In this article, we propose a variational inference formulation of auto-associative memories, allowing us to combine perceptual inference and memory retrieval into the same mathematical framework. In this formulation, the prior probability distribution onto latent representations is made memory dependent, thus pulling the inference process towards previously stored representations. We then study how different neural network approaches to variational inference can be applied in this framework. We compare methods relying on amortized inference such as Variational Auto Encoders and methods relying on iterative inference such as Predictive Coding and suggest combining both approaches to design new auto-associative memory models. We evaluate the obtained algorithms on the CIFAR10 and CLEVR image datasets and compare them with other associative memory models such as Hopfield Networks, End-to-End Memory Networks and Neural Turing Machines.

For each partition of a data set into a given number of parts there is a partition such that every part is as much as possible a good model (an "algorithmic sufficient statistic") for the data in that part. Since this can be done for every number between one and the number of data, the result is a function, the cluster structure function. It maps the number of parts of a partition to values related to the deficiencies of being good models by the parts. Such a function starts with a value at least zero for no partition of the data set and descents to zero for the partition of the data set into singleton parts. The optimal clustering is the one chosen to minimize the cluster structure function. The theory behind the method is expressed in algorithmic information theory (Kolmogorov complexity). In practice the Kolmogorov complexities involved are approximated by a concrete compressor. We give examples using real data sets: the MNIST handwritten digits and the segmentation of real cells as used in stem cell research.

Interactive reinforcement learning can effectively facilitate the agent training via human feedback. However, such methods often require the human teacher to know what is the correct action that the agent should take. In other words, if the human teacher is not always reliable, then it will not be consistently able to guide the agent through its training. In this paper, we propose a more effective interactive reinforcement learning system by introducing multiple trainers, namely Multi-Trainer Interactive Reinforcement Learning (MTIRL), which could aggregate the binary feedback from multiple non-perfect trainers into a more reliable reward for an agent training in a reward-sparse environment. In particular, our trainer feedback aggregation experiments show that our aggregation method has the best accuracy when compared with the majority voting, the weighted voting, and the Bayesian method. Finally, we conduct a grid-world experiment to show that the policy trained by the MTIRL with the review model is closer to the optimal policy than that without a review model.

We propose a family of First Hitting Diffusion Models (FHDM), deep generative models that generate data with a diffusion process that terminates at a random first hitting time. This yields an extension of the standard fixed-time diffusion models that terminate at a pre-specified deterministic time. Although standard diffusion models are designed for continuous unconstrained data, FHDM is naturally designed to learn distributions on continuous as well as a range of discrete and structure domains. Moreover, FHDM enables instance-dependent terminate time and accelerates the diffusion process to sample higher quality data with fewer diffusion steps. Technically, we train FHDM by maximum likelihood estimation on diffusion trajectories augmented from observed data with conditional first hitting processes (i.e., bridge) derived based on Doob's $h$-transform, deviating from the commonly used time-reversal mechanism. We apply FHDM to generate data in various domains such as point cloud (general continuous distribution), climate and geographical events on earth (continuous distribution on the sphere), unweighted graphs (distribution of binary matrices), and segmentation maps of 2D images (high-dimensional categorical distribution). We observe considerable improvement compared with the state-of-the-art approaches in both quality and speed.

The discovery of novel inhibitor molecules for emerging drug-target proteins is widely acknowledged as a challenging inverse design problem: Exhaustive exploration of the vast chemical search space is impractical, especially when the target structure or active molecules are unknown. Here we validate experimentally the broad utility of a deep generative framework trained at-scale on protein sequences, small molecules, and their mutual interactions -- that is unbiased toward any specific target. As demonstrators, we consider two dissimilar and relevant SARS-CoV-2 targets: the main protease and the spike protein (receptor binding domain, RBD). To perform target-aware design of novel inhibitor molecules, a protein sequence-conditioned sampling on the generative foundation model is performed. Despite using only the target sequence information, and without performing any target-specific adaptation of the generative model, micromolar-level inhibition was observed in in vitro experiments for two candidates out of only four synthesized for each target. The most potent spike RBD inhibitor also exhibited activity against several variants in live virus neutralization assays. These results therefore establish that a single, broadly deployable generative foundation model for accelerated hit discovery is effective and efficient, even in the most general case where neither target structure nor binder information is available.

Nonlinear dynamics are ubiquitous in science and engineering applications, but the physics of most complex systems is far from being fully understood. Discovering interpretable governing equations from measurement data can help us understand and predict the behavior of complex dynamic systems. Although extensive work has recently been done in this field, robustly distilling explicit model forms from very sparse data with considerable noise remains intractable. Moreover, quantifying and propagating the uncertainty of the identified system from noisy data is challenging, and relevant literature is still limited. To bridge this gap, we develop a novel Bayesian spline learning framework to identify parsimonious governing equations of nonlinear (spatio)temporal dynamics from sparse, noisy data with quantified uncertainty. The proposed method utilizes spline basis to handle the data scarcity and measurement noise, upon which a group of derivatives can be accurately computed to form a library of candidate model terms. The equation residuals are used to inform the spline learning in a Bayesian manner, where approximate Bayesian uncertainty calibration techniques are employed to approximate posterior distributions of the trainable parameters. To promote the sparsity, an iterative sequential-threshold Bayesian learning approach is developed, using the alternative direction optimization strategy to systematically approximate L0 sparsity constraints. The proposed algorithm is evaluated on multiple nonlinear dynamical systems governed by canonical ordinary and partial differential equations, and the merit/superiority of the proposed method is demonstrated by comparison with state-of-the-art methods.

Regime shifts in high-dimensional time series arise naturally in many applications, from neuroimaging to finance. This problem has received considerable attention in low-dimensional settings, with both Bayesian and frequentist methods used extensively for parameter estimation. The EM algorithm is a particularly popular strategy for parameter estimation in low-dimensional settings, although the statistical properties of the resulting estimates have not been well understood. Furthermore, its extension to high-dimensional time series has proved challenging. To overcome these challenges, in this paper we propose an approximate EM algorithm for Markov-switching VAR models that leads to efficient computation and also facilitates the investigation of asymptotic properties of the resulting parameter estimates. We establish the consistency of the proposed EM algorithm in high dimensions and investigate its performance via simulation studies.

This paper presents a fast algorithm for estimating hidden states of Bayesian state space models. The algorithm is a variation of amortized simulation-based inference algorithms, where a large number of artificial datasets are generated at the first stage, and then a flexible model is trained to predict the variables of interest. In contrast to those proposed earlier, the procedure described in this paper makes it possible to train estimators for hidden states by concentrating only on certain characteristics of the marginal posterior distributions and introducing inductive bias. Illustrations using the examples of the stochastic volatility model, nonlinear dynamic stochastic general equilibrium model, and seasonal adjustment procedure with breaks in seasonality show that the algorithm has sufficient accuracy for practical use. Moreover, after pretraining, which takes several hours, finding the posterior distribution for any dataset takes from hundredths to tenths of a second.

Most PAC-Bayesian bounds hold in the batch learning setting where data is collected at once, prior to inference or prediction. This somewhat departs from many contemporary learning problems where data streams are collected and the algorithms must dynamically adjust. We prove new PAC-Bayesian bounds in this online learning framework, leveraging an updated definition of regret, and we revisit classical PAC-Bayesian results with a batch-to-online conversion, extending their remit to the case of dependent data. Our results hold for bounded losses, potentially \emph{non-convex}, paving the way to promising developments in online learning.

Data augmentation is commonly applied to improve performance of deep learning by enforcing the knowledge that certain transformations on the input preserve the output. Currently, the data augmentation parameters are chosen by human effort and costly cross-validation, which makes it cumbersome to apply to new datasets. We develop a convenient gradient-based method for selecting the data augmentation without validation data during training of a deep neural network. Our approach relies on phrasing data augmentation as an invariance in the prior distribution on the functions of a neural network, which allows us to learn it using Bayesian model selection. This has been shown to work in Gaussian processes, but not yet for deep neural networks. We propose a differentiable Kronecker-factored Laplace approximation to the marginal likelihood as our objective, which can be optimised without human supervision or validation data. We show that our method can successfully recover invariances present in the data, and that this improves generalisation and data efficiency on image datasets.