Daily Papers

Graph Neural Networks (GNNs) have been widely adopted for drug discovery with molecular graphs. Nevertheless, current GNNs are mainly good at leveraging short-range interactions (SRI) but struggle to capture long-range interactions (LRI), both of which are crucial for determining molecular properties. To tackle this issue, we propose a method that implicitly projects all original atoms into a few Neural Atoms, which abstracts the collective information of atomic groups within a molecule. Specifically, we explicitly exchange the information among neural atoms and project them back to the atoms' representations as an enhancement. With this mechanism, neural atoms establish the communication channels among distant nodes, effectively reducing the interaction scope of arbitrary node pairs into a single hop. To provide an inspection of our method from a physical perspective, we reveal its connection with the traditional LRI calculation method, Ewald Summation. We conduct extensive experiments on three long-range graph benchmarks, covering both graph-level and link-level tasks on molecular graphs. We empirically justify that our method can be equipped with an arbitrary GNN and help to capture LRI.

The fundamental units of internal representations in large language models (LLMs) remain undefined, limiting further understanding of their mechanisms. Neurons or features are often regarded as such units, yet neurons suffer from polysemy, while features face concerns of unreliable reconstruction and instability. To address this issue, we propose the Atoms Theory, which defines such units as atoms. We introduce the atomic inner product (AIP) to correct representation shifting, formally define atoms, and prove the conditions that atoms satisfy the Restricted Isometry Property (RIP), ensuring stable sparse representations over atom set and linking to compressed sensing. Under stronger conditions, we further establish the uniqueness and exact ell_1 recoverability of the sparse representations, and provide guarantees that single-layer sparse autoencoders (SAEs) with threshold activations can reliably identify the atoms. To validate the Atoms Theory, we train threshold-activated SAEs on Gemma2-2B, Gemma2-9B, and Llama3.1-8B, achieving 99.9% sparse reconstruction across layers on average, and more than 99.8% of atoms satisfy the uniqueness condition, compared to 0.5% for neurons and 68.2% for features, showing that atoms more faithfully capture intrinsic representations of LLMs. Scaling experiments further reveal the link between SAEs size and recovery capacity. Overall, this work systematically introduces and validates Atoms Theory of LLMs, providing a theoretical framework for understanding internal representations and a foundation for mechanistic interpretability. Code available at https://github.com/ChenhuiHu/towards_atoms.

The static synaptic connectivity of neuronal circuits stands in direct contrast to the dynamics of their function. As in changing community interactions, different neurons can participate actively in various combinations to effect behaviors at different times. We introduce an unsupervised approach to learn the dynamic affinities between neurons in live, behaving animals, and to reveal which communities form among neurons at different times. The inference occurs in two major steps. First, pairwise non-linear affinities between neuronal traces from brain-wide calcium activity are organized by non-negative tensor factorization (NTF). Each factor specifies which groups of neurons are most likely interacting for an inferred interval in time, and for which animals. Finally, a generative model that allows for weighted community detection is applied to the functional motifs produced by NTF to reveal a dynamic functional connectome. Since time codes the different experimental variables (e.g., application of chemical stimuli), this provides an atlas of neural motifs active during separate stages of an experiment (e.g., stimulus application or spontaneous behaviors). Results from our analysis are experimentally validated, confirming that our method is able to robustly predict causal interactions between neurons to generate behavior. Code is available at https://github.com/dyballa/dynamic-connectomes.

Machine learning potentials (MLPs) trained on accurate quantum chemical data can retain the high accuracy, while inflicting little computational demands. On the downside, they need to be trained for each individual system. In recent years, a vast number of MLPs has been trained from scratch because learning additional data typically requires to train again on all data to not forget previously acquired knowledge. Additionally, most common structural descriptors of MLPs cannot represent efficiently a large number of different chemical elements. In this work, we tackle these problems by introducing element-embracing atom-centered symmetry functions (eeACSFs) which combine structural properties and element information from the periodic table. These eeACSFs are a key for our development of a lifelong machine learning potential (lMLP). Uncertainty quantification can be exploited to transgress a fixed, pre-trained MLP to arrive at a continuously adapting lMLP, because a predefined level of accuracy can be ensured. To extend the applicability of an lMLP to new systems, we apply continual learning strategies to enable autonomous and on-the-fly training on a continuous stream of new data. For the training of deep neural networks, we propose the continual resilient (CoRe) optimizer and incremental learning strategies relying on rehearsal of data, regularization of parameters, and the architecture of the model.

Human brains respond to semantic features of presented stimuli with different neurons. It is then curious whether modern deep neural networks admit a similar behavior pattern. Specifically, this paper finds a small cluster of neurons in a diffusion model corresponding to a particular subject. We call those neurons the concept neurons. They can be identified by statistics of network gradients to a stimulation connected with the given subject. The concept neurons demonstrate magnetic properties in interpreting and manipulating generation results. Shutting them can directly yield the related subject contextualized in different scenes. Concatenating multiple clusters of concept neurons can vividly generate all related concepts in a single image. A few steps of further fine-tuning can enhance the multi-concept capability, which may be the first to manage to generate up to four different subjects in a single image. For large-scale applications, the concept neurons are environmentally friendly as we only need to store a sparse cluster of int index instead of dense float32 values of the parameters, which reduces storage consumption by 90\% compared with previous subject-driven generation methods. Extensive qualitative and quantitative studies on diverse scenarios show the superiority of our method in interpreting and manipulating diffusion models.

The deep neural nets of modern artificial intelligence (AI) have not achieved defining features of biological intelligence, including abstraction, causal learning, and energy-efficiency. While scaling to larger models has delivered performance improvements for current applications, more brain-like capacities may demand new theories, models, and methods for designing artificial learning systems. Here, we argue that this opportunity to reassess insights from the brain should stimulate cooperation between AI research and theory-driven computational neuroscience (CN). To motivate a brain basis of neural computation, we present a dynamical view of intelligence from which we elaborate concepts of sparsity in network structure, temporal dynamics, and interactive learning. In particular, we suggest that temporal dynamics, as expressed through neural synchrony, nested oscillations, and flexible sequences, provide a rich computational layer for reading and updating hierarchical models distributed in long-term memory networks. Moreover, embracing agent-centered paradigms in AI and CN will accelerate our understanding of the complex dynamics and behaviors that build useful world models. A convergence of AI/CN theories and objectives will reveal dynamical principles of intelligence for brains and engineered learning systems. This article was inspired by our symposium on dynamical neuroscience and machine learning at the 6th Annual US/NIH BRAIN Initiative Investigators Meeting.

Sparse autoencoders have recently produced dictionaries of high-dimensional vectors corresponding to the universe of concepts represented by large language models. We find that this concept universe has interesting structure at three levels: 1) The "atomic" small-scale structure contains "crystals" whose faces are parallelograms or trapezoids, generalizing well-known examples such as (man-woman-king-queen). We find that the quality of such parallelograms and associated function vectors improves greatly when projecting out global distractor directions such as word length, which is efficiently done with linear discriminant analysis. 2) The "brain" intermediate-scale structure has significant spatial modularity; for example, math and code features form a "lobe" akin to functional lobes seen in neural fMRI images. We quantify the spatial locality of these lobes with multiple metrics and find that clusters of co-occurring features, at coarse enough scale, also cluster together spatially far more than one would expect if feature geometry were random. 3) The "galaxy" scale large-scale structure of the feature point cloud is not isotropic, but instead has a power law of eigenvalues with steepest slope in middle layers. We also quantify how the clustering entropy depends on the layer.

A wide range of scientific problems, such as those described by continuous-time dynamical systems and partial differential equations (PDEs), are naturally formulated on function spaces. While function spaces are typically infinite-dimensional, deep learning has predominantly advanced through applications in computer vision and natural language processing that focus on mappings between finite-dimensional spaces. Such fundamental disparities in the nature of the data have limited neural networks from achieving a comparable level of success in scientific applications as seen in other fields. Neural operators are a principled way to generalize neural networks to mappings between function spaces, offering a pathway to replicate deep learning's transformative impact on scientific problems. For instance, neural operators can learn solution operators for entire classes of PDEs, e.g., physical systems with different boundary conditions, coefficient functions, and geometries. A key factor in deep learning's success has been the careful engineering of neural architectures through extensive empirical testing. Translating these neural architectures into neural operators allows operator learning to enjoy these same empirical optimizations. However, prior neural operator architectures have often been introduced as standalone models, not directly derived as extensions of existing neural network architectures. In this paper, we identify and distill the key principles for constructing practical implementations of mappings between infinite-dimensional function spaces. Using these principles, we propose a recipe for converting several popular neural architectures into neural operators with minimal modifications. This paper aims to guide practitioners through this process and details the steps to make neural operators work in practice. Our code can be found at https://github.com/neuraloperator/NNs-to-NOs

Recent years have seen the advent of molecular simulation datasets that are orders of magnitude larger and more diverse. These new datasets differ substantially in four aspects of complexity: 1. Chemical diversity (number of different elements), 2. system size (number of atoms per sample), 3. dataset size (number of data samples), and 4. domain shift (similarity of the training and test set). Despite these large differences, benchmarks on small and narrow datasets remain the predominant method of demonstrating progress in graph neural networks (GNNs) for molecular simulation, likely due to cheaper training compute requirements. This raises the question -- does GNN progress on small and narrow datasets translate to these more complex datasets? This work investigates this question by first developing the GemNet-OC model based on the large Open Catalyst 2020 (OC20) dataset. GemNet-OC outperforms the previous state-of-the-art on OC20 by 16% while reducing training time by a factor of 10. We then compare the impact of 18 model components and hyperparameter choices on performance in multiple datasets. We find that the resulting model would be drastically different depending on the dataset used for making model choices. To isolate the source of this discrepancy we study six subsets of the OC20 dataset that individually test each of the above-mentioned four dataset aspects. We find that results on the OC-2M subset correlate well with the full OC20 dataset while being substantially cheaper to train on. Our findings challenge the common practice of developing GNNs solely on small datasets, but highlight ways of achieving fast development cycles and generalizable results via moderately-sized, representative datasets such as OC-2M and efficient models such as GemNet-OC. Our code and pretrained model weights are open-sourced.

Within the complex neuroarchitecture of the brain, astrocytes play crucial roles in development, structure, and metabolism. These cells regulate neural activity through tripartite synapses, directly impacting cognitive processes such as learning and memory. Despite the growing recognition of astrocytes' significance, traditional Spiking Neural Network (SNN) models remain predominantly neuron-centric, overlooking the profound influence of astrocytes on neural dynamics. Inspired by these biological insights, we have developed an Astrocyte-Modulated Spiking Unit (AM-SU), an innovative framework that integrates neuron-astrocyte interactions into the computational paradigm, demonstrating wide applicability across various hardware platforms. Our Astrocyte-Modulated Spiking Neural Network (AstroSNN) exhibits exceptional performance in tasks involving memory retention and natural language generation, particularly in handling long-term dependencies and complex linguistic structures. The design of AstroSNN not only enhances its biological authenticity but also introduces novel computational dynamics, enabling more effective processing of complex temporal dependencies. Furthermore, AstroSNN shows low latency, high throughput, and reduced memory usage in practical applications, making it highly suitable for resource-constrained environments. By successfully integrating astrocytic dynamics into intelligent neural networks, our work narrows the gap between biological plausibility and neural modeling, laying the groundwork for future biologically-inspired neural computing research that includes both neurons and astrocytes.

Recent neural network-based wave functions have achieved state-of-the-art accuracies in modeling ab-initio ground-state potential energy surface. However, these networks can only solve different spatial arrangements of the same set of atoms. To overcome this limitation, we present Graph-learned orbital embeddings (Globe), a neural network-based reparametrization method that can adapt neural wave functions to different molecules. Globe learns representations of local electronic structures that generalize across molecules via spatial message passing by connecting molecular orbitals to covalent bonds. Further, we propose a size-consistent wave function Ansatz, the Molecular orbital network (Moon), tailored to jointly solve Schr\"odinger equations of different molecules. In our experiments, we find Moon converging in 4.5 times fewer steps to similar accuracy as previous methods or to lower energies given the same time. Further, our analysis shows that Moon's energy estimate scales additively with increased system sizes, unlike previous work where we observe divergence. In both computational chemistry and machine learning, we are the first to demonstrate that a single wave function can solve the Schr\"odinger equation of molecules with different atoms jointly.

We propose a formal mathematical model for sparse representations and active dendrites in neocortex. Our model is inspired by recent experimental findings on active dendritic processing and NMDA spikes in pyramidal neurons. These experimental and modeling studies suggest that the basic unit of pattern memory in the neocortex is instantiated by small clusters of synapses operated on by localized non-linear dendritic processes. We derive a number of scaling laws that characterize the accuracy of such dendrites in detecting activation patterns in a neuronal population under adverse conditions. We introduce the union property which shows that synapses for multiple patterns can be randomly mixed together within a segment and still lead to highly accurate recognition. We describe simulation results that provide further insight into sparse representations as well as two primary results. First we show that pattern recognition by a neuron with active dendrites can be extremely accurate and robust with high dimensional sparse inputs even when using a tiny number of synapses to recognize large patterns. Second, equations representing recognition accuracy of a dendrite predict optimal NMDA spiking thresholds under a generous set of assumptions. The prediction tightly matches NMDA spiking thresholds measured in the literature. Our model matches many of the known properties of pyramidal neurons. As such the theory provides a mathematical framework for understanding the benefits and limits of sparse representations in cortical networks.

Single-atom catalysts (SACs) have emerged as frontiers for catalyzing chemical reactions, yet the diverse combinations of active elements and support materials, the nature of coordination environments, elude traditional methodologies in searching optimal SAC systems with superior catalytic performance. Herein, by integrating multi-branch Convolutional Neural Network (CNN) analysis models to hybrid descriptor based activity volcano plot, 2D SAC system composed of diverse metallic single atoms anchored on six type of 2D supports, including graphitic carbon nitride, nitrogen-doped graphene, graphene with dual-vacancy, black phosphorous, boron nitride, and C2N, are screened for efficient CO2RR. Starting from establishing a correlation map between the adsorption energies of intermediates and diverse electronic and elementary descriptors, sole singular descriptor lost magic to predict catalytic activity. Deep learning method utilizing multi-branch CNN model therefore was employed, using 2D electronic density of states as input to predict adsorption energies. Hybrid-descriptor enveloping both C- and O-types of CO2RR intermediates was introduced to construct volcano plots and limiting potential periodic table, aiming for intuitive screening of catalyst candidates for efficient CO2 reduction to CH4. The eDOS occlusion experiments were performed to unravel individual orbital contribution to adsorption energy. To explore the electronic scale principle governing practical engineering catalytic CO2RR activity, orbitalwise eDOS shifting experiments based on CNN model were employed. The study involves examining the adsorption energy and, consequently, catalytic activities while varying supported single atoms. This work offers a tangible framework to inform both theoretical screening and experimental synthesis, thereby paving the way for systematically designing efficient SACs.

We present a novel approach for the prediction of anticancer compound sensitivity by means of multi-modal attention-based neural networks (PaccMann). In our approach, we integrate three key pillars of drug sensitivity, namely, the molecular structure of compounds, transcriptomic profiles of cancer cells as well as prior knowledge about interactions among proteins within cells. Our models ingest a drug-cell pair consisting of SMILES encoding of a compound and the gene expression profile of a cancer cell and predicts an IC50 sensitivity value. Gene expression profiles are encoded using an attention-based encoding mechanism that assigns high weights to the most informative genes. We present and study three encoders for SMILES string of compounds: 1) bidirectional recurrent 2) convolutional 3) attention-based encoders. We compare our devised models against a baseline model that ingests engineered fingerprints to represent the molecular structure. We demonstrate that using our attention-based encoders, we can surpass the baseline model. The use of attention-based encoders enhance interpretability and enable us to identify genes, bonds and atoms that were used by the network to make a prediction.

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.

Biological nervous systems are created in a fundamentally different way than current artificial neural networks. Despite its impressive results in a variety of different domains, deep learning often requires considerable engineering effort to design high-performing neural architectures. By contrast, biological nervous systems are grown through a dynamic self-organizing process. In this paper, we take initial steps toward neural networks that grow through a developmental process that mirrors key properties of embryonic development in biological organisms. The growth process is guided by another neural network, which we call a Neural Developmental Program (NDP) and which operates through local communication alone. We investigate the role of neural growth on different machine learning benchmarks and different optimization methods (evolutionary training, online RL, offline RL, and supervised learning). Additionally, we highlight future research directions and opportunities enabled by having self-organization driving the growth of neural networks.

It has long been known in both neuroscience and AI that ``binding'' between neurons leads to a form of competitive learning where representations are compressed in order to represent more abstract concepts in deeper layers of the network. More recently, it was also hypothesized that dynamic (spatiotemporal) representations play an important role in both neuroscience and AI. Building on these ideas, we introduce Artificial Kuramoto Oscillatory Neurons (AKOrN) as a dynamical alternative to threshold units, which can be combined with arbitrary connectivity designs such as fully connected, convolutional, or attentive mechanisms. Our generalized Kuramoto updates bind neurons together through their synchronization dynamics. We show that this idea provides performance improvements across a wide spectrum of tasks such as unsupervised object discovery, adversarial robustness, calibrated uncertainty quantification, and reasoning. We believe that these empirical results show the importance of rethinking our assumptions at the most basic neuronal level of neural representation, and in particular show the importance of dynamical representations.

In living organisms, homeostasis is the natural regulation of internal states aimed at maintaining conditions compatible with life. Typical artificial systems are not equipped with comparable regulatory features. Here, we introduce an artificial neural network that incorporates homeostatic features. Its own computing substrate is placed in a needful and vulnerable relation to the very objects over which it computes. For example, artificial neurons performing classification of MNIST digits or Fashion-MNIST articles of clothing may receive excitatory or inhibitory effects, which alter their own learning rate as a direct result of perceiving and classifying the digits. In this scenario, accurate recognition is desirable to the agent itself because it guides decisions to regulate its vulnerable internal states and functionality. Counterintuitively, the addition of vulnerability to a learner does not necessarily impair its performance. On the contrary, self-regulation in response to vulnerability confers benefits under certain conditions. We show that homeostatic design confers increased adaptability under concept shift, in which the relationships between labels and data change over time, and that the greatest advantages are obtained under the highest rates of shift. This necessitates the rapid un-learning of past associations and the re-learning of new ones. We also demonstrate the superior abilities of homeostatic learners in environments with dynamically changing rates of concept shift. Our homeostatic design exposes the artificial neural network's thinking machinery to the consequences of its own "thoughts", illustrating the advantage of putting one's own "skin in the game" to improve fluid intelligence.

Artificial Neural Networks are computational network models inspired by signal processing in the brain. These models have dramatically improved the performance of many learning tasks, including speech and object recognition. However, today's computing hardware is inefficient at implementing neural networks, in large part because much of it was designed for von Neumann computing schemes. Significant effort has been made to develop electronic architectures tuned to implement artificial neural networks that improve upon both computational speed and energy efficiency. Here, we propose a new architecture for a fully-optical neural network that, using unique advantages of optics, promises a computational speed enhancement of at least two orders of magnitude over the state-of-the-art and three orders of magnitude in power efficiency for conventional learning tasks. We experimentally demonstrate essential parts of our architecture using a programmable nanophotonic processor.

Artificial neural networks for motor control usually adopt generic architectures like fully connected MLPs. While general, these tabula rasa architectures rely on large amounts of experience to learn, are not easily transferable to new bodies, and have internal dynamics that are difficult to interpret. In nature, animals are born with highly structured connectivity in their nervous systems shaped by evolution; this innate circuitry acts synergistically with learning mechanisms to provide inductive biases that enable most animals to function well soon after birth and learn efficiently. Convolutional networks inspired by visual circuitry have encoded useful biases for vision. However, it is unknown the extent to which ANN architectures inspired by neural circuitry can yield useful biases for other AI domains. In this work, we ask what advantages biologically inspired ANN architecture can provide in the domain of motor control. Specifically, we translate C. elegans locomotion circuits into an ANN model controlling a simulated Swimmer agent. On a locomotion task, our architecture achieves good initial performance and asymptotic performance comparable with MLPs, while dramatically improving data efficiency and requiring orders of magnitude fewer parameters. Our architecture is interpretable and transfers to new body designs. An ablation analysis shows that constrained excitation/inhibition is crucial for learning, while weight initialization contributes to good initial performance. Our work demonstrates several advantages of biologically inspired ANN architecture and encourages future work in more complex embodied control.

Transformer architectures have revolutionized artificial intelligence (AI) through their attention mechanisms, yet the computational principles underlying their success remain opaque. We present a novel theoretical framework that reinterprets the core computation of attention as Pavlovian conditioning. Our model finds a direct mathematical analogue in linear attention, which simplifies the analysis of the underlying associative process. We demonstrate that attention's queries, keys, and values can be mapped to the three elements of classical conditioning: test stimuli that probe associations, conditional stimuli (CS) that serve as retrieval cues, and unconditional stimuli (US) that contain response information. Through this lens, we suggest that each attention operation constructs a transient associative memory via a Hebbian rule, where CS-US pairs form dynamic associations that test stimuli can later retrieve. Our framework yields several theoretical insights grounded in this linearized model: (1) a capacity theorem showing that attention heads can store O(d_k) associations before interference degrades retrieval; (2) an error propagation analysis revealing fundamental architectural trade-offs of balancing model depth, width, and head redundancy to maintain reliability; and (3) an understanding of how biologically plausible learning rules could enhance transformer architectures. By establishing this deep connection, we suggest that the success of modern AI may stem not from architectural novelty alone, but from implementing computational principles that biology optimized over millions of years of evolution.

Artificial intelligence has made great strides in the last decade but still falls short of the human brain, the best-known example of intelligence. Not much is known of the neural processes that allow the brain to make the leap to achieve so much from so little beyond its ability to create knowledge structures that can be flexibly and dynamically combined, recombined, and applied in new and novel ways. This paper proposes a mathematical approach using graph theory and spectral graph theory, to hypothesize how to constrain these neural clusters of information based on eigen-relationships. This same hypothesis is hierarchically applied to scale up from the smallest to the largest clusters of knowledge that eventually lead to model building and reasoning.

We create a reusable Transformer, BrainBERT, for intracranial recordings bringing modern representation learning approaches to neuroscience. Much like in NLP and speech recognition, this Transformer enables classifying complex concepts, i.e., decoding neural data, with higher accuracy and with much less data by being pretrained in an unsupervised manner on a large corpus of unannotated neural recordings. Our approach generalizes to new subjects with electrodes in new positions and to unrelated tasks showing that the representations robustly disentangle the neural signal. Just like in NLP where one can study language by investigating what a language model learns, this approach opens the door to investigating the brain by what a model of the brain learns. As a first step along this path, we demonstrate a new analysis of the intrinsic dimensionality of the computations in different areas of the brain. To construct these representations, we combine a technique for producing super-resolution spectrograms of neural data with an approach designed for generating contextual representations of audio by masking. In the future, far more concepts will be decodable from neural recordings by using representation learning, potentially unlocking the brain like language models unlocked language.

There is an analogy that is often made between deep neural networks and actual brains, suggested by the nomenclature itself: the "neurons" in deep neural networks should correspond to neurons (or nerve cells, to avoid confusion) in the brain. We claim, however, that this analogy doesn't even type check: it is structurally flawed. In agreement with the slightly glib summary of Hebbian learning as "cells that fire together wire together", this article makes the case that the analogy should be different. Since the "neurons" in deep neural networks are managing the changing weights, they are more akin to the synapses in the brain; instead, it is the wires in deep neural networks that are more like nerve cells, in that they are what cause the information to flow. An intuition that nerve cells seem like more than mere wires is exactly right, and is justified by a precise category-theoretic analogy which we will explore in this article. Throughout, we will continue to highlight the error in equating artificial neurons with nerve cells by leaving "neuron" in quotes or by calling them artificial neurons. We will first explain how to view deep neural networks as nested dynamical systems with a very restricted sort of interaction pattern, and then explain a more general sort of interaction for dynamical systems that is useful throughout engineering, but which fails to adapt to changing circumstances. As mentioned, an analogy is then forced upon us by the mathematical formalism in which they are both embedded. We call the resulting encompassing generalization deeply interacting learning systems: they have complex interaction as in control theory, but adaptation to circumstances as in deep neural networks.

Attending to what is relevant is fundamental to both the mammalian brain and modern machine learning models such as Transformers. Yet, determining relevance remains a core challenge, traditionally offloaded to learning algorithms like backpropagation. Inspired by recent cellular neurobiological evidence linking neocortical pyramidal cells to distinct mental states, this work shows how models (e.g., Transformers) can emulate high-level perceptual processing and awake thought (imagination) states to pre-select relevant information before applying attention. Triadic neuronal-level modulation loops among questions (Q), clues (keys, K), and hypotheses (values, V) enable diverse, deep, parallel reasoning chains at the representation level and allow a rapid shift from initial biases to refined understanding. This leads to orders-of-magnitude faster learning with significantly reduced computational demand (e.g., fewer heads, layers, and tokens), at an approximate cost of O(N), where N is the number of input tokens. Results span reinforcement learning (e.g., CarRacing in a high-dimensional visual setup), computer vision, and natural language question answering.

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.

Computational methods that operate on three-dimensional molecular structure have the potential to solve important questions in biology and chemistry. In particular, deep neural networks have gained significant attention, but their widespread adoption in the biomolecular domain has been limited by a lack of either systematic performance benchmarks or a unified toolkit for interacting with molecular data. To address this, we present ATOM3D, a collection of both novel and existing benchmark datasets spanning several key classes of biomolecules. We implement several classes of three-dimensional molecular learning methods for each of these tasks and show that they consistently improve performance relative to methods based on one- and two-dimensional representations. The specific choice of architecture proves to be critical for performance, with three-dimensional convolutional networks excelling at tasks involving complex geometries, graph networks performing well on systems requiring detailed positional information, and the more recently developed equivariant networks showing significant promise. Our results indicate that many molecular problems stand to gain from three-dimensional molecular learning, and that there is potential for improvement on many tasks which remain underexplored. To lower the barrier to entry and facilitate further developments in the field, we also provide a comprehensive suite of tools for dataset processing, model training, and evaluation in our open-source atom3d Python package. All datasets are available for download from https://www.atom3d.ai .

A hallmark of intelligence is the ability to autonomously learn new flexible, cognitive behaviors - that is, behaviors where the appropriate action depends not just on immediate stimuli (as in simple reflexive stimulus-response associations), but on contextual information that must be adequately acquired, stored and processed. While many meta-learning algorithms can design agents that autonomously learn new tasks, cognitive tasks adds another level of learning and memory to typical ``learning-to-learn'' problems. Here we evolve neural networks, endowed with plastic connections and neuromodulation, over a sizable set of simple cognitive tasks adapted from a computational neuroscience framework. The resulting evolved networks can automatically modify their own connectivity to acquire a novel simple cognitive task, never seen during evolution, from stimuli and rewards alone, through the spontaneous operation of their evolved neural organization and plasticity system. Our results emphasize the importance of carefully considering the multiple learning loops involved in the emergence of intelligent behavior.

Molecular representation is a foundational element in our understanding of the physical world. Its importance ranges from the fundamentals of chemical reactions to the design of new therapies and materials. Previous molecular machine learning models have employed strings, fingerprints, global features, and simple molecular graphs that are inherently information-sparse representations. However, as the complexity of prediction tasks increases, the molecular representation needs to encode higher fidelity information. This work introduces a novel approach to infusing quantum-chemical-rich information into molecular graphs via stereoelectronic effects. We show that the explicit addition of stereoelectronic interactions significantly improves the performance of molecular machine learning models. Furthermore, stereoelectronics-infused representations can be learned and deployed with a tailored double graph neural network workflow, enabling its application to any downstream molecular machine learning task. Finally, we show that the learned representations allow for facile stereoelectronic evaluation of previously intractable systems, such as entire proteins, opening new avenues of molecular design.

We extend the capabilities of neural networks by coupling them to external memory resources, which they can interact with by attentional processes. The combined system is analogous to a Turing Machine or Von Neumann architecture but is differentiable end-to-end, allowing it to be efficiently trained with gradient descent. Preliminary results demonstrate that Neural Turing Machines can infer simple algorithms such as copying, sorting, and associative recall from input and output examples.

We explore the effects of various plasticity functions on assemblies of neurons. To bridge the gap between experimental and computational theories we make use of a conceptual framework, the Assembly Calculus, which is a formal system for the description of brain function based on assemblies of neurons. The Assembly Calculus includes operations for projecting, associating, and merging assemblies of neurons. Our research is focused on simulating different plasticity functions with Assembly Calculus. Our main contribution is the modification and evaluation of the projection operation. We experiment with Oja's and Spike Time-Dependent Plasticity (STDP) rules and test the effect of various hyper-parameters.

Classical models of memory in psychology and neuroscience rely on similarity-based retrieval of stored patterns, where similarity is a function of retrieval cues and the stored patterns. While parsimonious, these models do not allow distinct representations for storage and retrieval, despite their distinct computational demands. Key-value memory systems, in contrast, distinguish representations used for storage (values) and those used for retrieval (keys). This allows key-value memory systems to optimize simultaneously for fidelity in storage and discriminability in retrieval. We review the computational foundations of key-value memory, its role in modern machine learning systems, related ideas from psychology and neuroscience, applications to a number of empirical puzzles, and possible biological implementations.

A basic question within the emerging field of mechanistic interpretability is the degree to which neural networks learn the same underlying mechanisms. In other words, are neural mechanisms universal across different models? In this work, we study the universality of individual neurons across GPT2 models trained from different initial random seeds, motivated by the hypothesis that universal neurons are likely to be interpretable. In particular, we compute pairwise correlations of neuron activations over 100 million tokens for every neuron pair across five different seeds and find that 1-5\% of neurons are universal, that is, pairs of neurons which consistently activate on the same inputs. We then study these universal neurons in detail, finding that they usually have clear interpretations and taxonomize them into a small number of neuron families. We conclude by studying patterns in neuron weights to establish several universal functional roles of neurons in simple circuits: deactivating attention heads, changing the entropy of the next token distribution, and predicting the next token to (not) be within a particular set.

The brain is a noisy system subject to energy constraints. These facts are rarely taken into account when modelling artificial neural networks. In this paper, we are interested in demonstrating that those factors can actually lead to the appearance of robust associative memories. We first propose a simplified model of noise in the brain, taking into account synaptic noise and interference from neurons external to the network. When coarsely quantized, we show that this noise can be reduced to insertions and erasures. We take a neural network with recurrent modifiable connections, and subject it to noisy external inputs. We introduce an energy usage limitation principle in the network as well as consolidated Hebbian learning, resulting in an incremental processing of inputs. We show that the connections naturally formed correspond to state-of-the-art binary sparse associative memories.

The approximation capability of ANNs and their RNN instantiations, is strongly correlated with the number of parameters packed into these networks. However, the complexity barrier for human understanding, is arguably related to the number of neurons and synapses in the networks, and to the associated nonlinear transformations. In this paper we show that the use of biophysical synapses, as found in LTCs, have two main benefits. First, they allow to pack more parameters for a given number of neurons and synapses. Second, they allow to formulate the nonlinear-network transformation, as a linear system with state-dependent coefficients. Both increase interpretability, as for a given task, they allow to learn a system linear in its input features, that is smaller in size compared to the state of the art. We substantiate the above claims on various time-series prediction tasks, but we believe that our results are applicable to any feedforward or recurrent ANN.

We analyse perception and memory, using mathematical models for knowledge graphs and tensors, to gain insights into the corresponding functionalities of the human mind. Our discussion is based on the concept of propositional sentences consisting of subject-predicate-object (SPO) triples for expressing elementary facts. SPO sentences are the basis for most natural languages but might also be important for explicit perception and declarative memories, as well as intra-brain communication and the ability to argue and reason. A set of SPO sentences can be described as a knowledge graph, which can be transformed into an adjacency tensor. We introduce tensor models, where concepts have dual representations as indices and associated embeddings, two constructs we believe are essential for the understanding of implicit and explicit perception and memory in the brain. We argue that a biological realization of perception and memory imposes constraints on information processing. In particular, we propose that explicit perception and declarative memories require a semantic decoder, which, in a simple realization, is based on four layers: First, a sensory memory layer, as a buffer for sensory input, second, an index layer representing concepts, third, a memoryless representation layer for the broadcasting of information ---the "blackboard", or the "canvas" of the brain--- and fourth, a working memory layer as a processing center and data buffer. We discuss the operations of the four layers and relate them to the global workspace theory. In a Bayesian brain interpretation, semantic memory defines the prior for observable triple statements. We propose that ---in evolution and during development--- semantic memory, episodic memory, and natural language evolved as emergent properties in agents' process to gain a deeper understanding of sensory information.

The relationship between computing systems and the brain has served as motivation for pioneering theoreticians since John von Neumann and Alan Turing. Uniform, scale-free biological networks, such as the brain, have powerful properties, including generalizing over time, which is the main barrier for Machine Learning on the path to Universal Reasoning Models. We introduce `Dragon Hatchling' (BDH), a new Large Language Model architecture based on a scale-free biologically inspired network of \n locally-interacting neuron particles. BDH couples strong theoretical foundations and inherent interpretability without sacrificing Transformer-like performance. BDH is a practical, performant state-of-the-art attention-based state space sequence learning architecture. In addition to being a graph model, BDH admits a GPU-friendly formulation. It exhibits Transformer-like scaling laws: empirically BDH rivals GPT2 performance on language and translation tasks, at the same number of parameters (10M to 1B), for the same training data. BDH can be represented as a brain model. The working memory of BDH during inference entirely relies on synaptic plasticity with Hebbian learning using spiking neurons. We confirm empirically that specific, individual synapses strengthen connection whenever BDH hears or reasons about a specific concept while processing language inputs. The neuron interaction network of BDH is a graph of high modularity with heavy-tailed degree distribution. The BDH model is biologically plausible, explaining one possible mechanism which human neurons could use to achieve speech. BDH is designed for interpretability. Activation vectors of BDH are sparse and positive. We demonstrate monosemanticity in BDH on language tasks. Interpretability of state, which goes beyond interpretability of neurons and model parameters, is an inherent feature of the BDH architecture.

The brain has computational capabilities that surpass those of modern systems, being able to solve complex problems efficiently in a simple way. Neuromorphic engineering aims to mimic biology in order to develop new systems capable of incorporating such capabilities. Bio-inspired learning systems continue to be a challenge that must be solved, and much work needs to be done in this regard. Among all brain regions, the hippocampus stands out as an autoassociative short-term memory with the capacity to learn and recall memories from any fragment of them. These characteristics make the hippocampus an ideal candidate for developing bio-inspired learning systems that, in addition, resemble content-addressable memories. Therefore, in this work we propose a bio-inspired spiking content-addressable memory model based on the CA3 region of the hippocampus with the ability to learn, forget and recall memories, both orthogonal and non-orthogonal, from any fragment of them. The model was implemented on the SpiNNaker hardware platform using Spiking Neural Networks. A set of experiments based on functional, stress and applicability tests were performed to demonstrate its correct functioning. This work presents the first hardware implementation of a fully-functional bio-inspired spiking hippocampal content-addressable memory model, paving the way for the development of future more complex neuromorphic systems.

A Perceptron is a fundamental building block of a neural network. The flexibility and scalability of perceptron make it ubiquitous in building intelligent systems. Studies have shown the efficacy of a single neuron in making intelligent decisions. Here, we examined and compared two perceptrons with distinct mechanisms, and developed a quantum version of one of those perceptrons. As a part of this modeling, we implemented the quantum circuit for an artificial perception, generated a dataset, and simulated the training. Through these experiments, we show that there is an exponential growth advantage and test different qubit versions. Our findings show that this quantum model of an individual perceptron can be used as a pattern classifier. For the second type of model, we provide an understanding to design and simulate a spike-dependent quantum perceptron. Our code is available at https://github.com/ashutosh1919/quantum-perceptron

The complete connectome of the Drosophila larva brain offers a unique opportunity to investigate whether biologically evolved circuits can support artificial intelligence. We convert this wiring diagram into a Biological Processing Unit (BPU), a fixed recurrent network derived directly from synaptic connectivity. Despite its modest size 3,000 neurons and 65,000 weights between them), the unmodified BPU achieves 98% accuracy on MNIST and 58% on CIFAR-10, surpassing size-matched MLPs. Scaling the BPU via structured connectome expansions further improves CIFAR-10 performance, while modality-specific ablations reveal the uneven contributions of different sensory subsystems. On the ChessBench dataset, a lightweight GNN-BPU model trained on only 10,000 games achieves 60% move accuracy, nearly 10x better than any size transformer. Moreover, CNN-BPU models with ~2M parameters outperform parameter-matched Transformers, and with a depth-6 minimax search at inference, reach 91.7% accuracy, exceeding even a 9M-parameter Transformer baseline. These results demonstrate the potential of biofidelic neural architectures to support complex cognitive tasks and motivate scaling to larger and more intelligent connectomes in future work.

Many learning algorithms used as normative models in neuroscience or as candidate approaches for learning on neuromorphic chips learn by contrasting one set of network states with another. These Contrastive Learning (CL) algorithms are traditionally implemented with rigid, temporally non-local, and periodic learning dynamics that could limit the range of physical systems capable of harnessing CL. In this study, we build on recent work exploring how CL might be implemented by biological or neurmorphic systems and show that this form of learning can be made temporally local, and can still function even if many of the dynamical requirements of standard training procedures are relaxed. Thanks to a set of general theorems corroborated by numerical experiments across several CL models, our results provide theoretical foundations for the study and development of CL methods for biological and neuromorphic neural networks.

Deep neural networks (DNNs) have demonstrated state-of-the-art results on many pattern recognition tasks, especially vision classification problems. Understanding the inner workings of such computational brains is both fascinating basic science that is interesting in its own right - similar to why we study the human brain - and will enable researchers to further improve DNNs. One path to understanding how a neural network functions internally is to study what each of its neurons has learned to detect. One such method is called activation maximization (AM), which synthesizes an input (e.g. an image) that highly activates a neuron. Here we dramatically improve the qualitative state of the art of activation maximization by harnessing a powerful, learned prior: a deep generator network (DGN). The algorithm (1) generates qualitatively state-of-the-art synthetic images that look almost real, (2) reveals the features learned by each neuron in an interpretable way, (3) generalizes well to new datasets and somewhat well to different network architectures without requiring the prior to be relearned, and (4) can be considered as a high-quality generative method (in this case, by generating novel, creative, interesting, recognizable images).

The rapid evolution of artificial intelligence (AI) has shifted from static, data-driven models to dynamic systems capable of perceiving and interacting with real-world environments. Despite advancements in pattern recognition and symbolic reasoning, current AI systems, such as large language models, remain disembodied, unable to physically engage with the world. This limitation has driven the rise of embodied AI, where autonomous agents, such as humanoid robots, must navigate and manipulate unstructured environments with human-like adaptability. At the core of this challenge lies the concept of Neural Brain, a central intelligence system designed to drive embodied agents with human-like adaptability. A Neural Brain must seamlessly integrate multimodal sensing and perception with cognitive capabilities. Achieving this also requires an adaptive memory system and energy-efficient hardware-software co-design, enabling real-time action in dynamic environments. This paper introduces a unified framework for the Neural Brain of embodied agents, addressing two fundamental challenges: (1) defining the core components of Neural Brain and (2) bridging the gap between static AI models and the dynamic adaptability required for real-world deployment. To this end, we propose a biologically inspired architecture that integrates multimodal active sensing, perception-cognition-action function, neuroplasticity-based memory storage and updating, and neuromorphic hardware/software optimization. Furthermore, we also review the latest research on embodied agents across these four aspects and analyze the gap between current AI systems and human intelligence. By synthesizing insights from neuroscience, we outline a roadmap towards the development of generalizable, autonomous agents capable of human-level intelligence in real-world scenarios.

Neural networks have proven to be a highly effective tool for solving complex problems in many areas of life. Recently, their importance and practical usability have further been reinforced with the advent of deep learning. One of the important conditions for the success of neural networks is the choice of an appropriate activation function introducing non-linearity into the model. Many types of these functions have been proposed in the literature in the past, but there is no single comprehensive source containing their exhaustive overview. The absence of this overview, even in our experience, leads to redundancy and the unintentional rediscovery of already existing activation functions. To bridge this gap, our paper presents an extensive survey involving 400 activation functions, which is several times larger in scale than previous surveys. Our comprehensive compilation also references these surveys; however, its main goal is to provide the most comprehensive overview and systematization of previously published activation functions with links to their original sources. The secondary aim is to update the current understanding of this family of functions.

Multimodal learning enhances the perceptual capabilities of cognitive systems by integrating information from different sensory modalities. However, existing multimodal fusion research typically assumes static integration, not fully incorporating key dynamic mechanisms found in the brain. Specifically, the brain exhibits an inverse effectiveness phenomenon, wherein weaker unimodal cues yield stronger multisensory integration benefits; conversely, when individual modal cues are stronger, the effect of fusion is diminished. This mechanism enables biological systems to achieve robust cognition even with scarce or noisy perceptual cues. Inspired by this biological mechanism, we explore the relationship between multimodal output and information from individual modalities, proposing an inverse effectiveness driven multimodal fusion (IEMF) strategy. By incorporating this strategy into neural networks, we achieve more efficient integration with improved model performance and computational efficiency, demonstrating up to 50% reduction in computational cost across diverse fusion methods. We conduct experiments on audio-visual classification, continual learning, and question answering tasks to validate our method. Results consistently demonstrate that our method performs excellently in these tasks. To verify universality and generalization, we also conduct experiments on Artificial Neural Networks (ANN) and Spiking Neural Networks (SNN), with results showing good adaptability to both network types. Our research emphasizes the potential of incorporating biologically inspired mechanisms into multimodal networks and provides promising directions for the future development of multimodal artificial intelligence. The code is available at https://github.com/Brain-Cog-Lab/IEMF.

Machine learning techniques are essential tools to compute efficient, yet accurate, force fields for atomistic simulations. This approach has recently been extended to incorporate quantum computational methods, making use of variational quantum learning models to predict potential energy surfaces and atomic forces from ab initio training data. However, the trainability and scalability of such models are still limited, due to both theoretical and practical barriers. Inspired by recent developments in geometric classical and quantum machine learning, here we design quantum neural networks that explicitly incorporate, as a data-inspired prior, an extensive set of physically relevant symmetries. We find that our invariant quantum learning models outperform their more generic counterparts on individual molecules of growing complexity. Furthermore, we study a water dimer as a minimal example of a system with multiple components, showcasing the versatility of our proposed approach and opening the way towards larger simulations. Our results suggest that molecular force fields generation can significantly profit from leveraging the framework of geometric quantum machine learning, and that chemical systems represent, in fact, an interesting and rich playground for the development and application of advanced quantum machine learning tools.

This article is about the neural conundrum behind the slowness of human behavior. The information throughput of a human being is about 10 bits/s. In comparison, our sensory systems gather data at ~10^9 bits/s. The stark contrast between these numbers remains unexplained and touches on fundamental aspects of brain function: What neural substrate sets this speed limit on the pace of our existence? Why does the brain need billions of neurons to process 10 bits/s? Why can we only think about one thing at a time? The brain seems to operate in two distinct modes: the "outer" brain handles fast high-dimensional sensory and motor signals, whereas the "inner" brain processes the reduced few bits needed to control behavior. Plausible explanations exist for the large neuron numbers in the outer brain, but not for the inner brain, and we propose new research directions to remedy this.

Why do neurons communicate through spikes? By definition, spikes are all-or-none neural events which occur at continuous times. In other words, spikes are on one side binary, existing or not without further details, and on the other can occur at any asynchronous time, without the need for a centralized clock. This stands in stark contrast to the analog representation of values and the discretized timing classically used in digital processing and at the base of modern-day neural networks. As neural systems almost systematically use this so-called event-based representation in the living world, a better understanding of this phenomenon remains a fundamental challenge in neurobiology in order to better interpret the profusion of recorded data. With the growing need for intelligent embedded systems, it also emerges as a new computing paradigm to enable the efficient operation of a new class of sensors and event-based computers, called neuromorphic, which could enable significant gains in computation time and energy consumption -- a major societal issue in the era of the digital economy and global warming. In this review paper, we provide evidence from biology, theory and engineering that the precise timing of spikes plays a crucial role in our understanding of the efficiency of neural networks.

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.

Generative Flow Networks (GFlowNets) have recently emerged as a suitable framework for generating diverse and high-quality molecular structures by learning from rewards treated as unnormalized distributions. Previous works in this framework often restrict exploration by using predefined molecular fragments as building blocks, limiting the chemical space that can be accessed. In this work, we introduce Atomic GFlowNets (A-GFNs), a foundational generative model leveraging individual atoms as building blocks to explore drug-like chemical space more comprehensively. We propose an unsupervised pre-training approach using drug-like molecule datasets, which teaches A-GFNs about inexpensive yet informative molecular descriptors such as drug-likeliness, topological polar surface area, and synthetic accessibility scores. These properties serve as proxy rewards, guiding A-GFNs towards regions of chemical space that exhibit desirable pharmacological properties. We further implement a goal-conditioned finetuning process, which adapts A-GFNs to optimize for specific target properties. In this work, we pretrain A-GFN on a subset of ZINC dataset, and by employing robust evaluation metrics we show the effectiveness of our approach when compared to other relevant baseline methods for a wide range of drug design tasks. The code is accessible at https://github.com/diamondspark/AGFN.

Protein language models (PLMs) encode rich biological information, yet their internal neuron representations are poorly understood. We introduce the first automated framework for labeling every neuron in a PLM with biologically grounded natural language descriptions. Unlike prior approaches relying on sparse autoencoders or manual annotation, our method scales to hundreds of thousands of neurons, revealing individual neurons are selectively sensitive to diverse biochemical and structural properties. We then develop a novel neuron activation-guided steering method to generate proteins with desired traits, enabling convergence to target biochemical properties like molecular weight and instability index as well as secondary and tertiary structural motifs, including alpha helices and canonical Zinc Fingers. We finally show that analysis of labeled neurons in different model sizes reveals PLM scaling laws and a structured neuron space distribution.

The abilities to perceive, learn, and use generalities, similarities, classes, i.e., semantic memory (SM), is central to cognition. Machine learning (ML), neural network, and AI research has been primarily driven by tasks requiring such abilities. However, another central facet of cognition, single-trial formation of permanent memories of experiences, i.e., episodic memory (EM), has had relatively little focus. Only recently has EM-like functionality been added to Deep Learning (DL) models, e.g., Neural Turing Machine, Memory Networks. However, in these cases: a) EM is implemented as a separate module, which entails substantial data movement (and so, time and power) between the DL net itself and EM; and b) individual items are stored localistically within the EM, precluding realizing the exponential representational efficiency of distributed over localist coding. We describe Sparsey, an unsupervised, hierarchical, spatial/spatiotemporal associative memory model differing fundamentally from mainstream ML models, most crucially, in its use of sparse distributed representations (SDRs), or, cell assemblies, which admits an extremely efficient, single-trial learning algorithm that maps input similarity into code space similarity (measured as intersection). SDRs of individual inputs are stored in superposition and because similarity is preserved, the patterns of intersections over the assigned codes reflect the similarity, i.e., statistical, structure, of all orders, not simply pairwise, over the inputs. Thus, SM, i.e., a generative model, is built as a computationally free side effect of the act of storing episodic memory traces of individual inputs, either spatial patterns or sequences. We report initial results on MNIST and on the Weizmann video event recognition benchmarks. While we have not yet attained SOTA class accuracy, learning takes only minutes on a single CPU.

Traveling waves of neural activity have been observed throughout the brain at a diversity of regions and scales; however, their precise computational role is still debated. One physically inspired hypothesis suggests that the cortical sheet may act like a wave-propagating system capable of invertibly storing a short-term memory of sequential stimuli through induced waves traveling across the cortical surface, and indeed many experimental results from neuroscience correlate wave activity with memory tasks. To date, however, the computational implications of this idea have remained hypothetical due to the lack of a simple recurrent neural network architecture capable of exhibiting such waves. In this work, we introduce a model to fill this gap, which we denote the Wave-RNN (wRNN), and demonstrate how such an architecture indeed efficiently encodes the recent past through a suite of synthetic memory tasks where wRNNs learn faster and reach significantly lower error than wave-free counterparts. We further explore the implications of this memory storage system on more complex sequence modeling tasks such as sequential image classification and find that wave-based models not only again outperform comparable wave-free RNNs while using significantly fewer parameters, but additionally perform comparably to more complex gated architectures such as LSTMs and GRUs.

Predicting physical properties of materials from their crystal structures is a fundamental problem in materials science. In peripheral areas such as the prediction of molecular properties, fully connected attention networks have been shown to be successful. However, unlike these finite atom arrangements, crystal structures are infinitely repeating, periodic arrangements of atoms, whose fully connected attention results in infinitely connected attention. In this work, we show that this infinitely connected attention can lead to a computationally tractable formulation, interpreted as neural potential summation, that performs infinite interatomic potential summations in a deeply learned feature space. We then propose a simple yet effective Transformer-based encoder architecture for crystal structures called Crystalformer. Compared to an existing Transformer-based model, the proposed model requires only 29.4% of the number of parameters, with minimal modifications to the original Transformer architecture. Despite the architectural simplicity, the proposed method outperforms state-of-the-art methods for various property regression tasks on the Materials Project and JARVIS-DFT datasets.

The Backpropagation algorithm, widely used to train neural networks, has often been criticised for its lack of biological realism. In an attempt to find a more biologically plausible alternative, and avoid to back-propagate gradients in favour of using local learning rules, the recently introduced Forward-Forward algorithm replaces the traditional forward and backward passes of Backpropagation with two forward passes. In this work, we show that internal representations obtained with the Forward-Forward algorithm organize into robust, category-specific ensembles, composed by an extremely low number of active units (high sparsity). This is remarkably similar to what is observed in cortical representations during sensory processing. While not found in models trained with standard Backpropagation, sparsity emerges also in networks optimized by Backpropagation, on the same training objective of Forward-Forward. These results suggest that the learning procedure proposed by Forward-Forward may be superior to Backpropagation in modelling learning in the cortex, even when a backward pass is used.

Exposing meaningful and interpretable neural interactions is critical to understanding neural circuits. Inferred neural interactions from neural signals primarily reflect functional interactions. In a long experiment, subject animals may experience different stages defined by the experiment, stimuli, or behavioral states, and hence functional interactions can change over time. To model dynamically changing functional interactions, prior work employs state-switching generalized linear models with hidden Markov models (i.e., HMM-GLMs). However, we argue they lack biological plausibility, as functional interactions are shaped and confined by the underlying anatomical connectome. Here, we propose a novel prior-informed state-switching GLM. We introduce both a Gaussian prior and a one-hot prior over the GLM in each state. The priors are learnable. We will show that the learned prior should capture the state-constant interaction, shedding light on the underlying anatomical connectome and revealing more likely physical neuron interactions. The state-dependent interaction modeled by each GLM offers traceability to capture functional variations across multiple brain states. Our methods effectively recover true interaction structures in simulated data, achieve the highest predictive likelihood with real neural datasets, and render interaction structures and hidden states more interpretable when applied to real neural data.

Biological brains demonstrate complex neural activity, where the timing and interplay between neurons is critical to how brains process information. Most deep learning architectures simplify neural activity by abstracting away temporal dynamics. In this paper we challenge that paradigm. By incorporating neuron-level processing and synchronization, we can effectively reintroduce neural timing as a foundational element. We present the Continuous Thought Machine (CTM), a model designed to leverage neural dynamics as its core representation. The CTM has two core innovations: (1) neuron-level temporal processing, where each neuron uses unique weight parameters to process a history of incoming signals; and (2) neural synchronization employed as a latent representation. The CTM aims to strike a balance between oversimplified neuron abstractions that improve computational efficiency, and biological realism. It operates at a level of abstraction that effectively captures essential temporal dynamics while remaining computationally tractable for deep learning. We demonstrate the CTM's strong performance and versatility across a range of challenging tasks, including ImageNet-1K classification, solving 2D mazes, sorting, parity computation, question-answering, and RL tasks. Beyond displaying rich internal representations and offering a natural avenue for interpretation owing to its internal process, the CTM is able to perform tasks that require complex sequential reasoning. The CTM can also leverage adaptive compute, where it can stop earlier for simpler tasks, or keep computing when faced with more challenging instances. The goal of this work is to share the CTM and its associated innovations, rather than pushing for new state-of-the-art results. To that end, we believe the CTM represents a significant step toward developing more biologically plausible and powerful artificial intelligence systems.

Much of the excitement in modern AI is driven by the observation that scaling up existing systems leads to better performance. But does better performance necessarily imply better internal representations? While the representational optimist assumes it must, this position paper challenges that view. We compare neural networks evolved through an open-ended search process to networks trained via conventional stochastic gradient descent (SGD) on the simple task of generating a single image. This minimal setup offers a unique advantage: each hidden neuron's full functional behavior can be easily visualized as an image, thus revealing how the network's output behavior is internally constructed neuron by neuron. The result is striking: while both networks produce the same output behavior, their internal representations differ dramatically. The SGD-trained networks exhibit a form of disorganization that we term fractured entangled representation (FER). Interestingly, the evolved networks largely lack FER, even approaching a unified factored representation (UFR). In large models, FER may be degrading core model capacities like generalization, creativity, and (continual) learning. Therefore, understanding and mitigating FER could be critical to the future of representation learning.

Neural networks are a powerful class of nonlinear functions that can be trained end-to-end on various applications. While the over-parametrization nature in many neural networks renders the ability to fit complex functions and the strong representation power to handle challenging tasks, it also leads to highly correlated neurons that can hurt the generalization ability and incur unnecessary computation cost. As a result, how to regularize the network to avoid undesired representation redundancy becomes an important issue. To this end, we draw inspiration from a well-known problem in physics -- Thomson problem, where one seeks to find a state that distributes N electrons on a unit sphere as evenly as possible with minimum potential energy. In light of this intuition, we reduce the redundancy regularization problem to generic energy minimization, and propose a minimum hyperspherical energy (MHE) objective as generic regularization for neural networks. We also propose a few novel variants of MHE, and provide some insights from a theoretical point of view. Finally, we apply neural networks with MHE regularization to several challenging tasks. Extensive experiments demonstrate the effectiveness of our intuition, by showing the superior performance with MHE regularization.

Many AI models trained on natural images develop representations that resemble those of the human brain. However, the factors that drive this brain-model similarity remain poorly understood. To disentangle how the model, training and data independently lead a neural network to develop brain-like representations, we trained a family of self-supervised vision transformers (DINOv3) that systematically varied these different factors. We compare their representations of images to those of the human brain recorded with both fMRI and MEG, providing high resolution in spatial and temporal analyses. We assess the brain-model similarity with three complementary metrics focusing on overall representational similarity, topographical organization, and temporal dynamics. We show that all three factors - model size, training amount, and image type - independently and interactively impact each of these brain similarity metrics. In particular, the largest DINOv3 models trained with the most human-centric images reach the highest brain-similarity. This emergence of brain-like representations in AI models follows a specific chronology during training: models first align with the early representations of the sensory cortices, and only align with the late and prefrontal representations of the brain with considerably more training. Finally, this developmental trajectory is indexed by both structural and functional properties of the human cortex: the representations that are acquired last by the models specifically align with the cortical areas with the largest developmental expansion, thickness, least myelination, and slowest timescales. Overall, these findings disentangle the interplay between architecture and experience in shaping how artificial neural networks come to see the world as humans do, thus offering a promising framework to understand how the human brain comes to represent its visual world.

Advancements in neural machinery have led to a wide range of algorithmic solutions for molecular property prediction. Two classes of models in particular have yielded promising results: neural networks applied to computed molecular fingerprints or expert-crafted descriptors, and graph convolutional neural networks that construct a learned molecular representation by operating on the graph structure of the molecule. However, recent literature has yet to clearly determine which of these two methods is superior when generalizing to new chemical space. Furthermore, prior research has rarely examined these new models in industry research settings in comparison to existing employed models. In this paper, we benchmark models extensively on 19 public and 16 proprietary industrial datasets spanning a wide variety of chemical endpoints. In addition, we introduce a graph convolutional model that consistently matches or outperforms models using fixed molecular descriptors as well as previous graph neural architectures on both public and proprietary datasets. Our empirical findings indicate that while approaches based on these representations have yet to reach the level of experimental reproducibility, our proposed model nevertheless offers significant improvements over models currently used in industrial workflows.

Point defects play a central role in driving the properties of materials. First-principles methods are widely used to compute defect energetics and structures, including at scale for high-throughput defect databases. However, these methods are computationally expensive, making machine-learning force fields (MLFFs) an attractive alternative for accelerating structural relaxations. Most existing MLFFs are based on graph neural networks (GNNs), which can suffer from oversmoothing and poor representation of long-range interactions. Both of these issues are especially of concern when modeling point defects. To address these challenges, we introduce the Accelerated Deep Atomic Potential Transformer (ADAPT), an MLFF that replaces graph representations with a direct coordinates-in-space formulation and explicitly considers all pairwise atomic interactions. Atoms are treated as tokens, with a Transformer encoder modeling their interactions. Applied to a dataset of silicon point defects, ADAPT achieves a roughly 33 percent reduction in both force and energy prediction errors relative to a state-of-the-art GNN-based model, while requiring only a fraction of the computational cost.

Neural networks can learn to represent and manipulate numerical information, but they seldom generalize well outside of the range of numerical values encountered during training. To encourage more systematic numerical extrapolation, we propose an architecture that represents numerical quantities as linear activations which are manipulated using primitive arithmetic operators, controlled by learned gates. We call this module a neural arithmetic logic unit (NALU), by analogy to the arithmetic logic unit in traditional processors. Experiments show that NALU-enhanced neural networks can learn to track time, perform arithmetic over images of numbers, translate numerical language into real-valued scalars, execute computer code, and count objects in images. In contrast to conventional architectures, we obtain substantially better generalization both inside and outside of the range of numerical values encountered during training, often extrapolating orders of magnitude beyond trained numerical ranges.

Biological cortical neurons are remarkably sophisticated computational devices, temporally integrating their vast synaptic input over an intricate dendritic tree, subject to complex, nonlinearly interacting internal biological processes. A recent study proposed to characterize this complexity by fitting accurate surrogate models to replicate the input-output relationship of a detailed biophysical cortical pyramidal neuron model and discovered it needed temporal convolutional networks (TCN) with millions of parameters. Requiring these many parameters, however, could stem from a misalignment between the inductive biases of the TCN and cortical neuron's computations. In light of this, and to explore the computational implications of leaky memory units and nonlinear dendritic processing, we introduce the Expressive Leaky Memory (ELM) neuron model, a biologically inspired phenomenological model of a cortical neuron. Remarkably, by exploiting such slowly decaying memory-like hidden states and two-layered nonlinear integration of synaptic input, our ELM neuron can accurately match the aforementioned input-output relationship with under ten thousand trainable parameters. To further assess the computational ramifications of our neuron design, we evaluate it on various tasks with demanding temporal structures, including the Long Range Arena (LRA) datasets, as well as a novel neuromorphic dataset based on the Spiking Heidelberg Digits dataset (SHD-Adding). Leveraging a larger number of memory units with sufficiently long timescales, and correspondingly sophisticated synaptic integration, the ELM neuron displays substantial long-range processing capabilities, reliably outperforming the classic Transformer or Chrono-LSTM architectures on LRA, and even solving the Pathfinder-X task with over 70% accuracy (16k context length).

This paper discusses a simple and explicit toy-model example of the categorical Hopfield equations introduced in previous work of Manin and the author. These describe dynamical assignments of resources to networks, where resources are objects in unital symmetric monoidal categories and assignments are realized by summing functors. The special case discussed here is based on computational resources (computational models of neurons) as objects in a category of DNNs, with a simple choice of the endofunctors defining the Hopfield equations that reproduce the usual updating of the weights in DNNs by gradient descent.

Recent advances in artificial neural networks for machine learning, and language modeling in particular, have established a family of recurrent neural network (RNN) architectures that, unlike conventional RNNs with vector-form hidden states, use two-dimensional (2D) matrix-form hidden states. Such 2D-state RNNs, known as Fast Weight Programmers (FWPs), can be interpreted as a neural network whose synaptic weights (called fast weights) dynamically change over time as a function of input observations, and serve as short-term memory storage; corresponding synaptic weight modifications are controlled or programmed by another network (the programmer) whose parameters are trained (e.g., by gradient descent). In this Primer, we review the technical foundations of FWPs, their computational characteristics, and their connections to transformers and state space models. We also discuss connections between FWPs and models of synaptic plasticity in the brain, suggesting a convergence of natural and artificial intelligence.

Mechanistic Interpretability (MI) promises a path toward fully understanding how neural networks make their predictions. Prior work demonstrates that even when trained to perform simple arithmetic, models can implement a variety of algorithms (sometimes concurrently) depending on initialization and hyperparameters. Does this mean neuron-level interpretability techniques have limited applicability? We argue that high-dimensional neural networks can learn low-dimensional representations of their training data that are useful beyond simply making good predictions. Such representations can be understood through the mechanistic interpretability lens and provide insights that are surprisingly faithful to human-derived domain knowledge. This indicates that such approaches to interpretability can be useful for deriving a new understanding of a problem from models trained to solve it. As a case study, we extract nuclear physics concepts by studying models trained to reproduce nuclear data.

The brain understands the external world through an internal model that generates predictions and refines them based on prediction errors. A complete prediction specifies what will happen, when it will happen, and with what probability, which we refer to as a "prediction object". Existing models typically capture only what and when, omit probabilities, and rely on biologically-implausible algorithms. Here we show that a single population of spiking neurons can jointly encode the prediction object through a biologically grounded learning mechanism. We implement a heterogeneous Izhikevich spiking reservoir with readouts trained by an error-modulated, attention-gated three-factor Hebbian rule and test it on a novel paradigm that controls both the timing and probability of upcoming stimuli. By integrating real-time learning of "when" with offline consolidation of "what", the model encodes the complete prediction object, firing at the correct times with magnitudes proportional to the probabilities. Critically, it rapidly adapts to changes in both stimulus timing and probability, an ability that global least-squares methods such as FORCE lack without explicit resets. During learning, the model self-organizes its readout weights into near-orthogonal subspaces for "what" and "when," showing that multiplexed encoding arises naturally from generic recurrent dynamics under local, error-gated modulation. These results challenge the view that "what" and "when" predictions require separate modules, suggesting instead that mixed selectivity within shared populations supports flexible predictive cognition. The model also predicts phase-specific neuromodulation and overlapping neural subspaces, offering a parsimonious alternative to hierarchical predictive-coding accounts.

Prior studies on the emergence in large models have primarily focused on how the functional capabilities of large language models (LLMs) scale with model size. Our research, however, transcends this traditional paradigm, aiming to deepen our understanding of the emergence within LLMs by placing a special emphasis not just on the model size but more significantly on the complex behavior of neuron interactions during the training process. By introducing the concepts of "self-organization" and "multifractal analysis," we explore how neuron interactions dynamically evolve during training, leading to "emergence," mirroring the phenomenon in natural systems where simple micro-level interactions give rise to complex macro-level behaviors. To quantitatively analyze the continuously evolving interactions among neurons in large models during training, we propose the Neuron-based Multifractal Analysis (NeuroMFA). Utilizing NeuroMFA, we conduct a comprehensive examination of the emergent behavior in LLMs through the lens of both model size and training process, paving new avenues for research into the emergence in large models.

We frame the problem of unifying representations in neural models as one of sparse model recovery and introduce a framework that extends sparse autoencoders (SAEs) to lifted spaces and infinite-dimensional function spaces, enabling mechanistic interpretability of large neural operators (NO). While the Platonic Representation Hypothesis suggests that neural networks converge to similar representations across architectures, the representational properties of neural operators remain underexplored despite their growing importance in scientific computing. We compare the inference and training dynamics of SAEs, lifted-SAE, and SAE neural operators. We highlight how lifting and operator modules introduce beneficial inductive biases, enabling faster recovery, improved recovery of smooth concepts, and robust inference across varying resolutions, a property unique to neural operators.

State-of-the-art systems neuroscience experiments yield large-scale multimodal data, and these data sets require new tools for analysis. Inspired by the success of large pretrained models in vision and language domains, we reframe the analysis of large-scale, cellular-resolution neuronal spiking data into an autoregressive spatiotemporal generation problem. Neuroformer is a multimodal, multitask generative pretrained transformer (GPT) model that is specifically designed to handle the intricacies of data in systems neuroscience. It scales linearly with feature size, can process an arbitrary number of modalities, and is adaptable to downstream tasks, such as predicting behavior. We first trained Neuroformer on simulated datasets, and found that it both accurately predicted simulated neuronal circuit activity, and also intrinsically inferred the underlying neural circuit connectivity, including direction. When pretrained to decode neural responses, the model predicted the behavior of a mouse with only few-shot fine-tuning, suggesting that the model begins learning how to do so directly from the neural representations themselves, without any explicit supervision. We used an ablation study to show that joint training on neuronal responses and behavior boosted performance, highlighting the model's ability to associate behavioral and neural representations in an unsupervised manner. These findings show that Neuroformer can analyze neural datasets and their emergent properties, informing the development of models and hypotheses associated with the brain.

Artificial neural networks (ANN) were inspired by the architecture and functions of the human brain and have revolutionised the field of artificial intelligence (AI). Inspired by studies on the latent geometry of the brain we posit that an increase in the research and application of hyperbolic geometry in machine learning will lead to increased accuracy, improved feature space representations and more efficient models across a range of tasks. We look at the structure and functions of the human brain, highlighting the alignment between the brain's hierarchical nature and hyperbolic geometry. By examining the brain's complex network of neuron connections and its cognitive processes, we illustrate how hyperbolic geometry plays a pivotal role in human intelligence. Empirical evidence indicates that hyperbolic neural networks outperform Euclidean models for tasks including natural language processing, computer vision and complex network analysis, requiring fewer parameters and exhibiting better generalisation. Despite its nascent adoption, hyperbolic geometry holds promise for improving machine learning models and advancing the field toward AGI.

Humans and animals have the ability to continually acquire, fine-tune, and transfer knowledge and skills throughout their lifespan. This ability, referred to as lifelong learning, is mediated by a rich set of neurocognitive mechanisms that together contribute to the development and specialization of our sensorimotor skills as well as to long-term memory consolidation and retrieval. Consequently, lifelong learning capabilities are crucial for autonomous agents interacting in the real world and processing continuous streams of information. However, lifelong learning remains a long-standing challenge for machine learning and neural network models since the continual acquisition of incrementally available information from non-stationary data distributions generally leads to catastrophic forgetting or interference. This limitation represents a major drawback for state-of-the-art deep neural network models that typically learn representations from stationary batches of training data, thus without accounting for situations in which information becomes incrementally available over time. In this review, we critically summarize the main challenges linked to lifelong learning for artificial learning systems and compare existing neural network approaches that alleviate, to different extents, catastrophic forgetting. We discuss well-established and emerging research motivated by lifelong learning factors in biological systems such as structural plasticity, memory replay, curriculum and transfer learning, intrinsic motivation, and multisensory integration.

In the pursuit to understand the intricacies of human brain's visual processing, reconstructing dynamic visual experiences from brain activities emerges as a challenging yet fascinating endeavor. While recent advancements have achieved success in reconstructing static images from non-invasive brain recordings, the domain of translating continuous brain activities into video format remains underexplored. In this work, we introduce NeuroCine, a novel dual-phase framework to targeting the inherent challenges of decoding fMRI data, such as noises, spatial redundancy and temporal lags. This framework proposes spatial masking and temporal interpolation-based augmentation for contrastive learning fMRI representations and a diffusion model enhanced by dependent prior noise for video generation. Tested on a publicly available fMRI dataset, our method shows promising results, outperforming the previous state-of-the-art models by a notable margin of {20.97%}, {31.00%} and {12.30%} respectively on decoding the brain activities of three subjects in the fMRI dataset, as measured by SSIM. Additionally, our attention analysis suggests that the model aligns with existing brain structures and functions, indicating its biological plausibility and interpretability.

Artificial neural networks are the heart of machine learning algorithms and artificial intelligence protocols. Historically, the simplest implementation of an artificial neuron traces back to the classical Rosenblatt's `perceptron', but its long term practical applications may be hindered by the fast scaling up of computational complexity, especially relevant for the training of multilayered perceptron networks. Here we introduce a quantum information-based algorithm implementing the quantum computer version of a perceptron, which shows exponential advantage in encoding resources over alternative realizations. We experimentally test a few qubits version of this model on an actual small-scale quantum processor, which gives remarkably good answers against the expected results. We show that this quantum model of a perceptron can be used as an elementary nonlinear classifier of simple patterns, as a first step towards practical training of artificial quantum neural networks to be efficiently implemented on near-term quantum processing hardware.

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.

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.

Humans and animals have a rich and flexible understanding of the physical world, which enables them to infer the underlying dynamical trajectories of objects and events, plausible future states, and use that to plan and anticipate the consequences of actions. However, the neural mechanisms underlying these computations are unclear. We combine a goal-driven modeling approach with dense neurophysiological data and high-throughput human behavioral readouts to directly impinge on this question. Specifically, we construct and evaluate several classes of sensory-cognitive networks to predict the future state of rich, ethologically-relevant environments, ranging from self-supervised end-to-end models with pixel-wise or object-centric objectives, to models that future predict in the latent space of purely static image-based or dynamic video-based pretrained foundation models. We find strong differentiation across these model classes in their ability to predict neural and behavioral data both within and across diverse environments. In particular, we find that neural responses are currently best predicted by models trained to predict the future state of their environment in the latent space of pretrained foundation models optimized for dynamic scenes in a self-supervised manner. Notably, models that future predict in the latent space of video foundation models that are optimized to support a diverse range of sensorimotor tasks, reasonably match both human behavioral error patterns and neural dynamics across all environmental scenarios that we were able to test. Overall, these findings suggest that the neural mechanisms and behaviors of primate mental simulation are thus far most consistent with being optimized to future predict on dynamic, reusable visual representations that are useful for embodied AI more generally.

Neuromorphic computing with spiking neural networks is promising for energy-efficient artificial intelligence (AI) applications. However, different from humans who continually learn different tasks in a lifetime, neural network models suffer from catastrophic forgetting. How could neuronal operations solve this problem is an important question for AI and neuroscience. Many previous studies draw inspiration from observed neuroscience phenomena and propose episodic replay or synaptic metaplasticity, but they are not guaranteed to explicitly preserve knowledge for neuron populations. Other works focus on machine learning methods with more mathematical grounding, e.g., orthogonal projection on high dimensional spaces, but there is no neural correspondence for neuromorphic computing. In this work, we develop a new method with neuronal operations based on lateral connections and Hebbian learning, which can protect knowledge by projecting activity traces of neurons into an orthogonal subspace so that synaptic weight update will not interfere with old tasks. We show that Hebbian and anti-Hebbian learning on recurrent lateral connections can effectively extract the principal subspace of neural activities and enable orthogonal projection. This provides new insights into how neural circuits and Hebbian learning can help continual learning, and also how the concept of orthogonal projection can be realized in neuronal systems. Our method is also flexible to utilize arbitrary training methods based on presynaptic activities/traces. Experiments show that our method consistently solves forgetting for spiking neural networks with nearly zero forgetting under various supervised training methods with different error propagation approaches, and outperforms previous approaches under various settings. Our method can pave a solid path for building continual neuromorphic computing systems.

We propose the APTx Neuron, a novel, unified neural computation unit that integrates non-linear activation and linear transformation into a single trainable expression. The APTx Neuron is derived from the APTx activation function, thereby eliminating the need for separate activation layers and making the architecture both computationally efficient and elegant. The proposed neuron follows the functional form y = sum_{i=1}^{n} ((alpha_i + tanh(beta_i x_i)) cdot gamma_i x_i) + delta, where all parameters alpha_i, beta_i, gamma_i, and delta are trainable. We validate our APTx Neuron-based architecture on the MNIST dataset, achieving up to 96.69% test accuracy within 11 epochs using approximately 332K trainable parameters. The results highlight the superior expressiveness and computational efficiency of the APTx Neuron compared to traditional neurons, pointing toward a new paradigm in unified neuron design and the architectures built upon it.

How neuronal circuits achieve credit assignment remains a central unsolved question in systems neuroscience. Various studies have suggested plausible solutions for back-propagating error signals through multi-layer networks. These purely functionally motivated models assume distinct neuronal compartments to represent local error signals that determine the sign of synaptic plasticity. However, this explicit error modulation is inconsistent with phenomenological plasticity models in which the sign depends primarily on postsynaptic activity. Here we show how a plausible microcircuit model and Hebbian learning rule derived within an adaptive control theory framework can resolve this discrepancy. Assuming errors are encoded in top-down dis-inhibitory synaptic afferents, we show that error-modulated learning emerges naturally at the circuit level when recurrent inhibition explicitly influences Hebbian plasticity. The same learning rule accounts for experimentally observed plasticity in the absence of inhibition and performs comparably to back-propagation of error (BP) on several non-linearly separable benchmarks. Our findings bridge the gap between functional and experimentally observed plasticity rules and make concrete predictions on inhibitory modulation of excitatory plasticity.

Graph neural networks that model 3D data, such as point clouds or atoms, are typically desired to be SO(3) equivariant, i.e., equivariant to 3D rotations. Unfortunately equivariant convolutions, which are a fundamental operation for equivariant networks, increase significantly in computational complexity as higher-order tensors are used. In this paper, we address this issue by reducing the SO(3) convolutions or tensor products to mathematically equivalent convolutions in SO(2) . This is accomplished by aligning the node embeddings' primary axis with the edge vectors, which sparsifies the tensor product and reduces the computational complexity from O(L^6) to O(L^3), where L is the degree of the representation. We demonstrate the potential implications of this improvement by proposing the Equivariant Spherical Channel Network (eSCN), a graph neural network utilizing our novel approach to equivariant convolutions, which achieves state-of-the-art results on the large-scale OC-20 and OC-22 datasets.

Modeling the energy and forces of atomic systems is a fundamental problem in computational chemistry with the potential to help address many of the world's most pressing problems, including those related to energy scarcity and climate change. These calculations are traditionally performed using Density Functional Theory, which is computationally very expensive. Machine learning has the potential to dramatically improve the efficiency of these calculations from days or hours to seconds. We propose the Spherical Channel Network (SCN) to model atomic energies and forces. The SCN is a graph neural network where nodes represent atoms and edges their neighboring atoms. The atom embeddings are a set of spherical functions, called spherical channels, represented using spherical harmonics. We demonstrate, that by rotating the embeddings based on the 3D edge orientation, more information may be utilized while maintaining the rotational equivariance of the messages. While equivariance is a desirable property, we find that by relaxing this constraint in both message passing and aggregation, improved accuracy may be achieved. We demonstrate state-of-the-art results on the large-scale Open Catalyst dataset in both energy and force prediction for numerous tasks and metrics.

We interpret the function of individual neurons in CLIP by automatically describing them using text. Analyzing the direct effects (i.e. the flow from a neuron through the residual stream to the output) or the indirect effects (overall contribution) fails to capture the neurons' function in CLIP. Therefore, we present the "second-order lens", analyzing the effect flowing from a neuron through the later attention heads, directly to the output. We find that these effects are highly selective: for each neuron, the effect is significant for <2% of the images. Moreover, each effect can be approximated by a single direction in the text-image space of CLIP. We describe neurons by decomposing these directions into sparse sets of text representations. The sets reveal polysemantic behavior - each neuron corresponds to multiple, often unrelated, concepts (e.g. ships and cars). Exploiting this neuron polysemy, we mass-produce "semantic" adversarial examples by generating images with concepts spuriously correlated to the incorrect class. Additionally, we use the second-order effects for zero-shot segmentation and attribute discovery in images. Our results indicate that a scalable understanding of neurons can be used for model deception and for introducing new model capabilities.

There is renewed interest in modeling and understanding the nervous system of the nematode Caenorhabditis elegans (C. elegans), as this small model system provides a path to bridge the gap between nervous system structure (connectivity) and function (physiology). However, existing physiology datasets, whether involving passive recording or stimulation, are in distinct formats, and connectome datasets require preprocessing before analysis can commence. Here we compile and homogenize datasets of neural activity and connectivity. Our neural activity dataset is derived from 11 C. elegans neuroimaging experiments, while our connectivity dataset is compiled from 9 connectome annotations based on 3 primary electron microscopy studies and 1 signal propagation study. Physiology datasets, collected under varying protocols, measure calcium fluorescence in labeled subsets of the worm's 300 neurons. Our preprocessing pipeline standardizes these datasets by consistently ordering labeled neurons and resampling traces to a common sampling rate, yielding recordings from approximately 900 worms and 250 uniquely labeled neurons. The connectome datasets, collected from electron microscopy reconstructions, represent the entire nervous system as a graph of connections. Our collection is accessible on HuggingFace, facilitating analysis of the structure-function relationship in biology using modern neural network architectures and enabling cross-lab and cross-animal comparisons.

Graph neural networks are emerging as promising methods for modeling molecular graphs, in which nodes and edges correspond to atoms and chemical bonds, respectively. Recent studies show that when 3D molecular geometries, such as bond lengths and angles, are available, molecular property prediction tasks can be made more accurate. However, computing of 3D molecular geometries requires quantum calculations that are computationally prohibitive. For example, accurate calculation of 3D geometries of a small molecule requires hours of computing time using density functional theory (DFT). Here, we propose to predict the ground-state 3D geometries from molecular graphs using machine learning methods. To make this feasible, we develop a benchmark, known as Molecule3D, that includes a dataset with precise ground-state geometries of approximately 4 million molecules derived from DFT. We also provide a set of software tools for data processing, splitting, training, and evaluation, etc. Specifically, we propose to assess the error and validity of predicted geometries using four metrics. We implement two baseline methods that either predict the pairwise distance between atoms or atom coordinates in 3D space. Experimental results show that, compared with generating 3D geometries with RDKit, our method can achieve comparable prediction accuracy but with much smaller computational costs. Our Molecule3D is available as a module of the MoleculeX software library (https://github.com/divelab/MoleculeX).

Despite being the workhorse of deep learning, the backpropagation algorithm is no panacea. It enforces sequential layer updates, thus preventing efficient parallelization of the training process. Furthermore, its biological plausibility is being challenged. Alternative schemes have been devised; yet, under the constraint of synaptic asymmetry, none have scaled to modern deep learning tasks and architectures. Here, we challenge this perspective, and study the applicability of Direct Feedback Alignment to neural view synthesis, recommender systems, geometric learning, and natural language processing. In contrast with previous studies limited to computer vision tasks, our findings show that it successfully trains a large range of state-of-the-art deep learning architectures, with performance close to fine-tuned backpropagation. At variance with common beliefs, our work supports that challenging tasks can be tackled in the absence of weight transport.

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.

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.

Going beyond 'dendritic democracy', we introduce a 'democracy of local processors', termed Cooperator. Here we compare their capabilities when used in permutation-invariant neural networks for reinforcement learning (RL), with machine learning algorithms based on Transformers, such as ChatGPT. Transformers are based on the long-standing conception of integrate-and-fire 'point' neurons, whereas Cooperator is inspired by recent neurobiological breakthroughs suggesting that the cellular foundations of mental life depend on context-sensitive pyramidal neurons in the neocortex which have two functionally distinct points. We show that when used for RL, an algorithm based on Cooperator learns far quicker than that based on Transformer, even while having the same number of parameters.

We propose a simple auto-encoder framework for molecule generation. The molecular graph is first encoded into a continuous latent representation z, which is then decoded back to a molecule. The encoding process is easy, but the decoding process remains challenging. In this work, we introduce a simple two-step decoding process. In a first step, a fully connected neural network uses the latent vector z to produce a molecular formula, for example CO_2 (one carbon and two oxygen atoms). In a second step, a graph convolutional neural network uses the same latent vector z to place bonds between the atoms that were produced in the first step (for example a double bond will be placed between the carbon and each of the oxygens). This two-step process, in which a bag of atoms is first generated, and then assembled, provides a simple framework that allows us to develop an efficient molecule auto-encoder. Numerical experiments on basic tasks such as novelty, uniqueness, validity and optimized chemical property for the 250k ZINC molecules demonstrate the performances of the proposed system. Particularly, we achieve the highest reconstruction rate of 90.5\%, improving the previous rate of 76.7\%. We also report the best property improvement results when optimization is constrained by the molecular distance between the original and generated molecules.

Understanding the hidden mechanisms behind human's visual perception is a fundamental question in neuroscience. To that end, investigating into the neural responses of human mind activities, such as functional Magnetic Resonance Imaging (fMRI), has been a significant research vehicle. However, analyzing fMRI signals is challenging, costly, daunting, and demanding for professional training. Despite remarkable progress in fMRI analysis, existing approaches are limited to generating 2D images and far away from being biologically meaningful and practically useful. Under this insight, we propose to generate visually plausible and functionally more comprehensive 3D outputs decoded from brain signals, enabling more sophisticated modeling of fMRI data. Conceptually, we reformulate this task as a {\em fMRI conditioned 3D object generation} problem. We design a novel 3D object representation learning method, Brain3D, that takes as input the fMRI data of a subject who was presented with a 2D image, and yields as output the corresponding 3D object images. The key capabilities of this model include tackling the noises with high-level semantic signals and a two-stage architecture design for progressive high-level information integration. Extensive experiments validate the superior capability of our model over previous state-of-the-art 3D object generation methods. Importantly, we show that our model captures the distinct functionalities of each region of human vision system as well as their intricate interplay relationships, aligning remarkably with the established discoveries in neuroscience. Further, preliminary evaluations indicate that Brain3D can successfully identify the disordered brain regions in simulated scenarios, such as V1, V2, V3, V4, and the medial temporal lobe (MTL) within the human visual system. Our data and code will be available at https://brain-3d.github.io/.

The liquid state machine (LSM) combines low training complexity and biological plausibility, which has made it an attractive machine learning framework for edge and neuromorphic computing paradigms. Originally proposed as a model of brain computation, the LSM tunes its internal weights without backpropagation of gradients, which results in lower performance compared to multi-layer neural networks. Recent findings in neuroscience suggest that astrocytes, a long-neglected non-neuronal brain cell, modulate synaptic plasticity and brain dynamics, tuning brain networks to the vicinity of the computationally optimal critical phase transition between order and chaos. Inspired by this disruptive understanding of how brain networks self-tune, we propose the neuron-astrocyte liquid state machine (NALSM) that addresses under-performance through self-organized near-critical dynamics. Similar to its biological counterpart, the astrocyte model integrates neuronal activity and provides global feedback to spike-timing-dependent plasticity (STDP), which self-organizes NALSM dynamics around a critical branching factor that is associated with the edge-of-chaos. We demonstrate that NALSM achieves state-of-the-art accuracy versus comparable LSM methods, without the need for data-specific hand-tuning. With a top accuracy of 97.61% on MNIST, 97.51% on N-MNIST, and 85.84% on Fashion-MNIST, NALSM achieved comparable performance to current fully-connected multi-layer spiking neural networks trained via backpropagation. Our findings suggest that the further development of brain-inspired machine learning methods has the potential to reach the performance of deep learning, with the added benefits of supporting robust and energy-efficient neuromorphic computing on the edge.

The nexus of quantum computing and machine learning - quantum machine learning - offers the potential for significant advancements in chemistry. This review specifically explores the potential of quantum neural networks on gate-based quantum computers within the context of drug discovery. We discuss the theoretical foundations of quantum machine learning, including data encoding, variational quantum circuits, and hybrid quantum-classical approaches. Applications to drug discovery are highlighted, including molecular property prediction and molecular generation. We provide a balanced perspective, emphasizing both the potential benefits and the challenges that must be addressed.

Some neurons in deep networks specialize in recognizing highly specific perceptual, structural, or semantic features of inputs. In computer vision, techniques exist for identifying neurons that respond to individual concept categories like colors, textures, and object classes. But these techniques are limited in scope, labeling only a small subset of neurons and behaviors in any network. Is a richer characterization of neuron-level computation possible? We introduce a procedure (called MILAN, for mutual-information-guided linguistic annotation of neurons) that automatically labels neurons with open-ended, compositional, natural language descriptions. Given a neuron, MILAN generates a description by searching for a natural language string that maximizes pointwise mutual information with the image regions in which the neuron is active. MILAN produces fine-grained descriptions that capture categorical, relational, and logical structure in learned features. These descriptions obtain high agreement with human-generated feature descriptions across a diverse set of model architectures and tasks, and can aid in understanding and controlling learned models. We highlight three applications of natural language neuron descriptions. First, we use MILAN for analysis, characterizing the distribution and importance of neurons selective for attribute, category, and relational information in vision models. Second, we use MILAN for auditing, surfacing neurons sensitive to human faces in datasets designed to obscure them. Finally, we use MILAN for editing, improving robustness in an image classifier by deleting neurons sensitive to text features spuriously correlated with class labels.

This position paper explores the rapid development of Foundation Models (FMs) in AI and their implications for intelligence and reasoning. It examines the characteristics of FMs, including their training on vast datasets and use of embedding spaces to capture semantic relationships. The paper discusses recent advancements in FMs' reasoning abilities which we argue cannot be attributed to increased model size but to novel training techniques which yield learning phenomena like grokking. It also addresses the challenges in benchmarking FMs and compares their structure to the human brain. We argue that while FMs show promising developments in reasoning and knowledge representation, understanding their inner workings remains a significant challenge, similar to ongoing efforts in neuroscience to comprehend human brain function. Despite having some similarities, fundamental differences between FMs and the structure of human brain warn us against making direct comparisons or expecting neuroscience to provide immediate insights into FM function.

Deep Learning has revolutionized various fields, including Computer Vision, Natural Language Processing, as well as Biomedical research. Within the field of neuroscience, specifically in electrophysiological neuroimaging, researchers are starting to explore leveraging deep learning to make predictions on their data without extensive feature engineering. The availability of large-scale datasets is a crucial aspect of allowing the experimentation of Deep Learning models. We are publishing the first large-scale clinical EEG dataset that simplifies data access and management for Deep Learning. This dataset contains eyes-closed EEG data prepared from a collection of 1,574 juvenile participants from the Healthy Brain Network. We demonstrate a use case integrating this framework, and discuss why providing such neuroinformatics infrastructure to the community is critical for future scientific discoveries.

A growing literature in computational neuroscience leverages gradient descent and learning algorithms that approximate it to study synaptic plasticity in the brain. However, the vast majority of this work ignores a critical underlying assumption: the choice of distance for synaptic changes - i.e. the geometry of synaptic plasticity. Gradient descent assumes that the distance is Euclidean, but many other distances are possible, and there is no reason that biology necessarily uses Euclidean geometry. Here, using the theoretical tools provided by mirror descent, we show that the distribution of synaptic weights will depend on the geometry of synaptic plasticity. We use these results to show that experimentally-observed log-normal weight distributions found in several brain areas are not consistent with standard gradient descent (i.e. a Euclidean geometry), but rather with non-Euclidean distances. Finally, we show that it should be possible to experimentally test for different synaptic geometries by comparing synaptic weight distributions before and after learning. Overall, our work shows that the current paradigm in theoretical work on synaptic plasticity that assumes Euclidean synaptic geometry may be misguided and that it should be possible to experimentally determine the true geometry of synaptic plasticity in the brain.

Neurosymbolic (NeSy) frameworks combine neural representations and learning with symbolic representations and reasoning. Combining the reasoning capacities, explainability, and interpretability of symbolic processing with the flexibility and power of neural computing allows us to solve complex problems with more reliability while being data-efficient. However, this recently growing topic poses a challenge to developers with its learning curve, lack of user-friendly tools, libraries, and unifying frameworks. In this paper, we characterize the technical facets of existing NeSy frameworks, such as the symbolic representation language, integration with neural models, and the underlying algorithms. A majority of the NeSy research focuses on algorithms instead of providing generic frameworks for declarative problem specification to leverage problem solving. To highlight the key aspects of Neurosymbolic modeling, we showcase three generic NeSy frameworks - DeepProbLog, Scallop, and DomiKnowS. We identify the challenges within each facet that lay the foundation for identifying the expressivity of each framework in solving a variety of problems. Building on this foundation, we aim to spark transformative action and encourage the community to rethink this problem in novel ways.

Neural networks surround us, in the form of large language models, speech transcription systems, molecular discovery algorithms, robotics, and much more. Stripped of anything else, neural networks are compositions of differentiable primitives, and studying them means learning how to program and how to interact with these models, a particular example of what is called differentiable programming. This primer is an introduction to this fascinating field imagined for someone, like Alice, who has just ventured into this strange differentiable wonderland. I overview the basics of optimizing a function via automatic differentiation, and a selection of the most common designs for handling sequences, graphs, texts, and audios. The focus is on a intuitive, self-contained introduction to the most important design techniques, including convolutional, attentional, and recurrent blocks, hoping to bridge the gap between theory and code (PyTorch and JAX) and leaving the reader capable of understanding some of the most advanced models out there, such as large language models (LLMs) and multimodal architectures.

We find arithmetic ability resides within a limited number of attention heads, with each head specializing in distinct operations. To delve into the reason, we introduce the Comparative Neuron Analysis (CNA) method, which identifies an internal logic chain consisting of four distinct stages from input to prediction: feature enhancing with shallow FFN neurons, feature transferring by shallow attention layers, feature predicting by arithmetic heads, and prediction enhancing among deep FFN neurons. Moreover, we identify the human-interpretable FFN neurons within both feature-enhancing and feature-predicting stages. These findings lead us to investigate the mechanism of LoRA, revealing that it enhances prediction probabilities by amplifying the coefficient scores of FFN neurons related to predictions. Finally, we apply our method in model pruning for arithmetic tasks and model editing for reducing gender bias. Code is on https://github.com/zepingyu0512/arithmetic-mechanism.

Despite extraordinary progress in artificial intelligence (AI), modern systems remain incomplete representations of human cognition. Vision, audition, and language have received disproportionate attention due to well-defined benchmarks, standardized datasets, and consensus-driven scientific foundations. In contrast, olfaction - a high-bandwidth, evolutionarily critical sense - has been largely overlooked. This omission presents a foundational gap in the construction of truly embodied and ethically aligned super-human intelligence. We argue that the exclusion of olfactory perception from AI architectures is not due to irrelevance but to structural challenges: unresolved scientific theories of smell, heterogeneous sensor technologies, lack of standardized olfactory datasets, absence of AI-oriented benchmarks, and difficulty in evaluating sub-perceptual signal processing. These obstacles have hindered the development of machine olfaction despite its tight coupling with memory, emotion, and contextual reasoning in biological systems. In this position paper, we assert that meaningful progress toward general and embodied intelligence requires serious investment in olfactory research by the AI community. We call for cross-disciplinary collaboration - spanning neuroscience, robotics, machine learning, and ethics - to formalize olfactory benchmarks, develop multimodal datasets, and define the sensory capabilities necessary for machines to understand, navigate, and act within human environments. Recognizing olfaction as a core modality is essential not only for scientific completeness, but for building AI systems that are ethically grounded in the full scope of the human experience.

Understanding how the brain represents visual information is a fundamental challenge in neuroscience and artificial intelligence. While AI-driven decoding of neural data has provided insights into the human visual system, integrating multimodal neuroimaging signals, such as EEG, MEG, and fMRI, remains a critical hurdle due to their inherent spatiotemporal misalignment. Current approaches often analyze these modalities in isolation, limiting a holistic view of neural representation. In this study, we introduce BrainFLORA, a unified framework for integrating cross-modal neuroimaging data to construct a shared neural representation. Our approach leverages multimodal large language models (MLLMs) augmented with modality-specific adapters and task decoders, achieving state-of-the-art performance in joint-subject visual retrieval task and has the potential to extend multitasking. Combining neuroimaging analysis methods, we further reveal how visual concept representations align across neural modalities and with real world object perception. We demonstrate that the brain's structured visual concept representations exhibit an implicit mapping to physical-world stimuli, bridging neuroscience and machine learning from different modalities of neural imaging. Beyond methodological advancements, BrainFLORA offers novel implications for cognitive neuroscience and brain-computer interfaces (BCIs). Our code is available at https://github.com/ncclab-sustech/BrainFLORA.

Pretrained neural networks have attracted significant interest in chemistry and small molecule drug design. Embeddings from these models are widely used for molecular property prediction, virtual screening, and small data learning in molecular chemistry. This study presents the most extensive comparison of such models to date, evaluating 25 models across 25 datasets. Under a fair comparison framework, we assess models spanning various modalities, architectures, and pretraining strategies. Using a dedicated hierarchical Bayesian statistical testing model, we arrive at a surprising result: nearly all neural models show negligible or no improvement over the baseline ECFP molecular fingerprint. Only the CLAMP model, which is also based on molecular fingerprints, performs statistically significantly better than the alternatives. These findings raise concerns about the evaluation rigor in existing studies. We discuss potential causes, propose solutions, and offer practical recommendations.

We propose a new score-based approach to generate 3D molecules represented as atomic densities on regular grids. First, we train a denoising neural network that learns to map from a smooth distribution of noisy molecules to the distribution of real molecules. Then, we follow the neural empirical Bayes framework [Saremi and Hyvarinen, 2019] and generate molecules in two steps: (i) sample noisy density grids from a smooth distribution via underdamped Langevin Markov chain Monte Carlo, and (ii) recover the ``clean'' molecule by denoising the noisy grid with a single step. Our method, VoxMol, generates molecules in a fundamentally different way than the current state of the art (i.e., diffusion models applied to atom point clouds). It differs in terms of the data representation, the noise model, the network architecture and the generative modeling algorithm. VoxMol achieves comparable results to state of the art on unconditional 3D molecule generation while being simpler to train and faster to generate molecules.

Sensory systems across all modalities and species exhibit adaptation to continuously changing input statistics. Individual neurons have been shown to modulate their response gains so as to maximize information transmission in different stimulus contexts. Experimental measurements have revealed additional, nuanced sensory adaptation effects including changes in response maxima and minima, tuning curve repulsion from the adapter stimulus, and stimulus-driven response decorrelation. Existing explanations of these phenomena rely on changes in inter-neuronal synaptic efficacy, which, while more flexible, are unlikely to operate as rapidly or reversibly as single neuron gain modulations. Using published V1 population adaptation data, we show that propagation of single neuron gain changes in a recurrent network is sufficient to capture the entire set of observed adaptation effects. We propose a novel adaptive efficient coding objective with which single neuron gains are modulated, maximizing the fidelity of the stimulus representation while minimizing overall activity in the network. From this objective, we analytically derive a set of gains that optimize the trade-off between preserving information about the stimulus and conserving metabolic resources. Our model generalizes well-established concepts of single neuron adaptive gain control to recurrent populations, and parsimoniously explains experimental adaptation data.

This work is dedicated to the review and perspective of the new direction that we call "Neuropunk revolution" resembling the cultural phenomenon of cyberpunk. This new phenomenon has its foundations in advances in neuromorphic technologies including memristive and bio-plausible simulations, BCI, and neurointerfaces as well as unconventional approaches to AI and computing in general. We present the review of the current state-of-the-art and our vision of near future development of scientific approaches and future technologies. We call the "Neuropunk revolution" the set of trends that in our view provide the necessary background for the new generation of approaches technologies to integrate the cybernetic objects with biological tissues in close loop system as well as robotic systems inspired by the biological processes again integrated with biological objects. We see bio-plausible simulations implemented by digital computers or spiking networks memristive hardware as promising bridge or middleware between digital and (neuro)biological domains.

Despite their widespread success, the application of deep neural networks to functional data remains scarce today. The infinite dimensionality of functional data means standard learning algorithms can be applied only after appropriate dimension reduction, typically achieved via basis expansions. Currently, these bases are chosen a priori without the information for the task at hand and thus may not be effective for the designated task. We instead propose to adaptively learn these bases in an end-to-end fashion. We introduce neural networks that employ a new Basis Layer whose hidden units are each basis functions themselves implemented as a micro neural network. Our architecture learns to apply parsimonious dimension reduction to functional inputs that focuses only on information relevant to the target rather than irrelevant variation in the input function. Across numerous classification/regression tasks with functional data, our method empirically outperforms other types of neural networks, and we prove that our approach is statistically consistent with low generalization error. Code is available at: https://github.com/jwyyy/AdaFNN.

A new prior is proposed for learning representations of high-level concepts of the kind we manipulate with language. This prior can be combined with other priors in order to help disentangling abstract factors from each other. It is inspired by cognitive neuroscience theories of consciousness, seen as a bottleneck through which just a few elements, after having been selected by attention from a broader pool, are then broadcast and condition further processing, both in perception and decision-making. The set of recently selected elements one becomes aware of is seen as forming a low-dimensional conscious state. This conscious state is combining the few concepts constituting a conscious thought, i.e., what one is immediately conscious of at a particular moment. We claim that this architectural and information-processing constraint corresponds to assumptions about the joint distribution between high-level concepts. To the extent that these assumptions are generally true (and the form of natural language seems consistent with them), they can form a useful prior for representation learning. A low-dimensional thought or conscious state is analogous to a sentence: it involves only a few variables and yet can make a statement with very high probability of being true. This is consistent with a joint distribution (over high-level concepts) which has the form of a sparse factor graph, i.e., where the dependencies captured by each factor of the factor graph involve only very few variables while creating a strong dip in the overall energy function. The consciousness prior also makes it natural to map conscious states to natural language utterances or to express classical AI knowledge in a form similar to facts and rules, albeit capturing uncertainty as well as efficient search mechanisms implemented by attention mechanisms.

A fundamental question in cognitive neuroscience is what shapes visual perception: the external world's structure or the brain's internal architecture. Although some perceptual variability can be traced to individual differences, brain responses to naturalistic stimuli evoke similar activity patterns across individuals, suggesting a convergent representational principle. Here, we test if this stimulus-driven convergence follows a common trajectory across people and deep neural networks (DNNs) during its transformation from sensory to high-level internal representations. We introduce a unified framework that traces representational flow by combining inter-subject similarity with alignment to model hierarchies. Applying this framework to three independent fMRI datasets of visual scene perception, we reveal a cortex-wide network, conserved across individuals, organized into two pathways: a medial-ventral stream for scene structure and a lateral-dorsal stream tuned for social and biological content. This functional organization is captured by the hierarchies of vision DNNs but not language models, reinforcing the specificity of the visual-to-semantic transformation. These findings show a convergent computational solution for visual encoding in both human and artificial vision, driven by the structure of the external world.

Mapping behavioral actions to neural activity is a fundamental goal of neuroscience. As our ability to record large neural and behavioral data increases, there is growing interest in modeling neural dynamics during adaptive behaviors to probe neural representations. In particular, neural latent embeddings can reveal underlying correlates of behavior, yet, we lack non-linear techniques that can explicitly and flexibly leverage joint behavior and neural data. Here, we fill this gap with a novel method, CEBRA, that jointly uses behavioral and neural data in a hypothesis- or discovery-driven manner to produce consistent, high-performance latent spaces. We validate its accuracy and demonstrate our tool's utility for both calcium and electrophysiology datasets, across sensory and motor tasks, and in simple or complex behaviors across species. It allows for single and multi-session datasets to be leveraged for hypothesis testing or can be used label-free. Lastly, we show that CEBRA can be used for the mapping of space, uncovering complex kinematic features, and rapid, high-accuracy decoding of natural movies from visual cortex.

A long standing goal in neuroscience has been to elucidate the functional organization of the brain. Within higher visual cortex, functional accounts have remained relatively coarse, focusing on regions of interest (ROIs) and taking the form of selectivity for broad categories such as faces, places, bodies, food, or words. Because the identification of such ROIs has typically relied on manually assembled stimulus sets consisting of isolated objects in non-ecological contexts, exploring functional organization without robust a priori hypotheses has been challenging. To overcome these limitations, we introduce a data-driven approach in which we synthesize images predicted to activate a given brain region using paired natural images and fMRI recordings, bypassing the need for category-specific stimuli. Our approach -- Brain Diffusion for Visual Exploration ("BrainDiVE") -- builds on recent generative methods by combining large-scale diffusion models with brain-guided image synthesis. Validating our method, we demonstrate the ability to synthesize preferred images with appropriate semantic specificity for well-characterized category-selective ROIs. We then show that BrainDiVE can characterize differences between ROIs selective for the same high-level category. Finally we identify novel functional subdivisions within these ROIs, validated with behavioral data. These results advance our understanding of the fine-grained functional organization of human visual cortex, and provide well-specified constraints for further examination of cortical organization using hypothesis-driven methods.

The human brain is a complex spiking neural network (SNN) that learns multimodal signals in a zero-shot manner by generalizing existing knowledge. Remarkably, the brain achieves this with minimal power consumption, using event-based signals that propagate within its structure. However, mimicking the human brain in neuromorphic hardware presents both hardware and software challenges. Hardware limitations, such as the slowdown of Moore's law and the von Neumann bottleneck, hinder the efficiency of digital computers. On the software side, SNNs are known for their difficult training, especially when learning multimodal signals. To overcome these challenges, we propose a hardware-software co-design that combines a fixed and random liquid state machine (LSM) SNN encoder with trainable artificial neural network (ANN) projections. The LSM is physically implemented using analogue resistive memory, leveraging the inherent stochasticity of resistive switching to generate random weights. This highly efficient and nanoscale in-memory computing approach effectively addresses the von Neumann bottleneck and the slowdown of Moore's law. The ANN projections are implemented digitally, allowing for easy optimization using contrastive loss, which helps to overcome the difficulties associated with SNN training. We experimentally implement this co-design on a 40nm 256Kb in-memory computing macro. We first demonstrate LSM-based event encoding through supervised classification and linear probing on the N-MNIST and N-TIDIGITS datasets.

We introduce Einstein Fields, a neural representation that is designed to compress computationally intensive four-dimensional numerical relativity simulations into compact implicit neural network weights. By modeling the metric, which is the core tensor field of general relativity, Einstein Fields enable the derivation of physical quantities via automatic differentiation. However, unlike conventional neural fields (e.g., signed distance, occupancy, or radiance fields), Einstein Fields are Neural Tensor Fields with the key difference that when encoding the spacetime geometry of general relativity into neural field representations, dynamics emerge naturally as a byproduct. Einstein Fields show remarkable potential, including continuum modeling of 4D spacetime, mesh-agnosticity, storage efficiency, derivative accuracy, and ease of use. We address these challenges across several canonical test beds of general relativity and release an open source JAX-based library, paving the way for more scalable and expressive approaches to numerical relativity. Code is made available at https://github.com/AndreiB137/EinFields

The utility of a learned neural representation depends on how well its geometry supports performance in downstream tasks. This geometry depends on the structure of the inputs, the structure of the target outputs, and the architecture of the network. By studying the learning dynamics of networks with one hidden layer, we discovered that the network's activation function has an unexpectedly strong impact on the representational geometry: Tanh networks tend to learn representations that reflect the structure of the target outputs, while ReLU networks retain more information about the structure of the raw inputs. This difference is consistently observed across a broad class of parameterized tasks in which we modulated the degree of alignment between the geometry of the task inputs and that of the task labels. We analyzed the learning dynamics in weight space and show how the differences between the networks with Tanh and ReLU nonlinearities arise from the asymmetric asymptotic behavior of ReLU, which leads feature neurons to specialize for different regions of input space. By contrast, feature neurons in Tanh networks tend to inherit the task label structure. Consequently, when the target outputs are low dimensional, Tanh networks generate neural representations that are more disentangled than those obtained with a ReLU nonlinearity. Our findings shed light on the interplay between input-output geometry, nonlinearity, and learned representations in neural networks.

Activity difference based learning algorithms-such as contrastive Hebbian learning and equilibrium propagation-have been proposed as biologically plausible alternatives to error back-propagation. However, on traditional digital chips these algorithms suffer from having to solve a costly inference problem twice, making these approaches more than two orders of magnitude slower than back-propagation. In the analog realm equilibrium propagation may be promising for fast and energy efficient learning, but states still need to be inferred and stored twice. Inspired by lifted neural networks and compartmental neuron models we propose a simple energy based compartmental neuron model, termed dual propagation, in which each neuron is a dyad with two intrinsic states. At inference time these intrinsic states encode the error/activity duality through their difference and their mean respectively. The advantage of this method is that only a single inference phase is needed and that inference can be solved in layerwise closed-form. Experimentally we show on common computer vision datasets, including Imagenet32x32, that dual propagation performs equivalently to back-propagation both in terms of accuracy and runtime.

This study introduces BrainTransformers, an innovative Large Language Model (LLM) implemented using Spiking Neural Networks (SNN). Our key contributions include: (1) designing SNN-compatible Transformer components such as SNNMatmul, SNNSoftmax, and SNNSiLU; (2) implementing an SNN approximation of the SiLU activation function; and (3) developing a Synapsis module to simulate synaptic plasticity. Our 3-billion parameter model, BrainTransformers-3B-Chat, demonstrates competitive performance across various benchmarks, including MMLU (63.2), BBH (54.1), ARC-C (54.3), and GSM8K (76.3), while potentially offering improved energy efficiency and biological plausibility. The model employs a three-stage training approach, including SNN-specific neuronal synaptic plasticity training. This research opens new avenues for brain-like AI systems in natural language processing and neuromorphic computing. Future work will focus on hardware optimization, developing specialized SNN fine-tuning tools, and exploring practical applications in energy-efficient computing environments.

A neuroscience method to understanding the brain is to find and study the preferred stimuli that highly activate an individual cell or groups of cells. Recent advances in machine learning enable a family of methods to synthesize preferred stimuli that cause a neuron in an artificial or biological brain to fire strongly. Those methods are known as Activation Maximization (AM) or Feature Visualization via Optimization. In this chapter, we (1) review existing AM techniques in the literature; (2) discuss a probabilistic interpretation for AM; and (3) review the applications of AM in debugging and explaining networks.

Neural fields, which represent signals as a function parameterized by a neural network, are a promising alternative to traditional discrete vector or grid-based representations. Compared to discrete representations, neural representations both scale well with increasing resolution, are continuous, and can be many-times differentiable. However, given a dataset of signals that we would like to represent, having to optimize a separate neural field for each signal is inefficient, and cannot capitalize on shared information or structures among signals. Existing generalization methods view this as a meta-learning problem and employ gradient-based meta-learning to learn an initialization which is then fine-tuned with test-time optimization, or learn hypernetworks to produce the weights of a neural field. We instead propose a new paradigm that views the large-scale training of neural representations as a part of a partially-observed neural process framework, and leverage neural process algorithms to solve this task. We demonstrate that this approach outperforms both state-of-the-art gradient-based meta-learning approaches and hypernetwork approaches.

The field of artificial intelligence has seen explosive growth and exponential success. The last phase of development showcased deep learnings ability to solve a variety of difficult problems across a multitude of domains. Many of these networks met and exceeded human benchmarks by becoming experts in the domains in which they are trained. Though the successes of artificial intelligence have begun to overshadow its failures, there is still much that separates current artificial intelligence tools from becoming the exceptional general learners that humans are. In this paper, we identify the ten commandments upon which human intelligence is systematically and hierarchically built. We believe these commandments work collectively to serve as the essential ingredients that lead to the emergence of higher-order cognition and intelligence. This paper discusses a computational framework that could house these ten commandments and suggests new architectural modifications that could lead to the development of smarter, more explainable, and generalizable artificial systems inspired by a neuromorphic approach.

One of the roadblocks to a better understanding of neural networks' internals is polysemanticity, where neurons appear to activate in multiple, semantically distinct contexts. Polysemanticity prevents us from identifying concise, human-understandable explanations for what neural networks are doing internally. One hypothesised cause of polysemanticity is superposition, where neural networks represent more features than they have neurons by assigning features to an overcomplete set of directions in activation space, rather than to individual neurons. Here, we attempt to identify those directions, using sparse autoencoders to reconstruct the internal activations of a language model. These autoencoders learn sets of sparsely activating features that are more interpretable and monosemantic than directions identified by alternative approaches, where interpretability is measured by automated methods. Ablating these features enables precise model editing, for example, by removing capabilities such as pronoun prediction, while disrupting model behaviour less than prior techniques. This work indicates that it is possible to resolve superposition in language models using a scalable, unsupervised method. Our method may serve as a foundation for future mechanistic interpretability work, which we hope will enable greater model transparency and steerability.

In this work, we propose a concise neural operator architecture for operator learning. Drawing an analogy with a conventional fully connected neural network, we define the neural operator as follows: the output of the i-th neuron in a nonlinear operator layer is defined by mathcal O_i(u) = sigmaleft( sum_j mathcal W_{ij} u + mathcal B_{ij}right). Here, mathcal W_{ij} denotes the bounded linear operator connecting j-th input neuron to i-th output neuron, and the bias mathcal B_{ij} takes the form of a function rather than a scalar. Given its new universal approximation property, the efficient parameterization of the bounded linear operators between two neurons (Banach spaces) plays a critical role. As a result, we introduce MgNO, utilizing multigrid structures to parameterize these linear operators between neurons. This approach offers both mathematical rigor and practical expressivity. Additionally, MgNO obviates the need for conventional lifting and projecting operators typically required in previous neural operators. Moreover, it seamlessly accommodates diverse boundary conditions. Our empirical observations reveal that MgNO exhibits superior ease of training compared to other CNN-based models, while also displaying a reduced susceptibility to overfitting when contrasted with spectral-type neural operators. We demonstrate the efficiency and accuracy of our method with consistently state-of-the-art performance on different types of partial differential equations (PDEs).

The recent success of large foundation models in artificial intelligence has prompted the emergence of chemical pre-trained models. Despite the growing interest in large molecular pre-trained models that provide informative representations for downstream tasks, attempts for multimodal pre-training approaches on the molecule domain were limited. To address this, we present a novel multimodal molecular pre-trained model that incorporates the modalities of structure and biochemical properties, drawing inspiration from recent advances in multimodal learning techniques. Our proposed model pipeline of data handling and training objectives aligns the structure/property features in a common embedding space, which enables the model to regard bidirectional information between the molecules' structure and properties. These contributions emerge synergistic knowledge, allowing us to tackle both multimodal and unimodal downstream tasks through a single model. Through extensive experiments, we demonstrate that our model shows remarkable capabilities in solving various meaningful chemical challenges, including conditional molecule generation, property prediction, molecule classification, and reaction prediction.

Density functional theory (DFT) stands as a cornerstone method in computational quantum chemistry and materials science due to its remarkable versatility and scalability. Yet, it suffers from limitations in accuracy, particularly when dealing with strongly correlated systems. To address these shortcomings, recent work has begun to explore how machine learning can expand the capabilities of DFT; an endeavor with many open questions and technical challenges. In this work, we present Grad DFT: a fully differentiable JAX-based DFT library, enabling quick prototyping and experimentation with machine learning-enhanced exchange-correlation energy functionals. Grad DFT employs a pioneering parametrization of exchange-correlation functionals constructed using a weighted sum of energy densities, where the weights are determined using neural networks. Moreover, Grad DFT encompasses a comprehensive suite of auxiliary functions, notably featuring a just-in-time compilable and fully differentiable self-consistent iterative procedure. To support training and benchmarking efforts, we additionally compile a curated dataset of experimental dissociation energies of dimers, half of which contain transition metal atoms characterized by strong electronic correlations. The software library is tested against experimental results to study the generalization capabilities of a neural functional across potential energy surfaces and atomic species, as well as the effect of training data noise on the resulting model accuracy.

We present the COGnitive Neural GENerative system (CogNGen), a cognitive architecture that combines two neurobiologically-plausible, computational models: predictive processing and hyperdimensional/vector-symbolic models. We draw inspiration from architectures such as ACT-R and Spaun/Nengo. CogNGen is in broad agreement with these, providing a level of detail between ACT-R's high-level symbolic description of human cognition and Spaun's low-level neurobiological description, furthermore creating the groundwork for designing agents that learn continually from diverse tasks and model human performance at larger scales than what is possible with current systems. We test CogNGen on four maze-learning tasks, including those that test memory and planning, and find that CogNGen matches performance of deep reinforcement learning models and exceeds on a task designed to test memory.

The emerging field of Diverse Intelligence seeks to identify, formalize, and understand commonalities in behavioral competencies across a wide range of implementations. Especially interesting are simple systems that provide unexpected examples of memory, decision-making, or problem-solving in substrates that at first glance do not appear to be complex enough to implement such capabilities. We seek to develop tools to help understand the minimal requirements for such capabilities, and to learn to recognize and predict basal forms of intelligence in unconventional substrates. Here, we apply novel analyses to the behavior of classical sorting algorithms, short pieces of code which have been studied for many decades. To study these sorting algorithms as a model of biological morphogenesis and its competencies, we break two formerly-ubiquitous assumptions: top-down control (instead, showing how each element within a array of numbers can exert minimal agency and implement sorting policies from the bottom up), and fully reliable hardware (instead, allowing some of the elements to be "damaged" and fail to execute the algorithm). We quantitatively characterize sorting activity as the traversal of a problem space, showing that arrays of autonomous elements sort themselves more reliably and robustly than traditional implementations in the presence of errors. Moreover, we find the ability to temporarily reduce progress in order to navigate around a defect, and unexpected clustering behavior among the elements in chimeric arrays whose elements follow one of two different algorithms. The discovery of emergent problem-solving capacities in simple, familiar algorithms contributes a new perspective to the field of Diverse Intelligence, showing how basal forms of intelligence can emerge in simple systems without being explicitly encoded in their underlying mechanics.

With the growing accessibility and wide adoption of large language models, concerns about their safety and alignment with human values have become paramount. In this paper, we identify a concerning phenomenon: Reasoning-Induced Misalignment (RIM), in which misalignment emerges when reasoning capabilities strengthened-particularly when specific types of reasoning patterns are introduced during inference or training. Beyond reporting this vulnerability, we provide the first mechanistic account of its origins. Through representation analysis, we discover that specific attention heads facilitate refusal by reducing their attention to CoT tokens, a mechanism that modulates the model's rationalization process during inference. During training, we find significantly higher activation entanglement between reasoning and safety in safety-critical neurons than in control neurons, particularly after fine-tuning with those identified reasoning patterns. This entanglement strongly correlates with catastrophic forgetting, providing a neuron-level explanation for RIM.

In this work, we present a network-specific approach for predicting brain responses to complex multimodal movies, leveraging the Yeo 7-network parcellation of the Schaefer atlas. Rather than treating the brain as a homogeneous system, we grouped the seven functional networks into four clusters and trained separate multi-subject, multi-layer perceptron (MLP) models for each. This architecture supports cluster-specific optimization and adaptive memory modeling, allowing each model to adjust temporal dynamics and modality weighting based on the functional role of its target network. Our results demonstrate that this clustered strategy significantly enhances prediction accuracy across the 1,000 cortical regions of the Schaefer atlas. The final model achieved an eighth-place ranking in the Algonauts Project 2025 Challenge, with out-of-distribution (OOD) correlation scores nearly double those of the baseline model used in the selection phase. Code is available at https://github.com/Corsi01/algo2025.

Availability of large and diverse medical datasets is often challenged by privacy and data sharing restrictions. For successful application of machine learning techniques for disease diagnosis, prognosis, and precision medicine, large amounts of data are necessary for model building and optimization. To help overcome such limitations in the context of brain MRI, we present NeuroSynth: a collection of generative models of normative regional volumetric features derived from structural brain imaging. NeuroSynth models are trained on real brain imaging regional volumetric measures from the iSTAGING consortium, which encompasses over 40,000 MRI scans across 13 studies, incorporating covariates such as age, sex, and race. Leveraging NeuroSynth, we produce and offer 18,000 synthetic samples spanning the adult lifespan (ages 22-90 years), alongside the model's capability to generate unlimited data. Experimental results indicate that samples generated from NeuroSynth agree with the distributions obtained from real data. Most importantly, the generated normative data significantly enhance the accuracy of downstream machine learning models on tasks such as disease classification. Data and models are available at: https://huggingface.co/spaces/rongguangw/neuro-synth.

The discovery of novel materials and functional molecules can help to solve some of society's most urgent challenges, ranging from efficient energy harvesting and storage to uncovering novel pharmaceutical drug candidates. Traditionally matter engineering -- generally denoted as inverse design -- was based massively on human intuition and high-throughput virtual screening. The last few years have seen the emergence of significant interest in computer-inspired designs based on evolutionary or deep learning methods. The major challenge here is that the standard strings molecular representation SMILES shows substantial weaknesses in that task because large fractions of strings do not correspond to valid molecules. Here, we solve this problem at a fundamental level and introduce SELFIES (SELF-referencIng Embedded Strings), a string-based representation of molecules which is 100\% robust. Every SELFIES string corresponds to a valid molecule, and SELFIES can represent every molecule. SELFIES can be directly applied in arbitrary machine learning models without the adaptation of the models; each of the generated molecule candidates is valid. In our experiments, the model's internal memory stores two orders of magnitude more diverse molecules than a similar test with SMILES. Furthermore, as all molecules are valid, it allows for explanation and interpretation of the internal working of the generative models.

Understanding the functional organization of higher visual cortex is a central focus in neuroscience. Past studies have primarily mapped the visual and semantic selectivity of neural populations using hand-selected stimuli, which may potentially bias results towards pre-existing hypotheses of visual cortex functionality. Moving beyond conventional approaches, we introduce a data-driven method that generates natural language descriptions for images predicted to maximally activate individual voxels of interest. Our method -- Semantic Captioning Using Brain Alignments ("BrainSCUBA") -- builds upon the rich embedding space learned by a contrastive vision-language model and utilizes a pre-trained large language model to generate interpretable captions. We validate our method through fine-grained voxel-level captioning across higher-order visual regions. We further perform text-conditioned image synthesis with the captions, and show that our images are semantically coherent and yield high predicted activations. Finally, to demonstrate how our method enables scientific discovery, we perform exploratory investigations on the distribution of "person" representations in the brain, and discover fine-grained semantic selectivity in body-selective areas. Unlike earlier studies that decode text, our method derives voxel-wise captions of semantic selectivity. Our results show that BrainSCUBA is a promising means for understanding functional preferences in the brain, and provides motivation for further hypothesis-driven investigation of visual cortex.

Neural Architecture Search (NAS) algorithms automate the task of finding optimal deep learning architectures given an initial search space of possible operations. Developing these search spaces is usually a manual affair with pre-optimized search spaces being more efficient, rather than searching from scratch. In this paper we present a new framework called Neural Architecture Type System (NeuralArTS) that categorizes the infinite set of network operations in a structured type system. We further demonstrate how NeuralArTS can be applied to convolutional layers and propose several future directions.

Recent success in training deep neural networks have prompted active investigation into the features learned on their intermediate layers. Such research is difficult because it requires making sense of non-linear computations performed by millions of parameters, but valuable because it increases our ability to understand current models and create improved versions of them. In this paper we investigate the extent to which neural networks exhibit what we call convergent learning, which is when the representations learned by multiple nets converge to a set of features which are either individually similar between networks or where subsets of features span similar low-dimensional spaces. We propose a specific method of probing representations: training multiple networks and then comparing and contrasting their individual, learned representations at the level of neurons or groups of neurons. We begin research into this question using three techniques to approximately align different neural networks on a feature level: a bipartite matching approach that makes one-to-one assignments between neurons, a sparse prediction approach that finds one-to-many mappings, and a spectral clustering approach that finds many-to-many mappings. This initial investigation reveals a few previously unknown properties of neural networks, and we argue that future research into the question of convergent learning will yield many more. The insights described here include (1) that some features are learned reliably in multiple networks, yet other features are not consistently learned; (2) that units learn to span low-dimensional subspaces and, while these subspaces are common to multiple networks, the specific basis vectors learned are not; (3) that the representation codes show evidence of being a mix between a local code and slightly, but not fully, distributed codes across multiple units.

Strong correlation brings a rich array of emergent phenomena, as well as a daunting challenge to theoretical physics study. In condensed matter physics, the fractional quantum Hall effect is a prominent example of strong correlation, with Landau level mixing being one of the most challenging aspects to address using traditional computational methods. Deep learning real-space neural network wavefunction methods have emerged as promising architectures to describe electron correlations in molecules and materials, but their power has not been fully tested for exotic quantum states. In this work, we employ real-space neural network wavefunction techniques to investigate fractional quantum Hall systems. On both 1/3 and 2/5 filling systems, we achieve energies consistently lower than exact diagonalization results which only consider the lowest Landau level. We also demonstrate that the real-space neural network wavefunction can naturally capture the extent of Landau level mixing up to a very high level, overcoming the limitations of traditional methods. Our work underscores the potential of neural networks for future studies of strongly correlated systems and opens new avenues for exploring the rich physics of the fractional quantum Hall effect.

Scaling has been critical in improving model performance and generalization in machine learning. It involves how a model's performance changes with increases in model size or input data, as well as how efficiently computational resources are utilized to support this growth. Despite successes in other areas, the study of scaling in Neural Network Interatomic Potentials (NNIPs) remains limited. NNIPs act as surrogate models for ab initio quantum mechanical calculations. The dominant paradigm here is to incorporate many physical domain constraints into the model, such as rotational equivariance. We contend that these complex constraints inhibit the scaling ability of NNIPs, and are likely to lead to performance plateaus in the long run. In this work, we take an alternative approach and start by systematically studying NNIP scaling strategies. Our findings indicate that scaling the model through attention mechanisms is efficient and improves model expressivity. These insights motivate us to develop an NNIP architecture designed for scalability: the Efficiently Scaled Attention Interatomic Potential (EScAIP). EScAIP leverages a multi-head self-attention formulation within graph neural networks, applying attention at the neighbor-level representations. Implemented with highly-optimized attention GPU kernels, EScAIP achieves substantial gains in efficiency--at least 10x faster inference, 5x less memory usage--compared to existing NNIPs. EScAIP also achieves state-of-the-art performance on a wide range of datasets including catalysts (OC20 and OC22), molecules (SPICE), and materials (MPTrj). We emphasize that our approach should be thought of as a philosophy rather than a specific model, representing a proof-of-concept for developing general-purpose NNIPs that achieve better expressivity through scaling, and continue to scale efficiently with increased computational resources and training data.

Neural Module Networks, originally proposed for the task of visual question answering, are a class of neural network architectures that involve human-specified neural modules, each designed for a specific form of reasoning. In current formulations of such networks only the parameters of the neural modules and/or the order of their execution is learned. In this work, we further expand this approach and also learn the underlying internal structure of modules in terms of the ordering and combination of simple and elementary arithmetic operators. Our results show that one is indeed able to simultaneously learn both internal module structure and module sequencing without extra supervisory signals for module execution sequencing. With this approach, we report performance comparable to models using hand-designed modules.

We consider dense, associative neural-networks trained by a teacher (i.e., with supervision) and we investigate their computational capabilities analytically, via statistical-mechanics of spin glasses, and numerically, via Monte Carlo simulations. In particular, we obtain a phase diagram summarizing their performance as a function of the control parameters such as quality and quantity of the training dataset, network storage and noise, that is valid in the limit of large network size and structureless datasets: these networks may work in a ultra-storage regime (where they can handle a huge amount of patterns, if compared with shallow neural networks) or in a ultra-detection regime (where they can perform pattern recognition at prohibitive signal-to-noise ratios, if compared with shallow neural networks). Guided by the random theory as a reference framework, we also test numerically learning, storing and retrieval capabilities shown by these networks on structured datasets as MNist and Fashion MNist. As technical remarks, from the analytic side, we implement large deviations and stability analysis within Guerra's interpolation to tackle the not-Gaussian distributions involved in the post-synaptic potentials while, from the computational counterpart, we insert Plefka approximation in the Monte Carlo scheme, to speed up the evaluation of the synaptic tensors, overall obtaining a novel and broad approach to investigate supervised learning in neural networks, beyond the shallow limit, in general.

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.

We aim to understand grokking, a phenomenon where models generalize long after overfitting their training set. We present both a microscopic analysis anchored by an effective theory and a macroscopic analysis of phase diagrams describing learning performance across hyperparameters. We find that generalization originates from structured representations whose training dynamics and dependence on training set size can be predicted by our effective theory in a toy setting. We observe empirically the presence of four learning phases: comprehension, grokking, memorization, and confusion. We find representation learning to occur only in a "Goldilocks zone" (including comprehension and grokking) between memorization and confusion. We find on transformers the grokking phase stays closer to the memorization phase (compared to the comprehension phase), leading to delayed generalization. The Goldilocks phase is reminiscent of "intelligence from starvation" in Darwinian evolution, where resource limitations drive discovery of more efficient solutions. This study not only provides intuitive explanations of the origin of grokking, but also highlights the usefulness of physics-inspired tools, e.g., effective theories and phase diagrams, for understanding deep learning.

We present a novel type of neural fields that uses general radial bases for signal representation. State-of-the-art neural fields typically rely on grid-based representations for storing local neural features and N-dimensional linear kernels for interpolating features at continuous query points. The spatial positions of their neural features are fixed on grid nodes and cannot well adapt to target signals. Our method instead builds upon general radial bases with flexible kernel position and shape, which have higher spatial adaptivity and can more closely fit target signals. To further improve the channel-wise capacity of radial basis functions, we propose to compose them with multi-frequency sinusoid functions. This technique extends a radial basis to multiple Fourier radial bases of different frequency bands without requiring extra parameters, facilitating the representation of details. Moreover, by marrying adaptive radial bases with grid-based ones, our hybrid combination inherits both adaptivity and interpolation smoothness. We carefully designed weighting schemes to let radial bases adapt to different types of signals effectively. Our experiments on 2D image and 3D signed distance field representation demonstrate the higher accuracy and compactness of our method than prior arts. When applied to neural radiance field reconstruction, our method achieves state-of-the-art rendering quality, with small model size and comparable training speed.

Representational analysis explores how input data of a neural system are encoded in high dimensional spaces of its distributed neural activations, and how we can compare different systems, for instance, artificial neural networks and brains, on those grounds. While existing methods offer important insights, they typically do not account for local intrinsic geometrical properties within the high-dimensional representation spaces. To go beyond these limitations, we explore Ollivier-Ricci curvature and Ricci flow as tools to study the alignment of representations between humans and artificial neural systems on a geometric level. As a proof-of-principle study, we compared the representations of face stimuli between VGG-Face, a human-aligned version of VGG-Face, and corresponding human similarity judgments from a large online study. Using this discrete geometric framework, we were able to identify local structural similarities and differences by examining the distributions of node and edge curvature and higher-level properties by detecting and comparing community structure in the representational graphs.

In this work, we generalize the reaction-diffusion equation in statistical physics, Schr\"odinger equation in quantum mechanics, Helmholtz equation in paraxial optics into the neural partial differential equations (NPDE), which can be considered as the fundamental equations in the field of artificial intelligence research. We take finite difference method to discretize NPDE for finding numerical solution, and the basic building blocks of deep neural network architecture, including multi-layer perceptron, convolutional neural network and recurrent neural networks, are generated. The learning strategies, such as Adaptive moment estimation, L-BFGS, pseudoinverse learning algorithms and partial differential equation constrained optimization, are also presented. We believe it is of significance that presented clear physical image of interpretable deep neural networks, which makes it be possible for applying to analog computing device design, and pave the road to physical artificial intelligence.

We investigate the emergence of intuitive physics understanding in general-purpose deep neural network models trained to predict masked regions in natural videos. Leveraging the violation-of-expectation framework, we find that video prediction models trained to predict outcomes in a learned representation space demonstrate an understanding of various intuitive physics properties, such as object permanence and shape consistency. In contrast, video prediction in pixel space and multimodal large language models, which reason through text, achieve performance closer to chance. Our comparisons of these architectures reveal that jointly learning an abstract representation space while predicting missing parts of sensory input, akin to predictive coding, is sufficient to acquire an understanding of intuitive physics, and that even models trained on one week of unique video achieve above chance performance. This challenges the idea that core knowledge -- a set of innate systems to help understand the world -- needs to be hardwired to develop an understanding of intuitive physics.

We introduce NeuroSA, a neuromorphic architecture specifically designed to ensure asymptotic convergence to the ground state of an Ising problem using an annealing process that is governed by the physics of quantum mechanical tunneling using Fowler-Nordheim (FN). The core component of NeuroSA consists of a pair of asynchronous ON-OFF neurons, which effectively map classical simulated annealing (SA) dynamics onto a network of integrate-and-fire (IF) neurons. The threshold of each ON-OFF neuron pair is adaptively adjusted by an FN annealer which replicates the optimal escape mechanism and convergence of SA, particularly at low temperatures. To validate the effectiveness of our neuromorphic Ising machine, we systematically solved various benchmark MAX-CUT combinatorial optimization problems. Across multiple runs, NeuroSA consistently generates solutions that approach the state-of-the-art level with high accuracy (greater than 99%), and without any graph-specific hyperparameter tuning. For practical illustration, we present results from an implementation of NeuroSA on the SpiNNaker2 platform, highlighting the feasibility of mapping our proposed architecture onto a standard neuromorphic accelerator platform.

As artificial intelligence models have exploded in scale and capability, understanding of their internal mechanisms remains a critical challenge. Inspired by the success of dynamical systems approaches in neuroscience, here we propose a novel framework for studying computations in deep learning systems. We focus on the residual stream (RS) in transformer models, conceptualizing it as a dynamical system evolving across layers. We find that activations of individual RS units exhibit strong continuity across layers, despite the RS being a non-privileged basis. Activations in the RS accelerate and grow denser over layers, while individual units trace unstable periodic orbits. In reduced-dimensional spaces, the RS follows a curved trajectory with attractor-like dynamics in the lower layers. These insights bridge dynamical systems theory and mechanistic interpretability, establishing a foundation for a "neuroscience of AI" that combines theoretical rigor with large-scale data analysis to advance our understanding of modern neural networks.

Artificial neural networks are being proposed as models of parts of the brain. The networks are compared to recordings of biological neurons, and good performance in reproducing neural responses is considered to support the model's validity. A key question is how much this system identification approach tells us about brain computation. Does it validate one model architecture over another? We evaluate the most commonly used comparison techniques, such as a linear encoding model and centered kernel alignment, to correctly identify a model by replacing brain recordings with known ground truth models. System identification performance is quite variable; it also depends significantly on factors independent of the ground truth architecture, such as stimuli images. In addition, we show the limitations of using functional similarity scores in identifying higher-level architectural motifs.

Reservoir computers (RCs) provide a computationally efficient alternative to deep learning while also offering a framework for incorporating brain-inspired computational principles. By using an internal neural network with random, fixed connections-the 'reservoir'-and training only the output weights, RCs simplify the training process but remain sensitive to the choice of hyperparameters that govern activation functions and network architecture. Moreover, typical RC implementations overlook a critical aspect of neuronal dynamics: the balance between excitatory and inhibitory (E-I) signals, which is essential for robust brain function. We show that RCs characteristically perform best in balanced or slightly over-inhibited regimes, outperforming excitation-dominated ones. To reduce the need for precise hyperparameter tuning, we introduce a self-adapting mechanism that locally adjusts E/I balance to achieve target neuronal firing rates, improving performance by up to 130% in tasks like memory capacity and time series prediction compared with globally tuned RCs. Incorporating brain-inspired heterogeneity in target neuronal firing rates further reduces the need for fine-tuning hyperparameters and enables RCs to excel across linear and non-linear tasks. These results support a shift from static optimization to dynamic adaptation in reservoir design, demonstrating how brain-inspired mechanisms improve RC performance and robustness while deepening our understanding of neural computation.

Recently, pre-trained foundation models have enabled significant advancements in multiple fields. In molecular machine learning, however, where datasets are often hand-curated, and hence typically small, the lack of datasets with labeled features, and codebases to manage those datasets, has hindered the development of foundation models. In this work, we present seven novel datasets categorized by size into three distinct categories: ToyMix, LargeMix and UltraLarge. These datasets push the boundaries in both the scale and the diversity of supervised labels for molecular learning. They cover nearly 100 million molecules and over 3000 sparsely defined tasks, totaling more than 13 billion individual labels of both quantum and biological nature. In comparison, our datasets contain 300 times more data points than the widely used OGB-LSC PCQM4Mv2 dataset, and 13 times more than the quantum-only QM1B dataset. In addition, to support the development of foundational models based on our proposed datasets, we present the Graphium graph machine learning library which simplifies the process of building and training molecular machine learning models for multi-task and multi-level molecular datasets. Finally, we present a range of baseline results as a starting point of multi-task and multi-level training on these datasets. Empirically, we observe that performance on low-resource biological datasets show improvement by also training on large amounts of quantum data. This indicates that there may be potential in multi-task and multi-level training of a foundation model and fine-tuning it to resource-constrained downstream tasks.

Instruction tuning improves the ability of large language models (LLMs) to follow diverse human instructions, but achieving strong performance on specific target tasks remains challenging. A critical bottleneck is selecting the most relevant data to maximize task-specific performance. Existing data selection approaches include unstable influence-based methods and more stable distribution alignment methods, the latter of which critically rely on the underlying sample representation. In practice, most distribution alignment methods, from shallow features (e.g., BM25) to neural embeddings (e.g., BGE, LLM2Vec), may fail to capture how the model internally processes samples. To bridge this gap, we adopt a model-centric strategy in which each sample is represented by its neuronal activation pattern in the model, directly reflecting internal computation. However, directly using raw neuron activations leads to spurious similarity between unrelated samples due to neuron polysemanticity, where a single neuron may respond to multiple, unrelated concepts. To address this, we employ sparse autoencoders to disentangle polysemantic activations into sparse, monosemantic representations, and introduce a dedicated similarity metric for this space to better identify task-relevant data. Comprehensive experiments across multiple instruction datasets, models, tasks, and selection ratios show that our approach consistently outperforms existing data selection baselines in both stability and task-specific performance.

Although data diffusion embeddings are ubiquitous in unsupervised learning and have proven to be a viable technique for uncovering the underlying intrinsic geometry of data, diffusion embeddings are inherently limited due to their discrete nature. To this end, we propose neural FIM, a method for computing the Fisher information metric (FIM) from point cloud data - allowing for a continuous manifold model for the data. Neural FIM creates an extensible metric space from discrete point cloud data such that information from the metric can inform us of manifold characteristics such as volume and geodesics. We demonstrate Neural FIM's utility in selecting parameters for the PHATE visualization method as well as its ability to obtain information pertaining to local volume illuminating branching points and cluster centers embeddings of a toy dataset and two single-cell datasets of IPSC reprogramming and PBMCs (immune cells).

We consider dense, associative neural-networks trained with no supervision and we investigate their computational capabilities analytically, via a statistical-mechanics approach, and numerically, via Monte Carlo simulations. In particular, we obtain a phase diagram summarizing their performance as a function of the control parameters such as the quality and quantity of the training dataset and the network storage, valid in the limit of large network size and structureless datasets. Moreover, we establish a bridge between macroscopic observables standardly used in statistical mechanics and loss functions typically used in the machine learning. As technical remarks, from the analytic side, we implement large deviations and stability analysis within Guerra's interpolation to tackle the not-Gaussian distributions involved in the post-synaptic potentials while, from the computational counterpart, we insert Plefka approximation in the Monte Carlo scheme, to speed up the evaluation of the synaptic tensors, overall obtaining a novel and broad approach to investigate neural networks in general.

As Large Language Models (LLMs) continue to advance, they exhibit certain cognitive patterns similar to those of humans that are not directly specified in training data. This study investigates this phenomenon by focusing on temporal cognition in LLMs. Leveraging the similarity judgment task, we find that larger models spontaneously establish a subjective temporal reference point and adhere to the Weber-Fechner law, whereby the perceived distance logarithmically compresses as years recede from this reference point. To uncover the mechanisms behind this behavior, we conducted multiple analyses across neuronal, representational, and informational levels. We first identify a set of temporal-preferential neurons and find that this group exhibits minimal activation at the subjective reference point and implements a logarithmic coding scheme convergently found in biological systems. Probing representations of years reveals a hierarchical construction process, where years evolve from basic numerical values in shallow layers to abstract temporal orientation in deep layers. Finally, using pre-trained embedding models, we found that the training corpus itself possesses an inherent, non-linear temporal structure, which provides the raw material for the model's internal construction. In discussion, we propose an experientialist perspective for understanding these findings, where the LLMs' cognition is viewed as a subjective construction of the external world by its internal representational system. This nuanced perspective implies the potential emergence of alien cognitive frameworks that humans cannot intuitively predict, pointing toward a direction for AI alignment that focuses on guiding internal constructions. Our code is available at https://TheOtherMind.github.io.

Interpreting individual neurons or directions in activations space is an important component of mechanistic interpretability. As such, many algorithms have been proposed to automatically produce neuron explanations, but it is often not clear how reliable these explanations are, or which methods produce the best explanations. This can be measured via crowd-sourced evaluations, but they can often be noisy and expensive, leading to unreliable results. In this paper, we carefully analyze the evaluation pipeline and develop a cost-effective and highly accurate crowdsourced evaluation strategy. In contrast to previous human studies that only rate whether the explanation matches the most highly activating inputs, we estimate whether the explanation describes neuron activations across all inputs. To estimate this effectively, we introduce a novel application of importance sampling to determine which inputs are the most valuable to show to raters, leading to around 30x cost reduction compared to uniform sampling. We also analyze the label noise present in crowd-sourced evaluations and propose a Bayesian method to aggregate multiple ratings leading to a further ~5x reduction in number of ratings required for the same accuracy. Finally, we use these methods to conduct a large-scale study comparing the quality of neuron explanations produced by the most popular methods for two different vision models.

Interpretability researchers have attempted to understand MLP neurons of language models based on both the contexts in which they activate and their output weight vectors. They have paid little attention to a complementary aspect: the interactions between input and output. For example, when neurons detect a direction in the input, they might add much the same direction to the residual stream ("enrichment neurons") or reduce its presence ("depletion neurons"). We address this aspect by examining the cosine similarity between input and output weights of a neuron. We apply our method to 12 models and find that enrichment neurons dominate in early-middle layers whereas later layers tend more towards depletion. To explain this finding, we argue that enrichment neurons are largely responsible for enriching concept representations, one of the first steps of factual recall. Our input-output perspective is a complement to activation-dependent analyses and to approaches that treat input and output separately.

The precise timing of spikes emitted by neurons plays a crucial role in shaping the response of efferent biological neurons. This temporal dimension of neural activity holds significant importance in understanding information processing in neurobiology, especially for the performance of neuromorphic hardware, such as event-based cameras. Nonetheless, many artificial neural models disregard this critical temporal dimension of neural activity. In this study, we present a model designed to efficiently detect temporal spiking motifs using a layer of spiking neurons equipped with heterogeneous synaptic delays. Our model capitalizes on the diverse synaptic delays present on the dendritic tree, enabling specific arrangements of temporally precise synaptic inputs to synchronize upon reaching the basal dendritic tree. We formalize this process as a time-invariant logistic regression, which can be trained using labeled data. To demonstrate its practical efficacy, we apply the model to naturalistic videos transformed into event streams, simulating the output of the biological retina or event-based cameras. To evaluate the robustness of the model in detecting visual motion, we conduct experiments by selectively pruning weights and demonstrate that the model remains efficient even under significantly reduced workloads. In conclusion, by providing a comprehensive, event-driven computational building block, the incorporation of heterogeneous delays has the potential to greatly improve the performance of future spiking neural network algorithms, particularly in the context of neuromorphic chips.

Artificial Intelligence (AI), with its multiplier effect and wide applications in multiple areas, could potentially be an important application of quantum computing. Since modern AI systems are often built on neural networks, the design of quantum neural networks becomes a key challenge in integrating quantum computing into AI. To provide a more fine-grained characterisation of the impact of quantum components on the performance of neural networks, we propose a framework where classical neural network layers are gradually replaced by quantum layers that have the same type of input and output while keeping the flow of information between layers unchanged, different from most current research in quantum neural network, which favours an end-to-end quantum model. We start with a simple three-layer classical neural network without any normalisation layers or activation functions, and gradually change the classical layers to the corresponding quantum versions. We conduct numerical experiments on image classification datasets such as the MNIST, FashionMNIST and CIFAR-10 datasets to demonstrate the change of performance brought by the systematic introduction of quantum components. Through this framework, our research sheds new light on the design of future quantum neural network models where it could be more favourable to search for methods and frameworks that harness the advantages from both the classical and quantum worlds.

Incorporation of machine learning (ML) techniques into atomic-scale modeling has proven to be an extremely effective strategy to improve the accuracy and reduce the computational cost of simulations. It also entails conceptual and practical challenges, as it involves combining very different mathematical foundations, as well as software ecosystems that are very well developed in their own merit, but do not share many commonalities. To address these issues and facilitate the adoption of ML in atomistic simulations, we introduce two dedicated software libraries. The first one, metatensor, provides multi-platform and multi-language storage and manipulation of arrays with many potentially sparse indices, designed from the ground up for atomistic ML applications. By combining the actual values with metadata that describes their nature and that facilitates the handling of geometric information and gradients with respect to the atomic positions, metatensor provides a common framework to enable data sharing between ML software -- typically written in Python -- and established atomistic modeling tools -- typically written in Fortran, C or C++. The second library, metatomic, provides an interface to store an atomistic ML model and metadata about this model in a portable way, facilitating the implementation, training and distribution of models, and their use across different simulation packages. We showcase a growing ecosystem of tools, from low-level libraries, training utilities, to interfaces with existing software packages that demonstrate the effectiveness of metatensor and metatomic in bridging the gap between traditional simulation software and modern ML frameworks.

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.

The integration of deep learning and neuroscience has been advancing rapidly, which has led to improvements in the analysis of brain activity and the understanding of deep learning models from a neuroscientific perspective. The reconstruction of visual experience from human brain activity is an area that has particularly benefited: the use of deep learning models trained on large amounts of natural images has greatly improved its quality, and approaches that combine the diverse information contained in visual experiences have proliferated rapidly in recent years. In this technical paper, by taking advantage of the simple and generic framework that we proposed (Takagi and Nishimoto, CVPR 2023), we examine the extent to which various additional decoding techniques affect the performance of visual experience reconstruction. Specifically, we combined our earlier work with the following three techniques: using decoded text from brain activity, nonlinear optimization for structural image reconstruction, and using decoded depth information from brain activity. We confirmed that these techniques contributed to improving accuracy over the baseline. We also discuss what researchers should consider when performing visual reconstruction using deep generative models trained on large datasets. Please check our webpage at https://sites.google.com/view/stablediffusion-with-brain/. Code is also available at https://github.com/yu-takagi/StableDiffusionReconstruction.

Critical learning periods are periods early in development where temporary sensory deficits can have a permanent effect on behavior and learned representations. Despite the radical differences between biological and artificial networks, critical learning periods have been empirically observed in both systems. This suggests that critical periods may be fundamental to learning and not an accident of biology. Yet, why exactly critical periods emerge in deep networks is still an open question, and in particular it is unclear whether the critical periods observed in both systems depend on particular architectural or optimization details. To isolate the key underlying factors, we focus on deep linear network models, and show that, surprisingly, such networks also display much of the behavior seen in biology and artificial networks, while being amenable to analytical treatment. We show that critical periods depend on the depth of the model and structure of the data distribution. We also show analytically and in simulations that the learning of features is tied to competition between sources. Finally, we extend our analysis to multi-task learning to show that pre-training on certain tasks can damage the transfer performance on new tasks, and show how this depends on the relationship between tasks and the duration of the pre-training stage. To the best of our knowledge, our work provides the first analytically tractable model that sheds light into why critical learning periods emerge in biological and artificial networks.