Applications · neuroscience and cognitive science

Transformers have achieved great success in machine learning applications. Normalization techniques, such as Layer Normalization (LayerNorm, LN) and Root Mean Square Normalization (RMSNorm), play a critical role in accelerating and stabilizing the training of Transformers. While LayerNorm recenters and rescales input vectors, RMSNorm only rescales the vectors by their RMS value. Despite being more computationally efficient, RMSNorm may compromise the representation ability of Transformers. There is currently no consensus regarding the preferred normalization technique, as some models employ LayerNorm while others utilize RMSNorm, especially in recent large language models. It is challenging to convert Transformers with one normalization to the other type. While there is an ongoing disagreement between the two normalization types, we propose a solution to unify two mainstream Transformer architectures, Pre-LN and Pre-RMSNorm Transformers. By removing the inherent redundant mean information in the main branch of Pre-LN Transformers, we can reduce LayerNorm to RMSNorm, achieving higher efficiency. We further propose the Compressed RMSNorm (CRMSNorm) and Pre-CRMSNorm Transformer based on a lossless compression of the zero-mean vectors. We formally establish the equivalence of Pre-LN, Pre-RMSNorm, and Pre-CRMSNorm Transformer variants in both training and inference. It implies that Pre-LN Transformers can be substituted with Pre-(C)RMSNorm counterparts at almost no cost, offering the same arithmetic functionality along with free efficiency improvement. Experiments demonstrate that we can reduce the training and inference time of Pre-LN Transformers by 1% - 10%.

Spiking Neural Networks (SNNs) are biologically-inspired models that are capable of processing information in streams of action potentials. However, simulating and training SNNs is computationally expensive due to the need to solve large systems of coupled differential equations. In this paper, we propose a novel event-based algorithm called SparseProp for simulating and training sparse SNNs. Our algorithm reduces the computational cost of both forward pass and backward pass operations from O(N) to O(log(N)) per network spike, enabling numerically exact simulations of large spiking networks and their efficient training using backpropagation through time. By exploiting the sparsity of the network, SparseProp avoids iterating through all neurons at every spike and uses efficient state updates. We demonstrate the effectiveness of SparseProp for several classical integrate-and-fire neuron models, including simulating a sparse SNN with one million LIF neurons, which is sped up by more than four orders of magnitude compared to previous implementations. Our work provides an efficient and exact solution for training large-scale spiking neural networks and opens up new possibilities for building more sophisticated brain-inspired models.

Spectral clustering has gained popularity for clustering non-convex data due to its simplicity and effectiveness. It is essential to construct a similarity graph using a high-quality affinity measure that models the local neighborhood relations among the data samples. However, incomplete data can lead to inaccurate affinity measures, resulting in degraded clustering performance. To address these issues, we propose an imputation-free framework with two novel approaches to improve spectral clustering on incomplete data. Firstly, we introduce a new kernel correction method that enhances the quality of the kernel matrix estimated on incomplete data with a theoretical guarantee, benefiting classical spectral clustering on pre-defined kernels. Secondly, we develop a series of affinity learning methods that equip the self-expressive framework with $\ell_p$-norm to construct an intrinsic affinity matrix with an adaptive extension. Our methods outperform existing data imputation and distance calibration techniques on benchmark datasets, offering a promising solution to spectral clustering on incomplete data in various real-world applications.

Inverse optimal control can be used to characterize behavior in sequential decision-making tasks. Most existing work, however, is limited to fully observable or linear systems, or requires the action signals to be known. Here, we introduce a probabilistic approach to inverse optimal control for partially observable stochastic non-linear systems with unobserved action signals, which unifies previous approaches to inverse optimal control with maximum causal entropy formulations. Using an explicit model of the noise characteristics of the sensory and motor systems of the agent in conjunction with local linearization techniques, we derive an approximate likelihood function for the model parameters, which can be computed within a single forward pass. We present quantitative evaluations on stochastic and partially observable versions of two classic control tasks and two human behavioral tasks. Importantly, we show that our method can disentangle perceptual factors and behavioral costs despite the fact that epistemic and pragmatic actions are intertwined in sequential decision-making under uncertainty, such as in active sensing and active learning. The proposed method has broad applicability, ranging from imitation learning to sensorimotor neuroscience.

Deep neural networks are notorious for defying theoretical treatment. However, when the number of parameters in each layer tends to infinity, the network function is a Gaussian process (GP) and quantitatively predictive description is possible. Gaussian approximation allows one to formulate criteria for selecting hyperparameters, such as variances of weights and biases, as well as the learning rate. These criteria rely on the notion of criticality defined for deep neural networks. In this work we describe a new practical way to diagnose criticality. We introduce *partial Jacobians* of a network, defined as derivatives of preactivations in layer $l$ with respect to preactivations in layer $l_0\leq l$. We derive recurrence relations for the norms of partial Jacobians and utilize these relations to analyze criticality of deep fully connected neural networks with LayerNorm and/or residual connections. We derive and implement a simple and cheap numerical test that allows one to select optimal initialization for a broad class of deep neural networks; containing fully connected, convolutional and normalization layers. Using these tools we show quantitatively that proper stacking of the LayerNorm (applied to preactivations) and residual connections leads to an architecture that is critical for any initialization. Finally, we apply our methods to analyze ResNet and MLP-Mixer architectures; demonstrating the everywhere-critical regime.

While Gaussian processes are a mainstay for various engineering and scientific applications, the uncertainty estimates don't satisfy frequentist guarantees and can be miscalibrated in practice. State-of-the-art approaches for designing calibrated models rely on inflating the Gaussian process posterior variance, which yields confidence intervals that are potentially too coarse. To remedy this, we present a calibration approach that generates predictive quantiles using a computation inspired by the vanilla Gaussian process posterior variance but using a different set of hyperparameters chosen to satisfy an empirical calibration constraint. This results in a calibration approach that is considerably more flexible than existing approaches, which we optimize to yield tight predictive quantiles. Our approach is shown to yield a calibrated model under reasonable assumptions. Furthermore, it outperforms existing approaches in sharpness when employed for calibrated regression.

Naturalistic stimuli evoke complex neural responses with spatial and temporal properties that differ across individuals. Current alignment methods focus on either spatial hyperalignment (assuming exact temporal correspondence) or temporal alignment (assuming exact spatial correspondence). Here, we propose a hybrid model, the Hyper-HMM, that simultaneously aligns both temporal and spatial features across brains. The model learns to linearly project voxels to a reduced-dimension latent space, in which timecourses are segmented into corresponding temporal events. This approach allows tracking of each individual's mental trajectory through an event sequence, and also allows for alignment with other feature spaces such as stimulus content. Using an fMRI dataset in which students watch videos of class lectures, we demonstrate that the Hyper-HMM can be used to map all participants and the semantic content of the videos into a common low-dimensional space, and that these mappings generalize to held-out data. Our model provides a new window into individual cognitive dynamics evoked by complex naturalistic stimuli.

We introduce GAUCHE, an open-source library for GAUssian processes in CHEmistry. Gaussian processes have long been a cornerstone of probabilistic machine learning, affording particular advantages for uncertainty quantification and Bayesian optimisation. Extending Gaussian processes to molecular representations, however, necessitates kernels defined over structured inputs such as graphs, strings and bit vectors. By providing such kernels in a modular, robust and easy-to-use framework, we seek to enable expert chemists and materials scientists to make use of state-of-the-art black-box optimization techniques. Motivated by scenarios frequently encountered in practice, we showcase applications for GAUCHE in molecular discovery, chemical reaction optimisation and protein design. The codebase is made available at https://github.com/leojklarner/gauche.

Neurons in early sensory areas rapidly adapt to changing sensory statistics, both by normalizing the variance of their individual responses and by reducing correlations between their responses. Together, these transformations may be viewed as an adaptive form of statistical whitening. Existing mechanistic models of adaptive whitening exclusively use either synaptic plasticity or gain modulation as the biological substrate for adaptation; however, on their own, each of these models has significant limitations. In this work, we unify these approaches in a normative multi-timescale mechanistic model that adaptively whitens its responses with complementary computational roles for synaptic plasticity and gain modulation. Gains are modified on a fast timescale to adapt to the current statistical context, whereas synapses are modified on a slow timescale to match structural properties of the input statistics that are invariant across contexts. Our model is derived from a novel multi-timescale whitening objective that factorizes the inverse whitening matrix into basis vectors, which correspond to synaptic weights, and a diagonal matrix, which corresponds to neuronal gains. We test our model on synthetic and natural datasets and find that the synapses learn optimal configurations over long timescales that enable adaptive whitening on short timescales using gain modulation.

Self-consistent Field (SCF) equation is a type of nonlinear eigenvalue problem in which the matrix to be eigen-decomposed is a function of its own eigenvectors. It is of great significance in computational science for its connection to the Schrödinger equation. Traditional fixed-point iteration methods for solving such equations suffer from non-convergence issues. In this work, we present a novel perspective on such SCF equations as a principal component analysis (PCA) for non-stationary time series, in which a distribution and its own top principal components are mutually updated over time, and the equilibrium state of the model corresponds to the solution of the SCF equations. By the new perspective, online PCA techniques are able to engage in so as to enhance the convergence of the model towards the equilibrium state, acting as a new set of tools for converging the SCF equations. With several numerical adaptations, we then develop a new algorithm for converging the SCF equation, and demonstrated its high convergence capacity with experiments on both synthesized and real electronic structure scenarios.

This paper presents a comprehensive and quality collection of functional human brain network data for potential research in the intersection of neuroscience, machine learning, and graph analytics. Anatomical and functional MRI images have been used to understand the functional connectivity of the human brain and are particularly important in identifying underlying neurodegenerative conditions such as Alzheimer's, Parkinson's, and Autism. Recently, the study of the brain in the form of brain networks using machine learning and graph analytics has become increasingly popular, especially to predict the early onset of these conditions. A brain network, represented as a graph, retains rich structural and positional information that traditional examination methods are unable to capture. However, the lack of publicly accessible brain network data prevents researchers from data-driven explorations. One of the main difficulties lies in the complicated domain-specific preprocessing steps and the exhaustive computation required to convert the data from MRI images into brain networks. We bridge this gap by collecting a large amount of MRI images from public databases and a private source, working with domain experts to make sensible design choices, and preprocessing the MRI images to produce a collection of brain network datasets. The datasets originate from 6 different sources, cover 4 brain conditions, and consist of a total of 2,702 subjects. We test our graph datasets on 12 machine learning models to provide baselines and validate the data quality on a recent graph analysis model. To lower the barrier to entry and promote the research in this interdisciplinary field, we release our brain network data and complete preprocessing details including codes at https://doi.org/10.17608/k6.auckland.21397377 and https://github.com/brainnetuoa/data_driven_network_neuroscience.

Recent work has revealed many intriguing empirical phenomena in neural network training, despite the poorly understood and highly complex loss landscapes and training dynamics. One of these phenomena, Linear Mode Connectivity (LMC), has gained considerable attention due to the intriguing observation that different solutions can be connected by a linear path in the parameter space while maintaining near-constant training and test losses. In this work, we introduce a stronger notion of linear connectivity, Layerwise Linear Feature Connectivity (LLFC), which says that the feature maps of every layer in different trained networks are also linearly connected. We provide comprehensive empirical evidence for LLFC across a wide range of settings, demonstrating that whenever two trained networks satisfy LMC (via either spawning or permutation methods), they also satisfy LLFC in nearly all the layers. Furthermore, we delve deeper into the underlying factors contributing to LLFC, which reveal new insights into the permutation approaches. The study of LLFC transcends and advances our understanding of LMC by adopting a feature-learning perspective.

We study a novel variant of the parameterized bandits problem in which the learner can observe additional auxiliary feedback that is correlated with the observed reward. The auxiliary feedback is readily available in many real-life applications, e.g., an online platform that wants to recommend the best-rated services to its users can observe the user's rating of service (rewards) and collect additional information like service delivery time (auxiliary feedback). In this paper, we first develop a method that exploits auxiliary feedback to build a reward estimator with tight confidence bounds, leading to a smaller regret. We then characterize the regret reduction in terms of the correlation coefficient between reward and its auxiliary feedback. Experimental results in different settings also verify the performance gain achieved by our proposed method.

Modern recording techniques now allow us to record from distinct neuronal populations in different brain networks. However, especially as we consider multiple (more than two) populations, new conceptual and statistical frameworks are needed to characterize the multi-dimensional, concurrent flow of signals among these populations. Here, we develop a dimensionality reduction framework that determines (1) the subset of populations described by each latent dimension, (2) the direction of signal flow among those populations, and (3) how those signals evolve over time within and across experimental trials. We illustrate these features in simulation, and further validate the method by applying it to previously studied recordings from neuronal populations in macaque visual areas V1 and V2. Then we study interactions across select laminar compartments of areas V1, V2, and V3d, recorded simultaneously with multiple Neuropixels probes. Our approach uncovered signatures of selective communication across these three areas that related to their retinotopic alignment. This work advances the study of concurrent signaling across multiple neuronal populations.

Innovation is a major driver of economic and social development, and information about many kinds of innovation is embedded in semi-structured data from patents and patent applications. Though the impact and novelty of innovations expressed in patent data are difficult to measure through traditional means, machine learning offers a promising set of techniques for evaluating novelty, summarizing contributions, and embedding semantics. In this paper, we introduce the Harvard USPTO Patent Dataset (HUPD), a large-scale, well-structured, and multi-purpose corpus of English-language patent applications filed to the United States Patent and Trademark Office (USPTO) between 2004 and 2018. With more than 4.5 million patent documents, HUPD is two to three times larger than comparable corpora. Unlike other NLP patent datasets, HUPD contains the inventor-submitted versions of patent applications, not the final versions of granted patents, allowing us to study patentability at the time of filing using NLP methods for the first time. It is also novel in its inclusion of rich structured data alongside the text of patent filings: By providing each application’s metadata along with all of its text fields, HUPD enables researchers to perform new sets of NLP tasks that leverage variation in structured covariates. As a case study on the types of research HUPD makes possible, we introduce a new task to the NLP community -- patent acceptance prediction. We additionally show the structured metadata provided in HUPD allows us to conduct explicit studies of concept shifts for this task. We find that performance on patent acceptance prediction decays when models trained in one context are evaluated on different innovation categories and over time. Finally, we demonstrate how HUPD can be used for three additional tasks: Multi-class classification of patent subject areas, language modeling, and abstractive summarization. Put together, our publicly-available dataset aims to advance research extending language and classification models to diverse and dynamic real-world data distributions.

Visual motion processing is essential for humans to perceive and interact with dynamic environments. Despite extensive research in cognitive neuroscience, image-computable models that can extract informative motion flow from natural scenes in a manner consistent with human visual processing have yet to be established. Meanwhile, recent advancements in computer vision (CV), propelled by deep learning, have led to significant progress in optical flow estimation, a task closely related to motion perception. Here we propose an image-computable model of human motion perception by bridging the gap between biological and CV models. Specifically, we introduce a novel two-stages approach that combines trainable motion energy sensing with a recurrent self-attention network for adaptive motion integration and segregation. This model architecture aims to capture the computations in V1-MT, the core structure for motion perception in the biological visual system, while providing the ability to derive informative motion flow for a wide range of stimuli, including complex natural scenes. In silico neurophysiology reveals that our model's unit responses are similar to mammalian neural recordings regarding motion pooling and speed tuning. The proposed model can also replicate human responses to a range of stimuli examined in past psychophysical studies. The experimental results on the Sintel benchmark demonstrate that our model predicts human responses better than the ground truth, whereas the state-of-the-art CV models show the opposite. Our study provides a computational architecture consistent with human visual motion processing, although the physiological correspondence may not be exact.

A popular heuristic method for improving clustering results is to apply dimensionality reduction before running clustering algorithms. It has been observed that spectral-based dimensionality reduction tools, such as PCA or SVD, improve the performance of clustering algorithms in many applications. This phenomenon indicates that spectral method not only serves as a dimensionality reduction tool, but also contributes to the clustering procedure in some sense. It is an interesting question to understand the behavior of spectral steps in clustering problems. As an initial step in this direction, this paper studies the power of vanilla-SVD algorithm in the stochastic block model (SBM). We show that, in the symmetric setting, vanilla-SVD algorithm recovers all clusters correctly. This result answers an open question posed by Van Vu (Combinatorics Probability and Computing, 2018) in the symmetric setting.

Computerized adaptive testing (CAT), as a tool that can efficiently measure student's ability, has been widely used in various standardized tests (e.g., GMAT and GRE). The adaptivity of CAT refers to the selection of the most informative questions for each student, reducing test length. Existing CAT methods do not explicitly target ability estimation accuracy since there is no student's true ability as ground truth; therefore, these methods cannot be guaranteed to make the estimate converge to the true with such limited responses. In this paper, we analyze the statistical properties of estimation and find a theoretical approximation of the true ability: the ability estimated by full responses to question bank. Based on this, a Bounded Ability Estimation framework for CAT (BECAT) is proposed in a data-summary manner, which selects a question subset that closely matches the gradient of the full responses. Thus, we develop an expected gradient difference approximation to design a simple greedy selection algorithm, and show the rigorous theoretical and error upper-bound guarantees of its ability estimate. Experiments on both real-world and synthetic datasets, show that it can reach the same estimation accuracy using 15\% less questions on average, significantly reducing test length.

How does a single interconnected neural population perform multiple tasks, each with its own dynamical requirements? The relation between task requirements and neural dynamics in Recurrent Neural Networks (RNNs) has been investigated for single tasks. The forces shaping joint dynamics of multiple tasks, however, are largely unexplored. In this work, we first construct a systematic framework to study multiple tasks in RNNs, minimizing interference from input and output correlations with the hidden representation. This allows us to reveal how RNNs tend to share attractors and reuse dynamics, a tendency we define as the "simplicity bias". We find that RNNs develop attractors sequentially during training, preferentially reusing existing dynamics and opting for simple solutions when possible. This sequenced emergence and preferential reuse encapsulate the simplicity bias. Through concrete examples, we demonstrate that new attractors primarily emerge due to task demands or architectural constraints, illustrating a balance between simplicity bias and external factors. We examine the geometry of joint representations within a single attractor, by constructing a family of tasks from a set of functions. We show that the steepness of the associated functions controls their alignment within the attractor. This arrangement again highlights the simplicity bias, as points with similar input spacings undergo comparable transformations to reach the shared attractor. Our findings propose compelling applications. The geometry of shared attractors might allow us to infer the nature of unknown tasks. Furthermore, the simplicity bias implies that without specific incentives, modularity in RNNs may not spontaneously emerge, providing insights into the conditions required for network specialization.

Multimodal fusion has become an important research technique in neuroscience that completes downstream tasks by extracting complementary information from multiple modalities. Existing multimodal research on brain networks mainly focuses on two modalities, structural connectivity (SC) and functional connectivity (FC). Recently, extensive literature has shown that the relationship between SC and FC is complex and not a simple one-to-one mapping. The coupling of structure and function at the regional level is heterogeneous. However, all previous studies have neglected the modal regional heterogeneity between SC and FC and fused their representations via "simple patterns", which are inefficient ways of multimodal fusion and affect the overall performance of the model. In this paper, to alleviate the issue of regional heterogeneity of multimodal brain networks, we propose a novel Regional Heterogeneous multimodal Brain networks Fusion Strategy (RH-BrainFS). Briefly, we introduce a brain subgraph networks module to extract regional characteristics of brain networks, and further use a new transformer-based fusion bottleneck module to alleviate the issue of regional heterogeneity between SC and FC. To the best of our knowledge, this is the first paper to explicitly state the issue of structural-functional modal regional heterogeneity and to propose a solution. Extensive experiments demonstrate that the proposed method outperforms several state-of-the-art methods in a variety of neuroscience tasks.