ICLR 2024 论文列表

The predictions of small transformers, trained to calculate the greatest common divisor (GCD) of two positive integers, can be fully characterized by looking at model inputs and outputs. As training proceeds, the model learns a list $\mathcal D$ of integers, products of divisors of the base used to represent integers and small primes, and predicts the largest element of $\mathcal D$ that divides both inputs. Training distributions impact performance. Models trained from uniform operands only learn a handful of GCD (up to $38$ GCD $\leq100$). Log-uniform operands boost performance to $73$ GCD $\leq 100$, and a log-uniform distribution of outcomes (i.e. GCD) to $91$. However, training from uniform (balanced) GCD breaks explainability.

Visual prostheses are potential devices to restore vision for blind people, which highly depends on the quality of stimulation patterns of the implanted electrode array. However, existing processing frameworks prioritize the generation of stimulation while disregarding the potential impact of restoration effects and fail to assess the quality of the generated stimulation properly. In this paper, we propose for the first time an end-to-end visual prosthesis framework (StimuSEE) that generates stimulation patterns with proper quality verification using V1 neuron spike patterns as supervision. StimuSEE consists of a retinal network to predict the stimulation pattern, a phosphene model, and a primary vision system network (PVS-net) to simulate the signal processing from the retina to the visual cortex and predict the firing rate of V1 neurons. Experimental results show that the predicted stimulation shares similar patterns to the original scenes, whose different stimulus amplitudes contribute to a similar firing rate with normal cells. Numerically, the predicted firing rate and the recorded response of normal neurons achieve a Pearson correlation coefficient of 0.78.

The ability to predict upcoming events has been hypothesized to comprise a key aspect of natural and machine cognition. This is supported by trends in deep reinforcement learning (RL), where self-supervised auxiliary objectives such as prediction are widely used to support representation learning and improve task performance. Here, we study the effects predictive auxiliary objectives have on representation learning across different modules of an RL system and how these mimic representational changes observed in the brain. We find that predictive objectives improve and stabilize learning particularly in resource-limited architectures, and we identify settings where longer predictive horizons better support representational transfer. Furthermore, we find that representational changes in this RL system bear a striking resemblance to changes in neural activity observed in the brain across various experiments. Specifically, we draw a connection between the auxiliary predictive model of the RL system and hippocampus, an area thought to learn a predictive model to support memory-guided behavior. We also connect the encoder network and the value learning network of the RL system to visual cortex and striatum in the brain, respectively. This work demonstrates how representation learning in deep RL systems can provide an interpretable framework for modeling multi-region interactions in the brain. The deep RL perspective taken here also suggests an additional role of the hippocampus in the brain-- that of an auxiliary learning system that benefits representation learning in other regions.

Denoisers play a central role in many applications, from noise suppression in low-grade imaging sensors, to empowering score-based generative models. The latter category of methods makes use of Tweedie's formula, which links the posterior mean in Gaussian denoising (*i*.*e*., the minimum MSE denoiser) with the score of the data distribution. Here, we derive a fundamental relation between the higher-order central moments of the posterior distribution, and the higher-order derivatives of the posterior mean. We harness this result for uncertainty quantification of pre-trained denoisers. Particularly, we show how to efficiently compute the principal components of the posterior distribution for any desired region of an image, as well as to approximate the full marginal distribution along those (or any other) one-dimensional directions. Our method is fast and memory-efficient, as it does not explicitly compute or store the high-order moment tensors and it requires no training or fine tuning of the denoiser. Code and examples are available on the project [website](https://hilamanor.github.io/GaussianDenoisingPosterior/).

Characterizing the relationship between neural population activity and behavioral data is a central goal of neuroscience. While latent variable models (LVMs) are successful in describing high-dimensional data, they are typically only designed for a single type of data, making it difficult to identify structure shared across different experimental data modalities. Here, we address this shortcoming by proposing an unsupervised LVM which extracts shared and independent latents for distinct, simultaneously recorded experimental modalities. We do this by combining Gaussian Process Factor Analysis (GPFA), an interpretable LVM for neural spiking data with temporally smooth latent space, with Gaussian Process Variational Autoencoders (GP-VAEs), which similarly use a GP prior to characterize correlations in a latent space, but admit rich expressivity due to a deep neural network mapping to observations. We achieve interpretability in our model by partitioning latent variability into components that are either shared between or independent to each modality. We parameterize the latents of our model in the Fourier domain, and show improved latent identification using this approach over standard GP-VAE methods. We validate our model on simulated multi-modal data consisting of Poisson spike counts and MNIST images that scale and rotate smoothly over time. We show that the multi-modal GP-VAE (MM-GPVAE) is able to not only identify the shared and independent latent structure across modalities accurately, but provides good reconstructions of both images and neural rates on held-out trials. Finally, we demonstrate our framework on two real world multi-modal experimental settings: Drosophila whole-brain calcium imaging alongside tracked limb positions, and Manduca sexta spike train measurements from ten wing muscles as the animal tracks a visual stimulus.

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.

Modern neural recording techniques allow neuroscientists to obtain spiking activity of multiple neurons from different brain regions over long time periods, which requires new statistical methods to be developed for understanding structure of the large-scale data. In this paper, we develop a bi-clustering method to cluster the neural spiking activity spatially and temporally, according to their low-dimensional latent structures. The spatial (neuron) clusters are defined by the latent trajectories within each neural population, while the temporal (state) clusters are defined by (populationally) synchronous local linear dynamics shared with different periods. To flexibly extract the bi-clustering structure, we build the model non-parametrically, and develop an efficient Markov chain Monte Carlo (MCMC) algorithm to sample the posterior distributions of model parameters. Validating our proposed MCMC algorithm through simulations, we find the method can recover unknown parameters and true bi-clustering structures successfully. We then apply the proposed bi-clustering method to multi-regional neural recordings under different experiment settings, where we find that simultaneously considering latent trajectories and spatial-temporal clustering structures can provide us with a more accurate and interpretable result. Overall, the proposed method provides scientific insights for large-scale (counting) time series with elongated recording periods, and it can potentially have application beyond neuroscience.

Recent advances in the theory of Neural Operators (NOs) have enabled fast and accurate computation of the solutions to complex systems described by partial differential equations (PDEs). Despite their great success, current NO-based solutions face important challenges when dealing with spatio-temporal PDEs over long time scales. Specifically, the current theory of NOs does not present a systematic framework to perform data assimilation and efficiently correct the evolution of PDE solutions over time based on sparsely sampled noisy measurements. In this paper, we propose a learning-based state-space approach to compute the solution operators to infinite-dimensional semilinear PDEs. Exploiting the structure of semilinear PDEs and the theory of nonlinear observers in function spaces, we develop a flexible recursive method that allows for both prediction and data assimilation by combining prediction and correction operations. The proposed framework is capable of producing fast and accurate predictions over long time horizons, dealing with irregularly sampled noisy measurements to correct the solution, and benefits from the decoupling between the spatial and temporal dynamics of this class of PDEs. We show through experiments on the Kuramoto-Sivashinsky, Navier-Stokes and Korteweg-de Vries equations that the proposed model is robust to noise and can leverage arbitrary amounts of measurements to correct its prediction over a long time horizon with little computational overhead.

Gaussian processes (GPs) are popular nonparametric statistical models for learning unknown functions and quantifying the spatiotemporal uncertainty in data. Recent works have extended GPs to model scalar and vector quantities distributed over non-Euclidean domains, including smooth manifolds, appearing in numerous fields such as computer vision, dynamical systems, and neuroscience. However, these approaches assume that the manifold underlying the data is known, limiting their practical utility. We introduce RVGP, a generalisation of GPs for learning vector signals over latent Riemannian manifolds. Our method uses positional encoding with eigenfunctions of the connection Laplacian, associated with the tangent bundle, readily derived from common graph-based approximation of data. We demonstrate that RVGP possesses global regularity over the manifold, which allows it to super-resolve and inpaint vector fields while preserving singularities. Furthermore, we use RVGP to reconstruct high-density neural dynamics derived from low-density EEG recordings in healthy individuals and Alzheimer's patients. We show that vector field singularities are important disease markers and that their reconstruction leads to a comparable classification accuracy of disease states to high-density recordings. Thus, our method overcomes a significant practical limitation in experimental and clinical applications.

Spiking neural networks (SNNs) are energy-efficient and hold great potential for large-scale inference. Since training SNNs from scratch is costly and has limited performance, converting pretrained artificial neural networks (ANNs) to SNNs is an attractive approach that retains robust performance without additional training data and resources. However, while existing conversion methods work well on convolution networks, emerging Transformer models introduce unique mechanisms like self-attention and test-time normalization, leading to non-causal non-linear interactions unachievable by current SNNs. To address this, we approximate these operations in both temporal and spatial dimensions, thereby providing the first SNN conversion pipeline for Transformers. We propose \textit{Universal Group Operators} to approximate non-linear operations spatially and a \textit{Temporal-Corrective Self-Attention Layer} that approximates spike multiplications at inference through an estimation-correction approach. Our algorithm is implemented on a pretrained ViT-B/32 from CLIP, inheriting its zero-shot classification capabilities, while improving control over conversion losses. To our knowledge, this is the first direct training-free conversion of a pretrained Transformer to a purely event-driven SNN, promising for neuromorphic hardware deployment.

In this paper, we investigate the behavior of gradient descent algorithms in physics-informed machine learning methods like PINNs, which minimize residuals connected to partial differential equations (PDEs). Our key result is that the difficulty in training these models is closely related to the conditioning of a specific differential operator. This operator, in turn, is associated to the Hermitian square of the differential operator of the underlying PDE. If this operator is ill-conditioned, it results in slow or infeasible training. Therefore, preconditioning this operator is crucial. We employ both rigorous mathematical analysis and empirical evaluations to investigate various strategies, explaining how they better condition this critical operator, and consequently improve training.

Understanding how multiple brain regions interact to produce behavior is a major challenge in systems neuroscience, with many regions causally implicated in common tasks such as sensory processing and decision making. A precise description of interactions between regions remains an open problem. Moreover, neural dynamics are nonlinear and non-stationary. Here, we propose MR-SDS, a multiregion, switching nonlinear state space model that decomposes global dynamics into local and cross-communication components in the latent space. MR-SDS includes directed interactions between brain regions, allowing for estimation of state-dependent communication signals, and accounts for sensory inputs effects. We show that our model accurately recovers latent trajectories, vector fields underlying switching nonlinear dynamics, and cross-region communication profiles in three simulations. We then apply our method to two large-scale, multi-region neural datasets involving mouse decision making. The first includes hundreds of neurons per region, recorded simultaneously at single-cell-resolution across 3 distant cortical regions. The second is a mesoscale widefield dataset of 8 adjacent cortical regions imaged across both hemispheres. On these multi-region datasets, our model outperforms existing piece-wise linear multi-region models and reveals multiple distinct dynamical states and a rich set of cross-region communication profiles.

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 auto-regressive spatiotemporal generation problem. Neuroformer is a multimodal, multitask generative pre-trained 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.

Shannon and Weaver's seminal information theory divides communication into three levels: technical, semantic, and effectiveness. While the technical level deals with the accurate reconstruction of transmitted symbols, the semantic and effectiveness levels deal with the inferred meaning and its effect on the receiver. Large Language Models (LLMs), with their wide generalizability, make some progress towards the second level. However, LLMs and other communication models are not conventionally designed for predicting and optimizing communication for desired receiver behaviors and intents. As a result, the effectiveness level remains largely untouched by modern communication systems. In this paper, we introduce the receivers' "behavior tokens," such as shares, likes, clicks, purchases, and retweets, in the LLM's training corpora to optimize content for the receivers and predict their behaviors. Other than showing similar performance to LLMs on content understanding tasks, our trained models show generalization capabilities on the behavior dimension for behavior simulation, content simulation, behavior understanding, and behavior domain adaptation. We show results on all these capabilities using a wide range of tasks on three corpora. We call these models Large Content and Behavior Models (LCBMs). Further, to spur more research on LCBMs, we release our new Content Behavior Corpus (CBC), a repository containing communicator, message, and corresponding receiver behavior (https://behavior-in-the-wild.github.io/LCBM).

This paper introduces a novel approach to structural inference, combining a variational dynamics encoder with partial correlation coefficients. In contrast to prior methods, our approach leverages variational inference to encode node dynamics within latent variables, and structural reconstruction relies on the calculation of partial correlation coefficients derived from these latent variables. This unique design endows our method with scalability and extends its applicability to both one-dimensional and multi-dimensional feature spaces. Furthermore, by reorganizing latent variables according to temporal steps, our approach can effectively reconstruct directed graph structures. We validate our method through extensive experimentation on twenty datasets from a benchmark dataset and biological networks. Our results showcase the superior scalability, accuracy, and versatility of our proposed approach compared to existing methods. Moreover, experiments conducted on noisy data affirm the robustness of our method.

Research on conversation has put emphasis on the importance of a multi-level communication system, in which the interlocutors aim to establish and maintain common ground. In natural conversations, repair mechanisms such as clarification requests are frequently used to improve mutual understanding. Here we explore the effects of conversational repair on languages emerging in signaling games. We extend the basic Lewis signaling game setup with a feedback channel that allows for the transmission of messages backwards from the receiver to the sender. Further, we add noise to the communication channel so that repair mechanisms become necessary for optimal performance. We find that languages emerging in setups with feedback channel are less compositional. However, the models still achieve a substantially higher generalization performance in conditions with noise, putting to question the role of compositionality for generalization. These findings generalize also to a more realistic case involving a guessing game with naturalistic images. More broadly speaking, this study provides an important step towards the creation of signaling games that more closely resemble the conditions under which human languages emerged.

Despite many successful examples in which probabilistic inference can account for perception, we have little understanding of how the brain represents and uses structured priors that capture the complexity of natural input statistics. Here we construct a recurrent circuit model that can implicitly represent priors over latent variables, and combine them with sensory and contextual sources of information to encode task-specific posteriors. Inspired by the recent success of diffusion models as means of learning and using priors over images, our model uses dendritic nonlinearities optimized for denoising, and stochastic somatic integration with the degree of noise modulated by an oscillating global signal. Combining these elements into a recurrent network yields a stochastic dynamical system that samples from the prior at a rate prescribed by the period of the global oscillator. Additional inputs reflecting sensory or top-down contextual information alter these dynamics to generate samples from the corresponding posterior, with different input gating patterns selecting different inference tasks. We demonstrate that this architecture can sample from low dimensional nonlinear manifolds and multimodal posteriors. Overall, the model provides a new framework for circuit-level representation of probabilistic information, in a format that facilitates flexible inference.

Predictive coding networks are neuroscience-inspired models with roots in both Bayesian statistics and neuroscience. Training such models, however, is quite inefficient and unstable. In this work, we show how by simply changing the temporal scheduling of the update rule for the synaptic weights leads to an algorithm that is much more efficient and stable than the original one, and has theoretical guarantees in terms of convergence. The proposed algorithm, that we call incremental predictive coding (iPC) is also more biologically plausible than the original one, as it it fully automatic. In an extensive set of experiments, we show that iPC constantly performs better than the original formulation on a large number of benchmarks for image classification, as well as for the training of both conditional and masked language models, in terms of test accuracy, efficiency, and convergence with respect to a large set of hyperparameters.

We introduce the Brain Language Model (BrainLM), a foundation model for brain activity dynamics trained on 6,700 hours of fMRI recordings. Utilizing self-supervised masked-prediction training, BrainLM demonstrates proficiency in both fine-tuning and zero-shot inference tasks. Fine-tuning allows for the accurate prediction of clinical variables like age, anxiety, and PTSD as well as forecasting of future brain states. Critically, the model generalizes well to entirely new external cohorts not seen during training. In zero-shot inference mode, BrainLM can identify intrinsic functional networks directly from raw fMRI data without any network-based supervision during training. The model also generates interpretable latent representations that reveal relationships between brain activity patterns and cognitive states. Overall, BrainLM offers a versatile and interpretable framework for elucidating the complex spatiotemporal dynamics of human brain activity. It serves as a powerful "lens" through which massive repositories of fMRI data can be analyzed in new ways, enabling more effective interpretation and utilization at scale. The work demonstrates the potential of foundation models to advance computational neuroscience research.