specifically, domain-label bias restricts LLMs to random-level performance on many tasks regardless of the choice of in-context examples. To mitigate the effect of these biases, we propose a simple bias calibration method that estimates a language model's label bias using random in-domain words from the task corpus. After controlling for this estimated bias when making predictions, our novel domain-context calibration significantly improves the ICL performance of GPT-J and GPT-3 on a wide range of tasks. The gain is substantial on tasks with large domain-label bias (up to 37% in Macro-F1). Furthermore, our results generalize to models with different scales, pretraining methods, and manually-designed task instructions, showing the prevalence of label biases in ICL.

The structure of biological neural circuits-modular, hierarchical, and sparsely interconnected-reflects an efficient trade-off between wiring cost, functional specialization, and robustness. These principles offer valuable insights for artificial neural network (ANN) design, especially as networks grow in depth and scale. Sparsity, in particular, has been widely explored for reducing memory and computation, improving speed, and enhancing generalization. Motivated by systems neuroscience findings, we explore how patterns of functional connectivity in the mouse visual cortex-specifically, ensemble-to-ensemble communication, can inform ANN design. We introduce G2GNet, a novel architecture that imposes sparse, modular connectivity across feedforward layers. Despite having significantly fewer parameters than fully connected models, G2GNet achieves superior accuracy on standard vision benchmarks. To our knowledge, this is the first architecture to incorporate biologically observed functional connectivity patterns as a structural bias in ANN design. We complement this static bias with a dynamic sparse training (DST) mechanism that prunes and regrows edges during training. We also propose a Hebbian-inspired rewiring rule based on activation correlations, drawing on principles of biological plasticity. G2GNet achieves up to 75% sparsity while improving accuracy by up to 4.3% on benchmarks, including Fashion-MNIST, CIFAR-10, and CIFAR-100, outperforming dense baselines with far fewer computations.

Universality is a key hypothesis in mechanistic interpretability -- that different models learn similar features and circuits when trained on similar tasks. In this work, we study the universality hypothesis by examining how small neural networks learn to implement group composition. We present a novel algorithm by which neural networks may implement composition for any finite group via mathematical representation theory. We then show that networks consistently learn this algorithm by reverse engineering model logits and weights, and confirm our understanding using ablations. By studying networks of differing architectures trained on various groups, we find mixed evidence for universality: using our algorithm, we can completely characterize the family of circuits and features that networks learn on this task, but for a given network the precise circuits learned -- as well as the order they develop -- are arbitrary.

Although large multimodal models (LMMs) have demonstrated remarkable capabilities in visual scene interpretation and reasoning, their capacity for complex and precise 3-dimensional spatial reasoning remains uncertain. Existing benchmarks focus predominantly on 2D spatial understanding and lack a framework to comprehensively evaluate 6D spatial reasoning across varying complexities. To address this limitation, we present PulseCheck457, a scalable and unbiased synthetic dataset designed with 4 key capability for spatial reasoning: multi-object recognition, 2D location, 3D location, and 3D orientation. We develop a cascading evaluation structure, constructing 7 question types across 5 difficulty levels that range from basic single object recognition to our new proposed complex 6D spatial reasoning tasks. We evaluated various large multimodal models (LMMs) on PulseCheck457, observing a general decline in performance as task complexity increases, particularly in 3D reasoning and 6D spatial tasks. To quantify these challenges, we introduce the Relative Performance Dropping Rate (RPDR), highlighting key weaknesses in 3D reasoning capabilities. Leveraging the unbiased attribute design of our dataset, we also uncover prediction biases across different attributes, with similar patterns observed in real-world image settings.

Bias in text-to-image (T2I) models can propagate unfair social representations and may be used to aggressively market ideas or push controversial agendas. Existing T2I model bias evaluation methods only focus on social biases. We look beyond that and instead propose an evaluation methodology to quantify general biases in T2I generative models, without any preconceived notions. We assess four state-of-the-art T2I models and compare their baseline bias characteristics to their respective variants (two for each), where certain biases have been intentionally induced. We propose three evaluation metrics to assess model biases including: (i) Distribution bias, (ii) Jaccard hallucination and (iii) Generative miss-rate. We conduct two evaluation studies, modelling biases under general, and task-oriented conditions, using a marketing scenario as the domain for the latter. We also quantify social biases to compare our findings to related works. Finally, our methodology is transferred to evaluate captioned-image datasets and measure their bias. Our approach is objective, domain-agnostic and consistently measures different forms of T2I model biases. We have developed a web application and practical implementation of what has been proposed in this work, which is at https://huggingface.co/spaces/JVice/try-before-you-bias. A video series with demonstrations is available at https://www.youtube.com/channel/UCk-0xyUyT0MSd_hkp4jQt1Q

Interference is ubiquitous when conducting causal experiments over networks. Except for certain network structures, causal inference on the network in the presence of interference is difficult due to the entanglement between the treatment assignments and the interference levels. In this article, we conduct causal inference under interference on an observed, sparse but connected network, and we propose a novel design of experiments based on an independent set. Compared to conventional designs, the independent-set design focuses on an independent subset of data and controls their interference exposures through the assignments to the rest (auxiliary set). We provide a lower bound on the size of the independent set from a greedy algorithm , and justify the theoretical performance of estimators under the proposed design. Our approach is capable of estimating both spillover effects and treatment effects. We justify its superiority over conventional methods and illustrate the empirical performance through simulations.