A Low-Rank Space Captures Linear Alignment Between LLM and Human Neural Activity During Naturalistic Language Listening
Zach Paris, Emily Finn
AI 速览：作者用岭降秩回归发现，仅用LLM嵌入维度的1–3%即可恢复完整线性编码性能，且该脑预测子空间不同于嵌入的主方差方向。
Large language models (LLMs) are increasingly used as computational models of human language processing, yet it remains unclear which components of their representations drive alignment with neural activity. Here, we use ridge reduced-rank regression to identify the brain-predictive subspace of LLM representations: the representational directions that support linear prediction of neural responses. Across three naturalistic language-listening datasets spanning intracranial electrophysiology and fMRI, and six model conditions spanning autoregressive, bidirectional masked, and randomly initialized language models, we find that full linear encoding performance can be recovered using only 1-3% of the original embedding dimensionality. These low-dimensional subspaces generalize across held-out participants and, to a lesser extent, across datasets, suggesting that neural predictivity is concentrated in a compact and partially shared representational space. We next compare these brain-predictive directions with the principal axes of variation in the embeddings. Principal component analysis requires substantially more dimensions to recover neural prediction, demonstrating that the directions most useful for predicting neural activity are distinct from those capturing the most overall variance within LLM representations themselves. Finally, characterizing the learned subspaces allows us to surface interpretable features that are overrepresented in neural activity above and beyond the LLM representations. Together, these results show that LLM-brain alignment is supported by a small, structured subset of model representations and provides a framework for better understanding exactly why these representations align. Code can be found at: https://github.com/thefinnlab/low-rank-alignment
Serwan Jassim, Victoria Bosch, Daniel Anthes, Elia Bruni, Tim Kietzmann
Decoding sensory-evoked functional magnetic resonance imaging (fMRI) data is a central analytical tool in cognitive neuroscience. Here we ask whether self-supervised learning (SSL), which has been scarcely explored in this domain, can yield representations that support strong downstream performance. To do so, we adapt a joint embedding predictive architecture (JEPA) to train participant-specific encoders on brain data alone. The encoders never see the stimulus images or any representation derived from them. Applied to the Natural Scenes Dataset (NSD), we evaluate our learned brain embeddings on the downstream tasks of brain captioning and image reconstruction, as well as cross-participant generalization. Our self-supervised approach achieves competitive performance with parameter-rich supervised pipelines that are trained end-to-end with access to image and language data. We further find that encoders trained independently for different participants can be aligned fully unsupervised, using neither images nor stimuli shared between them. After alignment, a neural decoding head trained on one participant can be applied to another without fine-tuning and retains most of its within-subject performance on image reconstruction and brain captioning. By removing the need for images and shared stimuli, our approach is a step towards pooling fMRI data across participants and, eventually, across datasets.
Real-time forecasting of resting-state EEG signals is required by applications like brain-state-dependent stimulation, where computer generated actions are coupled with ongoing neural oscillations. Recently, the deep learning model WaveNet was proposed for the forecasting task. It shows superior accuracy compared to the prevailing method, the linear autoregressive (AR) model, and provides a built-in uncertainty measure due to its probabilistic modeling framework. However, inference using WaveNet is too slow for real-time use due to its sample-by-sample autoregressive operation: a single forecast requires evaluating the model tens or hundreds of times depending on the length of the prediction window. In this paper, we present REVBRAIN, a probabilistic deep learning method that produces forecasts in real time by generating the forecast over the whole prediction horizon at once. This is achieved by tokenizing the output space using residual vector quantization (RVQ) and generating forecasts over the items in the tokenized space. We tested REVBRAIN for forecasting 200 ms of EEG time series in the alpha-frequency band (8-13 Hz) and compared our results against WaveNet model. We found that REVBRAIN achieved real-time inference on a laptop GPU and an over $50\times$ speedup compared to WaveNet, while reaching superior prediction accuracy. By achieving real-time inference speed, REVBRAIN enables incorporating accurate and probabilistic EEG forecasting into BCI applications, opening up new ways for investigating the functioning of the human brain.
Paul Kurian, Tamoghna Chattopadhyay, Abhijith Shaji, Greg Ver Steeg, Paul M. Thompson, Jose Luis Ambite
Federated Learning (FL) allows for secure analysis of distributed data without data sharing. We and others have successfully applied FL to neuroimaging tasks, such as Alzheimer's disease classification from structural magnetic resonance imaging (MRI). FL trains a deep learning model locally at each site, encrypts the local model parameters and sends them to a federation controller that aggregates the local models under homomorphic encryption, the resulting community model is sent back to the sites for further training, and the process repeats for a number of rounds. FL often achieves learning performance (e.g., accuracy) close to centralized training, but no data leaves the sites and model parameters are protected through encryption and other measures. In this paper, we show that federations composed of sites with heterogeneous amounts of data (1 large site plus small sites) perform better than homogeneous (same data per site) federations, particularly in low data regimes, while reaching performance close to centralized training. Having a big site often results in faster convergence and higher final accuracy. Heterogeneous federations better exploit sites with small amounts of data, a common situation in large consortia such as ENIGMA.
How far can behaviour inside a group, and the group's performance, be predicted from members measured while alone? We tested this on three public datasets of human collective foraging (621, 128 and 1,133 participants). A low-dimensional individual representation estimated from private-phase movement was mapped onto behaviour inside the group through a mapping learned on other participants. Private information processing was stable between the two halves of a session (split-half reliability, the correlation between the halves, 0.60--0.83) and predicted behaviour inside the group with correlations of 0.30--0.66. Selective social learning, following those who have succeeded or stopped, showed stable individual differences inside the group (reliability 0.45--0.59) yet was not predicted at all from the same person's private behaviour. Group performance was predicted with a correlation of 0.55 in all three datasets by simulations never fitted to group outcomes or by the mean of individually measured performance, a prediction carried by mobility and individual performance rather than by social weights. We found no credible evidence for an effect of how members were combined (equivalence bound 0.06). Whom to follow thus emerges only in company, which delimits what solitary measurements can predict and compose.
Emma Reyner-Fuentes, Sebastian Rudolph, Carmen Peláez-Moreno, Francisco J. Valverde-Albacete
Brains do not simply add up every signal they receive: they select which routes dominate. Yet connectomes are usually analyzed with tools that sum over all paths and place neural states in Euclidean spaces, blurring the feedback circuits that may sustain internal states. Here we treat neural signaling as routing instead of diffusion and describe it with max-plus algebra, in which signals accumulate along a path and the strongest route prevails. We propose a model in which the functional connectome of Caenorhabditis elegans emerges from the time-varying combination of electrical, synaptic, monoaminergic, neuropeptidergic and hormonal layers, and analyze five networks within this framework. Each collapses onto a handful of dominant feedback loops, which recover well-characterized circuits and point to new candidates for experimental study. Unlike linear spectra, these structures keep the biological meaning of the data, and their order-based description suggests that brain states live in lattices rather than Euclidean spaces.
Mathis Immertreu, Achim Schilling, Thomas Kinfe, Patrick Krauss
Neural language models are typically trained on next-token prediction, although linguistic structure spans multiple temporal scales. Successor representations (SRs) make this horizon explicit by encoding discounted distributions over future states. Here, we ask whether such predictive representations can recover not only word classes, but also finer functional and construction-like structure from natural language. A residual network trained on WikiText-103 predicts SR distributions at three horizons without part-of-speech supervision. At the shortest horizon, unsupervised clustering robustly recovers nouns, verbs, and adjectives, while directed inter-cluster transitions reproduce familiar syntactic asymmetries. At finer resolutions and across 13 part-of-speech categories, the same geometry reveals semantic-functional groupings that cross category boundaries and directed relations tracing candidate date, measurement, and title-name constructions. Part-of-speech agreement declines as the predictive horizon lengthens. These results suggest that word classes are coarse regions within a richer predictive geometry in which categorical and construction-like linguistic structure emerge from future-word distributions.
Seungjae Han, Joshua Yedam You, Soi Kim, Minho Eom, Jinho Park, Seunghee Park, Byeongwook Lee, Young-Gyu Yoon
Individual neurons exhibit diverse molecular, morphological, and electrophysiological properties that shape their distinct roles in neural circuits. While these multimodal features are largely shared across individuals, they remain an underutilized source of information in analyzing neural population dynamics. We posit that these shared biological profiles provide a common reference for relating neural dynamics across subjects and recording sessions. Our framework leverages this structure by routing neurons into latent groups based on their biological profiles and analyzing population dynamics through group-level representations. Because these assignments are anchored in biological properties that are consistent across subjects, the learned organization supports transfer to unseen animals without retraining or neuron-wise correspondence. We evaluate our framework on whole-brain calcium imaging in larval zebrafish and large-scale electrophysiology in the mouse visual cortex. Across both species and recording modalities, the framework delivers state-of-the-art performance in both neural decoding and manifold analysis: it achieves superior decoding of behavior and stimulus labels while better preserving the temporal consistency and local geometric structure of latent trajectories on unseen data. Our experiments demonstrate that not only does providing biological features improve baseline performance, but our proposed framework achieves even stronger results by using these properties to explicitly structure the population rather than treating them as auxiliary inputs. Together, these results suggest that organizing neural populations by their multimodal biological features offers a promising framework for generalizing population dynamics across subjects and recording sessions.
Spike activity has been the dominant neural signal for behavior decoding because its high spatiotemporal resolution supports accurate decoding. However, as intracortical brain-computer interfaces (iBCIs) move toward higher channel counts and wireless operation, the high sampling rates required to record spikes create substantial power and bandwidth demands. Local field potentials (LFPs) offer complementary advantages, including greater long-term stability, lower energy consumption, and lower bandwidth requirements. However, LFP-based decoders often achieve lower accuracy and rely on non-causal architectures that cannot be used directly for real-time deployment. We propose REALM, a retrospective knowledge distillation (RKD) framework for causal LFP behavior decoding. Inspired by offline-to-online distillation in speech recognition, REALM transfers non-causal representational knowledge from a pretrained, multi-session bidirectional LFP teacher to a causal student model. We first pretrain a bidirectional Mamba-2 teacher across multiple recording sessions using continuous masked autoencoding (CMAE), and then distill its representation into a compact causal student using a combined objective of representation alignment and autoencoding. REALM achieves the highest mean accuracy among the compared decoders in both label-free and fine-tuned pipelines, with statistically significant improvements over each baseline, including the state-of-the-art CrossModalDistill. It does so using LFPs alone throughout pretraining, distillation, and decoding, with less than half the parameters of CrossModalDistill's published student and one-tenth of its pretraining time. These results show that a causal LFP-only model can achieve decoding accuracy competitive with a non-causal multi-modal model, offering a practical and scalable approach for next-generation wireless and implantable iBCIs.
Similarity scores are often offered as evidence that a model shares structure with the brain or across languages. We ask what such a score reads when that structure is removed, or when the instrument measuring it does not work, in two settings. Across seventeen languages, a grammaticality probe transfers worse between more distant languages (r = -0.66). But the probe's own accuracy falls along the same axis and is at chance in four languages, four of the five most distant. Dropping them halves the explained variance, and because it also narrows the range of distances, the design cannot say how much of the gradient is the instrument. Counting the 272 language pairs as independent gives p = 0.0006 for a steering effect that is null when the seventeen languages are the unit (p = 0.155). In brain alignment, a training objective raises a language model's similarity to fMRI responses from 0.10 to 0.34 (reliability ceiling 0.54), yet targets with the brain correspondence destroyed still reach 0.31. A shuffled target scores about k/n against the real one, for rank k and n sentences, a baseline that can be computed before any model is trained. Both interventions work, yet we detect no distance-graded steering effect and no syntactic benefit from alignment. Before reading a correspondence score, measure how much of it survives without the correspondence.
Kianté Fernandez, Caitlin Chen, Jialu Zhou, Bartek Sadowski, Anthony C. Miceli, Ian Krajbich
Claims about the cognitive capabilities of large language models are typically tested by translating behavioral paradigms into text prompts, bypassing the visual interfaces and time pressure through which human participants actually engage with experiments. At the same time, AI agents can now complete online behavioral tasks and produce human-like data, which raises concerns that online datasets in the social and behavioral sciences are increasingly open to contamination. We introduce CogArena, a benchmark of ten experimental paradigms from the social and behavioral sciences. Agents complete the experiments through a standard web browser, working with the same visual stimuli and response interfaces that online participants use. A three-level scoring procedure evaluates whether the agent completed the task, how accurately it performed, and whether its data show the behavioral signatures each paradigm reliably produces in people. Across four multimodal models, each run ten times per task, we find that finishing an experiment and reproducing its signatures are different things. Many sessions did not finish, and those that did reproduced some signatures reliably and others not at all. CogArena provides the tasks, scoring code, and a public leaderboard for new submissions.
Rajkumar Vasudeva Raju, Zhe Li, Scott Linderman, Xaq Pitkow
Patterns of microcircuitry in the cerebral cortex suggest that the brain has an array of repeated canonical computational units. However, neural representations are distributed, so the relevant computations may only be related indirectly to single-neuron transformations. It thus remains an open challenge how to define canonical distributed computations. Here we integrate normative and algorithmic theories of neural computation to present a mathematical framework for inferring canonical distributed computations from large-scale neural activity patterns. At the normative level, we hypothesize that the brain learns a structured internal model of its environment and its latent causes. At the algorithmic level, we propose that this inference process is a nonlinear message-passing algorithm on a graph-structured model of the world. Given a time series of neural activity during a perceptual inference task, our analysis framework finds (i) the neural representation of the relevant latent variables, (ii) interactions between these latent variables that define the brain's internal model of the world, and (iii) message functions that specify the inference algorithm. With enough data, key computational properties are identifiable due to constraints from the symmetries inherent in any canonical computation, up to a joint global transformation of all interactions and the message-passing functions. As a demonstration of this framework, we analyze artificial neural recordings generated by a simulated brain that implicitly implements an approximate inference algorithm. Given simulated inputs and neural activity we successfully recover the latent variables, their neural representation and dynamics, and canonical message functions that govern the dynamics. Analysis of these models reveals features of experimental design required to extract canonical computations from neural data.
Matea Tashkovska, Naël Ouerghemi, Haozhe Qi, Alexander Mathis
Perceiving human body motion is critical for multimodal systems that understand and assist people. Yet current evaluations of Multimodal Large Language Models (MLLMs) largely focus on objects, scenes, and coarse actions, leaving their ability to reason about the body itself poorly assessed. This is especially challenging from the egocentric perspective, in which the body is only partially visible and motion must be inferred from occluded and temporally distributed cues. We introduce SOMA, a benchmark for fine-grained body-motion understanding from egocentric video, comprising 1,632 human-verified questions across three capability axes: body configuration, motion dynamics, and temporal reasoning. We evaluate 37 leading closed-source, open-source, and specialized egocentric MLLMs, complemented by an extensive human evaluation. We find that humans also find this task difficult from video alone (68.5% accuracy), yet clearly outperform the strongest MLLM (Qwen3.6-27B), which reaches 50.0% zero-shot accuracy. Our error analysis shows that MLLMs often misread the wearer's own body, misjudge events in time, and are prone to biases such as favoring the right hand or under-counting repetitions. To narrow the gap to human performance and support further progress, we introduce a training dataset of aligned video, body motion, and language supervision, and a multimodal baseline that jointly learns from these modalities. By identifying common failure modes and missing capabilities in current MLLMs, we hope SOMA will inspire future research on body-motion understanding and multimodal reasoning. Full benchmark, training data, and code will be released at: https://cnai.epfl.ch/soma
Learning algorithms are usually analyzed under the assumption that informative gradients are continuously available. But this is not always true---learning signals in biological neural networks, for example, may be sparse, local, and only intermittently available at any given synapse. In this work, we show that if gradient information is noisy and only intermittently available, learning may be unstable. In particular, even if average learning dynamics converge to the correct optimum, variance in learning may be asymptotically infinite. We explore this point in a number of analytically tractable settings, including single-layer and multi-layer linear networks, and derive explicit conditions under which learning is stable. These conditions complement, but are conceptually distinct from, existing conditions related to the stability of stochastic gradient descent. Our work demonstrates that unbiased credit assignment is not enough for reliable learning; sufficiently frequent and informative feedback is also required, which yields an additional constraint on models of biologically plausible learning.
Biological neural networks are noisy: their dynamics involve difficult-to-predict fluctuations which are likely due not just to chaos, but also to a variety of low-level biophysical processes. Despite the omnipresence of intrinsic noise, its theoretical consequences are incompletely understood, especially in the context of learning. For example, does noise meaningfully shape representation learning, or is it better viewed as a nuisance factor whose presence or absence changes little about what solution is found and when? Here, we argue that intrinsic noise can significantly modulate representation learning in recurrent neural networks (RNNs), since it can strongly break solution-space degeneracies and in some cases control whether a non-degenerate solution exists at all. We show that this is true for an analytically tractable model of noisy RNN learning with a linear activation function and white noise inputs. We find that, in the so-called rich regime (where weights are initialized with small values), noise strongly modulates the directions in which the read-in, readout, and recurrent weights align. Moreover, we find that noise produces a kind of phase transition: for sufficiently high noise, a non-degenerate solution is not even optimal if parameter scales are limited (e.g., via regularization). These results extend recent analytic work on RNN representation learning and show that noise can act as a fundamental determinant of representations.
Declan Kutscher, Reece Keller, Alyn Kirsch, Felix Pei, Aran Nayebi
Animals have a remarkable capacity for autonomy---driven by intrinsic motivation---without external sensory cues or extrinsic objectives, yet the computational mechanisms behind this ability largely remain a mystery. We combine whole-brain recordings in the fruit fly (Drosophila melanogaster), which reveal neural representations of spontaneous exploratory decisions more than 10 seconds in advance, with a neuromechanical digital twin to test whether optimizing intrinsic goals yields realistically embodied artificial agents that quantitatively match fly behavior and internal representations of future volitional action during exploration. Our hierarchical policy selects from a discrete library of low-level motor primitives, consistent with ethological theories of behavioral syllables. We train agents without external reward using 20 intrinsic motivation algorithms spanning curiosity, entropy, and competency methods. The agents are evaluated in a virtual tethered-ball assay modeled on the fly experiment, comparing spontaneous locomotor statistics and internal representations and decoding future turn direction from kinematics and neural activity on the same timescales observed in flies. DIAYN, a hierarchical competency algorithm learning discrete policies that maximize behavioral entropy and the separability of induced sensory observations, achieves the strongest joint behavioral and neural prospective coding performance relative to flies. Its learned policies closely capture individual variability in fly exploration strategies, suggesting that this diversity serves to maximize state-space coverage at the population level. DIAYN's latent activity also closely captures the sum-difference rule for interhemispheric encoding of kinematics in biological flies. These results establish hierarchical, intrinsically motivated agents as a powerful framework for reverse-engineering animal autonomy.
Jan-Matthis Lueckmann, Viren Jain, Michał Januszewski
Constructing mechanistic models of neural circuits is a fundamental goal of neuroscience, yet verifying such models is limited by the lack of ground truth. To rigorously test model discovery, we establish an in silico testbed using neuromechanical simulations of a larval zebrafish as a transparent ground truth. We find that LLM-based tree search autonomously discovers predictive models that significantly outperform established forecasting baselines. Conditioning on sensory drive is necessary but not sufficient for faithful system identification, as models exploit statistical shortcuts. Structural priors prove essential for enabling robust out-of-distribution generalization and recovery of interpretable mechanistic models. Our insights provide guidance for modeling real-world neural recordings and offer a broader template for AI-driven scientific discovery.
We obtain an analytic, interpretable and predictive theory of creativity in convolutional diffusion models. Indeed, score-matching diffusion models can generate highly original images that lie far from their training data. However, optimal score-matching theory suggests that these models should only be able to produce memorized training examples. To reconcile this theory-experiment gap, we identify two simple inductive biases, locality and equivariance, that: (1) induce a form of combinatorial creativity by preventing optimal score-matching; (2) result in fully analytic, completely mechanistically interpretable, local score (LS) and equivariant local score (ELS) machines that, (3) after calibrating a single time-dependent hyperparameter can quantitatively predict the outputs of trained convolution only diffusion models (like ResNets and UNets) with high accuracy (median $r^2$ of $0.95, 0.94, 0.94, 0.96$ for our top model on CIFAR10, FashionMNIST, MNIST, and CelebA). Our model reveals a locally consistent patch mosaic mechanism of creativity, in which diffusion models create exponentially many novel images by mixing and matching different local training set patches at different scales and image locations. Our theory also partially predicts the outputs of pre-trained self-attention enabled UNets (median $r^2 \sim 0.77$ on CIFAR10), revealing an intriguing role for attention in carving out semantic coherence from local patch mosaics.
Jan-Matthis Lueckmann, Alexander Immer, Alex Bo-Yuan Chen, Peter H. Li, Mariela D. Petkova, Nirmala A. Iyer, Luuk Willem Hesselink, Aparna Dev 等 18 位作者
Data-driven benchmarks have led to significant progress in key scientific modeling domains including weather and structural biology. Here, we introduce the Zebrafish Activity Prediction Benchmark (ZAPBench) to measure progress on the problem of predicting cellular-resolution neural activity throughout an entire vertebrate brain. The benchmark is based on a novel dataset containing 4d light-sheet microscopy recordings of over 70,000 neurons in a larval zebrafish brain, along with motion stabilized and voxel-level cell segmentations of these data that facilitate development of a variety of forecasting methods. Initial results from a selection of time series and volumetric video modeling approaches achieve better performance than naive baseline methods, but also show room for further improvement. The specific brain used in the activity recording is also undergoing synaptic-level anatomical mapping, which will enable future integration of detailed structural information into forecasting methods.
Jascha Sohl-Dickstein, Eric A. Weiss, Niru Maheswaranathan, Surya Ganguli
A central problem in machine learning involves modeling complex data-sets using highly flexible families of probability distributions in which learning, sampling, inference, and evaluation are still analytically or computationally tractable. Here, we develop an approach that simultaneously achieves both flexibility and tractability. The essential idea, inspired by non-equilibrium statistical physics, is to systematically and slowly destroy structure in a data distribution through an iterative forward diffusion process. We then learn a reverse diffusion process that restores structure in data, yielding a highly flexible and tractable generative model of the data. This approach allows us to rapidly learn, sample from, and evaluate probabilities in deep generative models with thousands of layers or time steps, as well as to compute conditional and posterior probabilities under the learned model. We additionally release an open source reference implementation of the algorithm.