ICLR 2025 Papers

Functional magnetic resonance imaging (fMRI) is essential for mapping brain activity but faces challenges like lengthy acquisition time and sensitivity to patient movement, limiting its clinical and machine learning applications. While generative models such as diffusion models can synthesize fMRI signals to alleviate these issues, they often underperform due to neglecting the brain's complex structural and dynamic properties. To address these limitations, we propose the Physiological Dynamics-Driven Hierarchical Diffusion Model, a novel framework integrating two key brain physiological properties into the diffusion process: brain hierarchical regional interactions and multifractal dynamics. To model complex interactions among brain regions, we construct hypergraphs based on the prior knowledge of brain functional parcellation reflected by resting-state functional connectivity (rsFC). This enables the aggregation of fMRI signals across multiple scales and generates hierarchical signals. Additionally, by incorporating the prediction of two key dynamics properties of fMRI—the multifractal spectrum and generalized Hurst exponent—our framework effectively guides the diffusion process, ensuring the preservation of the scale-invariant characteristics inherent in real fMRI data. Our framework employs progressive diffusion generation, with signals representing broader brain region information conditioning those that capture localized details, and unifies multiple inputs during denoising for balanced integration. Experiments demonstrate that our model generates physiologically realistic fMRI signals, potentially reducing acquisition time and enhancing data quality, benefiting clinical diagnostics and machine learning in neuroscience.

Understanding the relationship between behavior and neural activity is crucial for understanding brain function. An effective method is to learn embeddings for interconnected modalities. For simple behavioral tasks, neural features can be learned based on labels. However, complex behaviors, such as social interactions, require the joint extraction of behavioral and neural characteristics. In this paper, we present an autoencoder (AE) framework, called Shared-AE, which includes a novel regularization term that automatically identifies features shared between neural activity and behavior, while simultaneously capturing the unique private features specific to each modality. We apply Shared-AE to large-scale neural activity recorded across the entire dorsal cortex of the mouse, during two very different behaviors: (i) head-fixed mice performing a self-initiated decision-making task, and (ii) freely-moving social behavior amongst two mice. Our model successfully captures both `shared features', shared across neural and behavioral activity, and `private features', unique to each modality, significantly enhancing our understanding of the alignment between neural activity and complex behaviors. The original code for the entire Shared-AE framework on Pytorch has been made publicly available at: \url{https://github.com/saxenalab-neuro/Shared-AE}.

Molecular docking is a key task in computational biology that has attracted increasing interest from the machine learning community. While existing methods have achieved success, they generally treat each protein-ligand pair in isolation. Inspired by the biochemical observation that ligands binding to the same target protein tend to adopt similar poses, we propose \textsc{GroupBind}, a novel molecular docking framework that simultaneously considers multiple ligands docking to a protein. This is achieved by introducing an interaction layer for the group of ligands and a triangle attention module for embedding protein-ligand and group-ligand pairs. By integrating our approach with diffusion based docking model, we set a new state-of-the-art performance on the PDBBind blind docking benchmark, demonstrating the effectiveness of our paradigm in enhancing molecular docking accuracy.

Kolmogorov-Arnold Networks (KAN) \cite{liu2024kan} were very recently proposed as a potential alternative to the prevalent architectural backbone of many deep learning models, the multi-layer perceptron (MLP). KANs have seen success in various tasks of AI for science, with their empirical efficiency and accuracy demonstrated in function regression, PDE solving, and many more scientific problems. In this article, we revisit the comparison of KANs and MLPs, with emphasis on a theoretical perspective. On the one hand, we compare the representation and approximation capabilities of KANs and MLPs. We establish that MLPs can be represented using KANs of a comparable size. This shows that the approximation and representation capabilities of KANs are at least as good as MLPs. Conversely, we show that KANs can be represented using MLPs, but that in this representation the number of parameters increases by a factor of the KAN grid size. This suggests that KANs with a large grid size may be more efficient than MLPs at approximating certain functions. On the other hand, from the perspective of learning and optimization, we study the spectral bias of KANs compared with MLPs. We demonstrate that KANs are less biased toward low frequencies than MLPs. We highlight that the multi-level learning feature specific to KANs, i.e. grid extension of splines, improves the learning process for high-frequency components. Detailed comparisons with different choices of depth, width, and grid sizes of KANs are made, shedding some light on how to choose the hyperparameters in practice.

Intelligent perception and interaction with the world hinges on internal representations that capture its underlying structure ("disentangled" or "abstract" representations). Disentangled representations serve as world models, isolating latent factors of variation in the world along approximately orthogonal directions, thus facilitating feature-based generalization. We provide experimental and theoretical results guaranteeing the emergence of disentangled representations in agents that optimally solve multi-task evidence accumulation classification tasks, canonical in the neuroscience literature. The key conceptual finding is that, by producing accurate multi-task classification estimates, a system implicitly represents a set of coordinates specifying a disentangled representation of the underlying latent state of the data it receives. The theory provides conditions for the emergence of these representations in terms of noise, number of tasks, and evidence accumulation time, when the classification boundaries are affine in the latent space. Surprisingly, the theory also produces closed-form expressions for extracting the disentangled representation from the model's latent state $\mathbf Z(t)$. We experimentally validate these predictions in RNNs trained on multi-task classification, which learn disentangled representations in the form of continuous attractors, leading to zero-shot out-of-distribution (OOD) generalization in predicting latent factors. We demonstrate the robustness of our framework across autoregressive architectures, decision boundary geometries and in tasks requiring classification confidence estimation. We find that transformers are particularly suited for disentangling representations, which might explain their unique world understanding abilities. Overall, our framework establishes a formal link between competence at multiple tasks and the formation of disentangled, interpretable world models in both biological and artificial systems, and helps explain why ANNs often arrive at human-interpretable concepts, and how they both may acquire exceptional zero-shot generalization capabilities.

A fundamental part of human cognition is the ability to not only recall previous memories, but also reason across them to draw conclusions. In cognitive science and psychology, this is termed relational reasoning and a number of effects and biases have been observed in human cognition. Designing experiments to measure these reasoning effects is effortful and does not transfer easily to analyzing language model reasoning patterns. To make exploring language models on relational reasoning easier, we introduce ReCogLab – a generative framework for constructing reasoning examples. Unlike static datasets, our framework has a number of benefits that help us in our goal of flexible evaluation of LLMs. First, our framework allows us to control the difficulty and context-length of the problem, allowing us to scale with model capability and evaluate LLMs at a variety of scales. Second, the ability to change the configuration of a dataset dynamically allows us to probe models on different aspects and capabilities. Finally, the flexibility of our approach enables the recreation of classic cognitive science experiments and the systematic study of relational reasoning biases in language models. We demonstrate several such experiments and present our findings on a wide variety of open and closed-source language models. We release all data and code at https://github.com/google-deepmind/recoglab.

We introduce BrainSAIL (Semantic Attribution and Image Localization), a method for linking neural selectivity with spatially distributed semantic visual concepts in natural scenes. BrainSAIL leverages recent advances in large-scale artificial neural networks, using them to provide insights into the functional topology of the brain. To overcome the challenge presented by the co-occurrence of multiple categories in natural images, BrainSAIL exploits semantically consistent, dense spatial features from pre-trained vision models, building upon their demonstrated ability to robustly predict neural activity. This method derives clean, spatially dense embeddings without requiring any additional training, and employs a novel denoising process that leverages the semantic consistency of images under random augmentations. By unifying the space of whole-image embeddings and dense visual features and then applying voxel-wise encoding models to these features, we enable the identification of specific subregions of each image which drive selectivity patterns in different areas of the higher visual cortex. This provides a powerful tool for dissecting the neural mechanisms that underlie semantic visual processing for natural images. We validate BrainSAIL on cortical regions with known category selectivity, demonstrating its ability to accurately localize and disentangle selectivity to diverse visual concepts. Next, we demonstrate BrainSAIL's ability to characterize high-level visual selectivity to scene properties and low-level visual features such as depth, luminance, and saturation, providing insights into the encoding of complex visual information. Finally, we use BrainSAIL to directly compare the feature selectivity of different brain encoding models across different regions of interest in visual cortex. Our innovative method paves the way for significant advances in mapping and decomposing high-level visual representations in the human brain.

In subsurface imaging, learning the mapping from velocity maps to seismic waveforms (forward problem) and waveforms to velocity (inverse problem) is important for several applications. While traditional techniques for solving forward and inverse problems are computationally prohibitive, there is a growing interest to leverage recent advances in deep learning to learn the mapping between velocity maps and seismic waveform images directly from data. Despite the variety of architectures explored in previous works, several open questions still remain unanswered such as the effect of latent space sizes, the importance of manifold learning, the complexity of translation models, and the value of jointly solving forward and inverse problems. We propose a unified framework to systematically characterize prior research in this area termed the Generalized Forward-Inverse (GFI) framework, building on the assumption of manifolds and latent space translations. We show that GFI encompasses previous works in deep learning for subsurface imaging, which can be viewed as specific instantiations of GFI. We also propose two new model architectures within the framework of GFI: Latent U-Net and Invertible X-Net, leveraging the power of U-Nets for domain translation and the ability of IU-Nets to simultaneously learn forward and inverse translations, respectively. We show that our proposed models achieve state-of-the-art (SOTA) performance for forward and inverse problems on a wide range of synthetic datasets, and also investigate their zero-shot effectiveness on two real-world-like datasets. The code is available at https://github.com/KGML-lab/Generalized-Forward-Inverse-Framework-for-DL4SI

A wide range of LM applications require generating text that conforms to syntactic or semantic constraints. Imposing such constraints can be naturally framed as _probabilistic conditioning_, but exact generation from the resulting distribution—which can differ substantially from the LM’s base distribution—is generally intractable. In this work, we develop an architecture for controlled LM generation based on sequential Monte Carlo (SMC). Our SMC framework allows us to flexibly incorporate domain- and problem-specific constraints at inference time, and efficiently reallocate computational resources in light of new information during the course of generation. By comparing to a number of alternatives and ablations on four challenging domains---Python code generation for data science, text-to-SQL, goal inference, and molecule synthesis—we demonstrate that, with little overhead, our approach allows small open-source language models to outperform models over 8$\times$ larger, as well as closed-source, fine-tuned ones. In support of the probabilistic perspective, we show that these performance improvements are driven by better approximation to the posterior distribution. [Our system](https://github.com/probcomp/genlm-control) builds on the framework of Lew et al. (2023) and integrates with its _language model probabilistic programming language_, giving users a simple, programmable way to apply SMC to a broad variety of controlled generation problems.

Transformer-based language models, though not explicitly trained to mimic brain recordings, have demonstrated surprising alignment with brain activity. Progress in these models—through increased size, instruction-tuning, and multimodality—has led to better representational alignment with neural data. Recently, a new class of instruction-tuned multimodal LLMs (MLLMs) have emerged, showing remarkable zero-shot capabilities in open-ended multimodal vision tasks. However, it is unknown whether MLLMs, when prompted with natural instructions, lead to better brain alignment and effectively capture instruction-specific representations. To address this, we first investigate the brain alignment, i.e., measuring the degree of predictivity of neural visual activity using text output response embeddings from MLLMs as participants engage in watching natural scenes. Experiments with 10 different instructions (like image captioning, visual question answering, etc.) show that MLLMs exhibit significantly better brain alignment than vision-only models and perform comparably to non-instruction-tuned multimodal models like CLIP. We also find that while these MLLMs are effective at generating high-quality responses suitable to the task-specific instructions, not all instructions are relevant for brain alignment. Further, by varying instructions, we make the MLLMs encode instruction-specific visual concepts related to the input image. This analysis shows that MLLMs effectively capture count-related and recognition-related concepts, demonstrating strong alignment with brain activity. Notably, the majority of the explained variance of the brain encoding models is shared between MLLM embeddings of image captioning and other instructions. These results indicate that enhancing MLLMs' ability to capture more task-specific information could allow for better differentiation between various types of instructions, and hence improve their precision in predicting brain responses.

Humans excel at learning abstract patterns across different sequences, filtering out irrelevant details, and transferring these generalized concepts to new sequences. In contrast, many sequence learning models lack the ability to abstract, which leads to memory inefficiency and poor transfer. We introduce a non-parametric hierarchical variable learning model (HVM) that learns chunks from sequences and abstracts contextually similar chunks as variables. HVM efficiently organizes memory while uncovering abstractions, leading to compact sequence representations. When learning on language datasets such as babyLM, HVM learns a more efficient dictionary than standard compression algorithms such as Lempel-Ziv. In a sequence recall task requiring the acquisition and transfer of variables embedded in sequences, we demonstrate HVM’s sequence likelihood correlates with human recall times. In contrast, large language models (LLMs) struggle to transfer abstract variables as effectively as humans. From HVM’s adjustable layer of abstraction, we demonstrate that the model realizes a precise trade-off between compression and generalization. Our work offers a cognitive model that captures the learning and transfer of abstract representations in human cognition and differentiates itself from LLMs.

In the primate neocortex, neurons with similar function are often found to be spatially close. Kohonen's self-organizing map (SOM) has been one of the most influential approaches for simulating brain-like topographical organization in artificial neural network models. However, integrating these maps into deep neural networks with multitude of layers has been challenging, with self-organized deep neural networks suffering from substantially diminished capacity to perform visual recognition. We identified a key factor leading to the performance degradation in self-organized topographical neural network models: the discord between predominantly bottom-up learning updates in the self-organizing maps, and those derived from top-down, credit-based learning approaches. To address this, we propose an alternative self organization algorithm, tailored to align with the top-down learning processes in deep neural networks. This model not only emulates critical aspects of cortical topography but also significantly narrows the performance gap between non-topographical and topographical models. This advancement underscores the substantial importance of top-down assigned credits in shaping topographical organization. Our findings are a step in reconciling topographical modeling with the functional efficacy of neural network models, paving the way for more brain-like neural architectures.

Deep learning models trained on computer vision tasks are widely considered the most successful models of human vision to date. The majority of work that supports this idea evaluates how accurately these models predict behavior and brain responses to static images of objects and scenes. Real-world vision, however, is highly dynamic, and far less work has evaluated deep learning models on human responses to moving stimuli, especially those that involve more complicated, higher-order phenomena like social interactions. Here, we extend a dataset of natural videos depicting complex multi-agent interactions by collecting human-annotated sentence captions for each video, and we benchmark 350+ image, video, and language models on behavior and neural responses to the videos. As in prior work, we find that many vision models reach the noise ceiling in predicting visual scene features and responses along the ventral visual stream (often considered the primary neural substrate of object and scene recognition). In contrast, vision models poorly predict human action and social interaction ratings and neural responses in the lateral stream (a neural pathway theorized to specialize in dynamic, social vision), though video models show a striking advantage in predicting mid-level lateral stream regions. Language models (given human sentence captions of the videos) predict action and social ratings better than image and video models, but perform poorly at predicting neural responses in the lateral stream. Together, these results identify a major gap in AI's ability to match human social vision and provide insights to guide future model development for dynamic, natural contexts.

Concept-selective regions within the human cerebral cortex exhibit significant activation in response to specific visual stimuli associated with particular concepts. Precisely localizing these regions stands as a crucial long-term goal in neuroscience to grasp essential brain functions and mechanisms. Conventional experiment-driven approaches hinge on manually constructed visual stimulus collections and corresponding brain activity recordings, constraining the support and coverage of concept localization. Additionally, these stimuli often consist of concept objects in unnatural contexts and are potentially biased by subjective preferences, thus prompting concerns about the validity and generalizability of the identified regions. To address these limitations, we propose a data-driven exploration approach. By synthesizing extensive brain activity recordings, we statistically localize various concept-selective regions. Our proposed MindSimulator leverages advanced generative technologies to learn the probability distribution of brain activity conditioned on concept-oriented visual stimuli. This enables the creation of simulated brain recordings that reflect real neural response patterns. Using the synthetic recordings, we successfully localize several well-studied concept-selective regions and validate them against empirical findings, achieving promising prediction accuracy. The feasibility opens avenues for exploring novel concept-selective regions and provides prior hypotheses for future neuroscience research.

How do we know if two systems - biological or artificial - process information in a similar way? Similarity measures such as linear regression, Centered Kernel Alignment (CKA), Normalized Bures Similarity (NBS), and angular Procrustes distance, are often used to quantify this similarity. However, it is currently unclear what drives high similarity scores and even what constitutes a "good" score. Here, we introduce a novel tool to investigate these questions by differentiating through similarity measures to directly maximize the score. Surprisingly, we find that high similarity scores do not guarantee encoding task-relevant information in a manner consistent with neural data; and this is particularly acute for CKA and even some variations of cross-validated and regularized linear regression. We find no consistent threshold for a good similarity score - it depends on both the measure and the dataset. In addition, synthetic datasets optimized to maximize similarity scores initially learn the highest variance principal component of the target dataset, but some methods like angular Procrustes capture lower variance dimensions much earlier than methods like CKA. To shed light on this, we mathematically derive the sensitivity of CKA, angular Procrustes, and NBS to the variance of principal component dimensions, and explain the emphasis CKA places on high variance components. Finally, by jointly optimizing multiple similarity measures, we characterize their allowable ranges and reveal that some similarity measures are more constraining than others. While current measures offer a seemingly straightforward way to quantify the similarity between neural systems, our work underscores the need for careful interpretation. We hope the tools we developed will be used by practitioners to better understand current and future similarity measures.

The Platonic Representation Hypothesis posits that behind different modalities of data (what we sense or detect), there exists a universal, modality-independent representation of reality. Inspired by this, we treat each neuron as a system, where we can detect the neuron’s multi-segment activity data under different peripheral conditions. We believe that, similar to the Platonic idea, there exists a time-invariant representation behind the different segments of the same neuron, which reflects the intrinsic properties of the neuron’s system. Intrinsic properties include the molecular profiles, brain regions and morphological structure, etc. The optimization objective for obtaining the intrinsic representation of neurons should satisfy two criteria: (I) segments from the same neuron should have a higher similarity than segments from different neurons; (II) the representations should generalize well to out-of-domain data. To achieve this, we employ contrastive learning, treating different segments from the same neuron as positive pairs and segments from different neurons as negative pairs. During the implementation, we chose the VICReg, which uses only positive pairs for optimization but indirectly separates dissimilar samples via regularization terms. To validate the efficacy of our method, we first applied it to simulated neuron population dynamics data generated using the Izhikevich model. We successfully confirmed that our approach captures the type of each neuron as defined by preset hyperparameters. We then applied our method to two real-world neuron dynamics datasets, including spatial transcriptomics-derived neuron type annotations and the brain regions where each neuron is located. The learned representations from our model not only predict neuron type and location but also show robustness when tested on out-of-domain data (unseen animals). This demonstrates the potential of our approach in advancing the understanding of neuronal systems and offers valuable insights for future neuroscience research.

Precipitation nowcasting plays a pivotal role in socioeconomic sectors, especially in severe convective weather warnings. Although notable progress has been achieved by approaches mining the spatiotemporal correlations with deep learning, these methods still suffer severe blurriness as the lead time increases, which hampers accurate predictions for extreme precipitation. To alleviate blurriness, researchers explore generative methods conditioned on blurry predictions. However, the pairs of blurry predictions and corresponding ground truth need to be given in advance, making the training pipeline cumbersome and limiting the generality of generative models within blurry modes that appear in training data. By rethinking the blurriness in precipitation nowcasting as a blur kernel acting on predictions, we propose an unsupervised postprocessing method to eliminate the blurriness without the requirement of training with the pairs of blurry predictions and corresponding ground truth. Specifically, we utilize blurry predictions to guide the generation process of a pre-trained unconditional denoising diffusion probabilistic model (DDPM) to obtain high-fidelity predictions with eliminated blurriness. A zero-shot blur kernel estimation mechanism and an auto-scale denoise guidance strategy are introduced to adapt the unconditional DDPM to any blurriness modes varying from datasets and lead times in precipitation nowcasting. Extensive experiments are conducted on 7 precipitation radar datasets, demonstrating the generality and superiority of our method.

In traditional machine learning, models are defined by a set of parameters, which are optimized to perform specific tasks. In neural networks, these parameters correspond to the synaptic weights. However, in reality, it is often infeasible to control or update all weights. This challenge is not limited to artificial networks but extends to biological networks, such as the brain, where the extent of distributed synaptic weight modification during learning remains unclear. Motivated by these insights, we theoretically investigate how different allocations of a fixed number of learnable weights influence the capacity of neural networks. Using a teacher-student setup, we introduce a benchmark to quantify the expressivity associated with each allocation. We establish conditions under which allocations have \`maximal' or \`minimal' expressive power in linear recurrent neural networks and linear multi-layer feedforward networks. For suboptimal allocations, we propose heuristic principles to estimate their expressivity. These principles extend to shallow ReLU networks as well. Finally, we validate our theoretical findings with empirical experiments. Our results emphasize the critical role of strategically distributing learnable weights across the network, showing that a more widespread allocation generally enhances the network’s expressive power.

Image representations (artificial or biological) are often compared in terms of their global geometric structure; however, representations with similar global structure can have strikingly different local geometries. Here, we propose a framework for comparing a set of image representations in terms of their local geometries. We quantify the local geometry of a representation using the Fisher information matrix, a standard statistical tool for characterizing the sensitivity to local stimulus distortions, and use this as a substrate for a metric on the local geometry in the vicinity of a base image. This metric may then be used to optimally differentiate a set of models, by finding a pair of "principal distortions" that maximize the variance of the models under this metric. As an example, we use this framework to compare a set of simple models of the early visual system, identifying a novel set of image distortions that allow immediate comparison of the models by visual inspection. In a second example, we apply our method to a set of deep neural network models and reveal differences in the local geometry that arise due to architecture and training types. These examples demonstrate how our framework can be used to probe for informative differences in local sensitivities between complex models, and suggest how it could be used to compare model representations with human perception.