In the realm of interpretability and out-of-distribution generalisation, the identifiability of latent variable models has emerged as a captivating field of inquiry. In this work, we delve into the identifiability of Switching Dynamical Systems, taking an initial stride toward extending identifiability analysis to sequential latent variable models. We first prove the identifiability of Markov Switching Models, which commonly serve as the prior distribution for the continuous latent variables in Switching Dynamical Systems. We present identification conditions for first-order Markov dependency structures, whose transition distribution is parametrised via non-linear Gaussians. We then establish the identifiability of the latent variables and non-linear mappings in Switching Dynamical Systems up to affine transformations, by leveraging identifiability analysis techniques from identifiable deep latent variable models. We finally develop estimation algorithms for identifiable Switching Dynamical Systems. Throughout empirical studies, we demonstrate the practicality of identifiable Switching Dynamical Systems for segmenting high-dimensional time series such as videos, and showcase the use of identifiable Markov Switching Models for regime-dependent causal discovery in climate data.

Molecular dynamics (MD) simulation is a widely used technique to simulate molecular systems, most commonly at the all-atom resolution where equations of motion are integrated with timesteps on the order of femtoseconds ($1\textrm{fs}=10^{-15}\textrm{s}$). MD is often used to compute equilibrium properties, which requires sampling from an equilibrium distribution such as the Boltzmann distribution. However, many important processes, such as binding and folding, occur over timescales of milliseconds or beyond, and cannot be efficiently sampled with conventional MD. Furthermore, new MD simulations need to be performed for each molecular system studied. We present Timewarp, an enhanced sampling method which uses a normalising flow as a proposal distribution in a Markov chain Monte Carlo method targeting the Boltzmann distribution. The flow is trained offline on MD trajectories and learns to make large steps in time, simulating the molecular dynamics of $10^{5} - 10^{6}\:\textrm{fs}$. Crucially, Timewarp is transferable between molecular systems: once trained, we show that it generalises to unseen small peptides (2-4 amino acids) at all-atom resolution, exploring their metastable states and providing wall-clock acceleration of sampling compared to standard MD. Our method constitutes an important step towards general, transferable algorithms for accelerating MD.

Protein-nucleic acid interactions play a very important role in a variety of biological activities. Accurate identification of nucleic acid-binding residues is a critical step in understanding the interaction mechanisms. Although many computationally based methods have been developed to predict nucleic acid-binding residues, challenges remain. In this study, a fast and accurate sequence-based method, called ESM-NBR, is proposed. In ESM-NBR, we first use the large protein language model ESM2 to extract discriminative biological properties feature representation from protein primary sequences; then, a multi-task deep learning model composed of stacked bidirectional long short-term memory (BiLSTM) and multi-layer perceptron (MLP) networks is employed to explore common and private information of DNA- and RNA-binding residues with ESM2 feature as input. Experimental results on benchmark data sets demonstrate that the prediction performance of ESM2 feature representation comprehensively outperforms evolutionary information-based hidden Markov model (HMM) features. Meanwhile, the ESM-NBR obtains the MCC values for DNA-binding residues prediction of 0.427 and 0.391 on two independent test sets, which are 18.61 and 10.45% higher than those of the second-best methods, respectively. Moreover, by completely discarding the time-cost multiple sequence alignment process, the prediction speed of ESM-NBR far exceeds that of existing methods (5.52s for a protein sequence of length 500, which is about 16 times faster than the second-fastest method). A user-friendly standalone package and the data of ESM-NBR are freely available for academic use at: https://github.com/wwzll123/ESM-NBR.

Robots operating in an open world will encounter novel objects with unknown physical properties, such as mass, friction, or size. These robots will need to sense these properties through interaction prior to performing downstream tasks with the objects. We propose a method that autonomously learns tactile exploration policies by developing a generative world model that is leveraged to 1) estimate the object's physical parameters using a differentiable Bayesian filtering algorithm and 2) develop an exploration policy using an information-gathering model predictive controller. We evaluate our method on three simulated tasks where the goal is to estimate a desired object property (mass, height or toppling height) through physical interaction. We find that our method is able to discover policies that efficiently gather information about the desired property in an intuitive manner. Finally, we validate our method on a real robot system for the height estimation task, where our method is able to successfully learn and execute an information-gathering policy from scratch.

To ensure the usefulness of Reinforcement Learning (RL) in real systems, it is crucial to ensure they are robust to noise and adversarial attacks. In adversarial RL, an external attacker has the power to manipulate the victim agent's interaction with the environment. We study the full class of online manipulation attacks, which include (i) state attacks, (ii) observation attacks (which are a generalization of perceived-state attacks), (iii) action attacks, and (iv) reward attacks. We show the attacker's problem of designing a stealthy attack that maximizes its own expected reward, which often corresponds to minimizing the victim's value, is captured by a Markov Decision Process (MDP) that we call a meta-MDP since it is not the true environment but a higher level environment induced by the attacked interaction. We show that the attacker can derive optimal attacks by planning in polynomial time or learning with polynomial sample complexity using standard RL techniques. We argue that the optimal defense policy for the victim can be computed as the solution to a stochastic Stackelberg game, which can be further simplified into a partially-observable turn-based stochastic game (POTBSG). Neither the attacker nor the victim would benefit from deviating from their respective optimal policies, thus such solutions are truly robust. Although the defense problem is NP-hard, we show that optimal Markovian defenses can be computed (learned) in polynomial time (sample complexity) in many scenarios.

In this paper, we address the problem of detecting anomalies among a given set of binary processes via learning-based controlled sensing. Each process is parameterized by a binary random variable indicating whether the process is anomalous. To identify the anomalies, the decision-making agent is allowed to observe a subset of the processes at each time instant. Also, probing each process has an associated cost. Our objective is to design a sequential selection policy that dynamically determines which processes to observe at each time with the goal to minimize the delay in making the decision and the total sensing cost. We cast this problem as a sequential hypothesis testing problem within the framework of Markov decision processes. This formulation utilizes both a Bayesian log-likelihood ratio-based reward and an entropy-based reward. The problem is then solved using two approaches: 1) a deep reinforcement learning-based approach where we design both deep Q-learning and policy gradient actor-critic algorithms; and 2) a deep active inference-based approach. Using numerical experiments, we demonstrate the efficacy of our algorithms and show that our algorithms adapt to any unknown statistical dependence pattern of the processes.

Imitation Learning (IL) holds great promise for enabling agile locomotion in embodied agents. However, many existing locomotion benchmarks primarily focus on simplified toy tasks, often failing to capture the complexity of real-world scenarios and steering research toward unrealistic domains. To advance research in IL for locomotion, we present a novel benchmark designed to facilitate rigorous evaluation and comparison of IL algorithms. This benchmark encompasses a diverse set of environments, including quadrupeds, bipeds, and musculoskeletal human models, each accompanied by comprehensive datasets, such as real noisy motion capture data, ground truth expert data, and ground truth sub-optimal data, enabling evaluation across a spectrum of difficulty levels. To increase the robustness of learned agents, we provide an easy interface for dynamics randomization and offer a wide range of partially observable tasks to train agents across different embodiments. Finally, we provide handcrafted metrics for each task and ship our benchmark with state-of-the-art baseline algorithms to ease evaluation and enable fast benchmarking.

It is widely known that Boltzmann machines are capable of representing arbitrary probability distributions over the values of their visible neurons, given enough hidden ones. However, sampling -- and thus training -- these models can be numerically hard. Recently we proposed a regularisation of the connections of Boltzmann machines, in order to control the energy landscape of the model, paving a way for efficient sampling and training. Here we formally prove that such regularised Boltzmann machines preserve the ability to represent arbitrary distributions. This is in conjunction with controlling the number of energy local minima, thus enabling easy \emph{guided} sampling and training. Furthermore, we explicitly show that regularised Boltzmann machines can store exponentially many arbitrarily correlated visible patterns with perfect retrieval, and we connect them to the Dense Associative Memory networks.

Many machine learning tasks can be solved by minimizing a convex function of an occupancy measure over the policies that generate them. These include reinforcement learning, imitation learning, among others. This more general paradigm is called the Concave Utility Reinforcement Learning problem (CURL). Since CURL invalidates classical Bellman equations, it requires new algorithms. We introduce MD-CURL, a new algorithm for CURL in a finite horizon Markov decision process. MD-CURL is inspired by mirror descent and uses a non-standard regularization to achieve convergence guarantees and a simple closed-form solution, eliminating the need for computationally expensive projection steps typically found in mirror descent approaches. We then extend CURL to an online learning scenario and present Greedy MD-CURL, a new method adapting MD-CURL to an online, episode-based setting with partially unknown dynamics. Like MD-CURL, the online version Greedy MD-CURL benefits from low computational complexity, while guaranteeing sub-linear or even logarithmic regret, depending on the level of information available on the underlying dynamics.

In this paper, we propose a policy gradient method for confounded partially observable Markov decision processes (POMDPs) with continuous state and observation spaces in the offline setting. We first establish a novel identification result to non-parametrically estimate any history-dependent policy gradient under POMDPs using the offline data. The identification enables us to solve a sequence of conditional moment restrictions and adopt the min-max learning procedure with general function approximation for estimating the policy gradient. We then provide a finite-sample non-asymptotic bound for estimating the gradient uniformly over a pre-specified policy class in terms of the sample size, length of horizon, concentratability coefficient and the measure of ill-posedness in solving the conditional moment restrictions. Lastly, by deploying the proposed gradient estimation in the gradient ascent algorithm, we show the global convergence of the proposed algorithm in finding the history-dependent optimal policy under some technical conditions. To the best of our knowledge, this is the first work studying the policy gradient method for POMDPs under the offline setting.