QuantFormer: Learning to Quantize for Neural Activity Forecasting in Mouse Visual Cortex

Understanding complex animal behaviors hinges on deciphering the neural activity patterns within brain circuits, making the ability to forecast neural activity crucial for developing predictive models of brain dynamics. This capability holds immense value for neuroscience, particularly in applications such as real-time optogenetic interventions. While traditional encoding and decoding methods have been used to map external variables to neural activity and vice versa, they focus on interpreting past data. In contrast, neural forecasting aims to predict future neural activity, presenting a unique and challenging task due to the spatiotemporal sparsity and complex dependencies of neural signals. Existing transformer-based forecasting methods, while effective in many domains, struggle to capture the distinctiveness of neural signals characterized by spatiotemporal sparsity and intricate dependencies. To address this challenge, we here introduce QuantFormer, a transformer-based model specifically designed for forecasting neural activity from two-photon calcium imaging data. Unlike conventional regression-based approaches, QuantFormerreframes the forecasting task as a classification problem via dynamic signal quantization, enabling more effective learning of sparse neural activation patterns. Additionally, QuantFormer tackles the challenge of analyzing multivariate signals from an arbitrary number of neurons by incorporating neuron-specific tokens, allowing scalability across diverse neuronal populations. Trained with unsupervised quantization on the Allen dataset, QuantFormer sets a new benchmark in forecasting mouse visual cortex activity. It demonstrates robust performance and generalization across various stimuli and individuals, paving the way for a foundational model in neural signal prediction.

Unlocking State-Tracking in Linear RNNs Through Negative Eigenvalues

Linear Recurrent Neural Networks (LRNNs) such as Mamba, RWKV, GLA, mLSTM, and DeltaNet have emerged as efficient alternatives to Transformers in large language modeling, offering linear scaling with sequence length and improved training efficiency. However, LRNNs struggle to perform state-tracking which may impair performance in tasks such as code evaluation or tracking a chess game. Even parity, the simplest state-tracking task, which non-linear RNNs like LSTM handle effectively, cannot be solved by current LRNNs. Recently, Sarrof et al. (2024) demonstrated that the failure of LRNNs like Mamba to solve parity stems from restricting the value range of their diagonal state-transition matrices to $[0, 1]$ and that incorporating negative values can resolve this issue. We extend this result to non-diagonal LRNNs, which have recently shown promise in models such as DeltaNet. We prove that finite precision LRNNs with state-transition matrices having only positive eigenvalues cannot solve parity, while complex eigenvalues are needed to count modulo $3$. Notably, we also prove that LRNNs can learn any regular language when their state-transition matrices are products of identity minus vector outer product matrices, each with eigenvalues in the range $[-1, 1]$. Our empirical results confirm that extending the eigenvalue range of models like Mamba and DeltaNet to include negative values not only enables them to solve parity but consistently improves their performance on state-tracking tasks. Furthermore, pre-training LRNNs with an extended eigenvalue range for language modeling achieves comparable performance and stability while showing promise on code and math data. Our work enhances the expressivity of modern LRNNs, broadening their applicability without changing the cost of training or inference.

Hyperparameter Optimization in Machine Learning

Hyperparameters are configuration variables controlling the behavior of machine learning algorithms. They are ubiquitous in machine learning and artificial intelligence and the choice of their values determine the effectiveness of systems based on these technologies. Manual hyperparameter search is often unsatisfactory and becomes unfeasible when the number of hyperparameters is large. Automating the search is an important step towards automating machine learning, freeing researchers and practitioners alike from the burden of finding a good set of hyperparameters by trial and error. In this survey, we present a unified treatment of hyperparameter optimization, providing the reader with examples and insights into the state-of-the-art. We cover the main families of techniques to automate hyperparameter search, often referred to as hyperparameter optimization or tuning, including random and quasi-random search, bandit-, model- and gradient- based approaches. We further discuss extensions, including online, constrained, and multi-objective formulations, touch upon connections with other fields such as meta-learning and neural architecture search, and conclude with open questions and future research directions.

Laplace Transform Based Low-Complexity Learning of Continuous Markov Semigroups

Markov processes serve as a universal model for many real-world random processes. This paper presents a data-driven approach for learning these models through the spectral decomposition of the infinitesimal generator (IG) of the Markov semigroup. The unbounded nature of IGs complicates traditional methods such as vector-valued regression and Hilbert-Schmidt operator analysis. Existing techniques, including physics-informed kernel regression, are computationally expensive and limited in scope, with no recovery guarantees for transfer operator methods when the time-lag is small. We propose a novel method that leverages the IG's resolvent, characterized by the Laplace transform of transfer operators. This approach is robust to time-lag variations, ensuring accurate eigenvalue learning even for small time-lags. Our statistical analysis applies to a broader class of Markov processes than current methods while reducing computational complexity from quadratic to linear in the state dimension. Finally, we illustrate the behaviour of our method in two experiments.

Adaptive AI-Driven Material Synthesis: Towards Autonomous 2D Materials Growth

Two-dimensional (2D) materials are poised to revolutionize current solid-state technology with their extraordinary properties. Yet, the primary challenge remains their scalable production. While there have been significant advancements, much of the scientific progress has depended on the exfoliation of materials, a method that poses severe challenges for large-scale applications. With the advent of artificial intelligence (AI) in materials science, innovative synthesis methodologies are now on the horizon. This study explores the forefront of autonomous materials synthesis using an artificial neural network (ANN) trained by evolutionary methods, focusing on the efficient production of graphene. Our approach demonstrates that a neural network can iteratively and autonomously learn a time-dependent protocol for the efficient growth of graphene, without requiring pretraining on what constitutes an effective recipe. Evaluation criteria are based on the proximity of the Raman signature to that of monolayer graphene: higher scores are granted to outcomes whose spectrum more closely resembles that of an ideal continuous monolayer structure. This feedback mechanism allows for iterative refinement of the ANN's time-dependent synthesis protocols, progressively improving sample quality. Through the advancement and application of AI methodologies, this work makes a substantial contribution to the field of materials engineering, fostering a new era of innovation and efficiency in the synthesis process.

Neural Conditional Probability for Inference

We introduce NCP (Neural Conditional Probability), a novel operator-theoretic approach for learning conditional distributions with a particular focus on inference tasks. NCP can be used to build conditional confidence regions and extract important statistics like conditional quantiles, mean, and covariance. It offers streamlined learning through a single unconditional training phase, facilitating efficient inference without the need for retraining even when conditioning changes. By tapping into the powerful approximation capabilities of neural networks, our method efficiently handles a wide variety of complex probability distributions, effectively dealing with nonlinear relationships between input and output variables. Theoretical guarantees ensure both optimization consistency and statistical accuracy of the NCP method. Our experiments show that our approach matches or beats leading methods using a simple Multi-Layer Perceptron (MLP) with two hidden layers and GELU activations. This demonstrates that a minimalistic architecture with a theoretically grounded loss function can achieve competitive results without sacrificing performance, even in the face of more complex architectures.

Operator World Models for Reinforcement Learning

Policy Mirror Descent (PMD) is a powerful and theoretically sound methodology for sequential decision-making. However, it is not directly applicable to Reinforcement Learning (RL) due to the inaccessibility of explicit action-value functions. We address this challenge by introducing a novel approach based on learning a world model of the environment using conditional mean embeddings. We then leverage the operatorial formulation of RL to express the action-value function in terms of this quantity in closed form via matrix operations. Combining these estimators with PMD leads to POWR, a new RL algorithm for which we prove convergence rates to the global optimum. Preliminary experiments in finite and infinite state settings support the effectiveness of our method.

From Biased to Unbiased Dynamics: An Infinitesimal Generator Approach

We investigate learning the eigenfunctions of evolution operators for time-reversal invariant stochastic processes, a prime example being the Langevin equation used in molecular dynamics. Many physical or chemical processes described by this equation involve transitions between metastable states separated by high potential barriers that can hardly be crossed during a simulation. To overcome this bottleneck, data are collected via biased simulations that explore the state space more rapidly. We propose a framework for learning from biased simulations rooted in the infinitesimal generator of the process and the associated resolvent operator. We contrast our approach to more common ones based on the transfer operator, showing that it can provably learn the spectral properties of the unbiased system from biased data. In experiments, we highlight the advantages of our method over transfer operator approaches and recent developments based on generator learning, demonstrating its effectiveness in estimating eigenfunctions and eigenvalues. Importantly, we show that even with datasets containing only a few relevant transitions due to sub-optimal biasing, our approach recovers relevant information about the transition mechanism.

Contextual Continuum Bandits: Static Versus Dynamic Regret

We study the contextual continuum bandits problem, where the learner sequentially receives a side information vector and has to choose an action in a convex set, minimizing a function associated to the context. The goal is to minimize all the underlying functions for the received contexts, leading to a dynamic (contextual) notion of regret, which is stronger than the standard static regret. Assuming that the objective functions are H\"older with respect to the contexts, we demonstrate that any algorithm achieving a sub-linear static regret can be extended to achieve a sub-linear dynamic regret. We further study the case of strongly convex and smooth functions when the observations are noisy. Inspired by the interior point method and employing self-concordant barriers, we propose an algorithm achieving a sub-linear dynamic regret. Lastly, we present a minimax lower bound, implying two key facts. First, no algorithm can achieve sub-linear dynamic regret over functions that are not continuous with respect to the context. Second, for strongly convex and smooth functions, the algorithm that we propose achieves, up to a logarithmic factor, the minimax optimal rate of dynamic regret as a function of the number of queries.

Learning the Infinitesimal Generator of Stochastic Diffusion Processes

We address data-driven learning of the infinitesimal generator of stochastic diffusion processes, essential for understanding numerical simulations of natural and physical systems. The unbounded nature of the generator poses significant challenges, rendering conventional analysis techniques for Hilbert-Schmidt operators ineffective. To overcome this, we introduce a novel framework based on the energy functional for these stochastic processes. Our approach integrates physical priors through an energy-based risk metric in both full and partial knowledge settings. We evaluate the statistical performance of a reduced-rank estimator in reproducing kernel Hilbert spaces (RKHS) in the partial knowledge setting. Notably, our approach provides learning bounds independent of the state space dimension and ensures non-spurious spectral estimation. Additionally, we elucidate how the distortion between the intrinsic energy-induced metric of the stochastic diffusion and the RKHS metric used for generator estimation impacts the spectral learning bounds.