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.

Our work presents a novel approach to shape optimization, with the twofold objective to improve the efficiency of global optimization algorithms while promoting the generation of high-quality designs during the optimization process free of geometrical anomalies. This is accomplished by reducing the number of the original design variables defining a new reduced subspace where the geometrical variance is maximized and modeling the underlying generative process of the data via probabilistic linear latent variable models such as factor analysis and probabilistic principal component analysis. We show that the data follows approximately a Gaussian distribution when the shape modification method is linear and the design variables are sampled uniformly at random, due to the direct application of the central limit theorem. The degree of anomalousness is measured in terms of Mahalanobis distance, and the paper demonstrates that abnormal designs tend to exhibit a high value of this metric. This enables the definition of a new optimization model where anomalous geometries are penalized and consequently avoided during the optimization loop. The procedure is demonstrated for hull shape optimization of the DTMB 5415 model, extensively used as an international benchmark for shape optimization problems. The global optimization routine is carried out using Bayesian optimization and the DIRECT algorithm. From the numerical results, the new framework improves the convergence of global optimization algorithms, while only designs with high-quality geometrical features are generated through the optimization routine thereby avoiding the wastage of precious computationally expensive simulations.

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.

Artificial intelligence (AI) technology has become increasingly prevalent and transforms our everyday life. One important application of AI technology is the development of autonomous vehicles (AV). However, the reliability of an AV needs to be carefully demonstrated via an assurance test so that the product can be used with confidence in the field. To plan for an assurance test, one needs to determine how many AVs need to be tested for how many miles and the standard for passing the test. Existing research has made great efforts in developing reliability demonstration tests in the other fields of applications for product development and assessment. However, statistical methods have not been utilized in AV test planning. This paper aims to fill in this gap by developing statistical methods for planning AV reliability assurance tests based on recurrent events data. We explore the relationship between multiple criteria of interest in the context of planning AV reliability assurance tests. Specifically, we develop two test planning strategies based on homogeneous and non-homogeneous Poisson processes while balancing multiple objectives with the Pareto front approach. We also offer recommendations for practical use. The disengagement events data from the California Department of Motor Vehicles AV testing program is used to illustrate the proposed assurance test planning methods.

Next-generation radio interferometers like the Square Kilometer Array have the potential to unlock scientific discoveries thanks to their unprecedented angular resolution and sensitivity. One key to unlocking their potential resides in handling the deluge and complexity of incoming data. This challenge requires building radio interferometric imaging methods that can cope with the massive data sizes and provide high-quality image reconstructions with uncertainty quantification (UQ). This work proposes a method coined QuantifAI to address UQ in radio-interferometric imaging with data-driven (learned) priors for high-dimensional settings. Our model, rooted in the Bayesian framework, uses a physically motivated model for the likelihood. The model exploits a data-driven convex prior, which can encode complex information learned implicitly from simulations and guarantee the log-concavity of the posterior. We leverage probability concentration phenomena of high-dimensional log-concave posteriors that let us obtain information about the posterior, avoiding MCMC sampling techniques. We rely on convex optimisation methods to compute the MAP estimation, which is known to be faster and better scale with dimension than MCMC sampling strategies. Our method allows us to compute local credible intervals, i.e., Bayesian error bars, and perform hypothesis testing of structure on the reconstructed image. In addition, we propose a novel blazing-fast method to compute pixel-wise uncertainties at different scales. We demonstrate our method by reconstructing radio-interferometric images in a simulated setting and carrying out fast and scalable UQ, which we validate with MCMC sampling. Our method shows an improved image quality and more meaningful uncertainties than the benchmark method based on a sparsity-promoting prior. QuantifAI's source code: https://github.com/astro-informatics/QuantifAI.

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.

Human behavior is inherently hierarchical, resulting from the decomposition of a task into subtasks or an abstract action into concrete actions. However, behavior is typically measured as a sequence of actions, which makes it difficult to infer its hierarchical structure. In this paper, we explore how people form hierarchically-structured plans, using an experimental paradigm that makes hierarchical representations observable: participants create programs that produce sequences of actions in a language with explicit hierarchical structure. This task lets us test two well-established principles of human behavior: utility maximization (i.e. using fewer actions) and minimum description length (MDL; i.e. having a shorter program). We find that humans are sensitive to both metrics, but that both accounts fail to predict a qualitative feature of human-created programs, namely that people prefer programs with reuse over and above the predictions of MDL. We formalize this preference for reuse by extending the MDL account into a generative model over programs, modeling hierarchy choice as the induction of a grammar over actions. Our account can explain the preference for reuse and provides the best prediction of human behavior, going beyond simple accounts of compressibility to highlight a principle that guides hierarchical planning.

Unlearnable datasets lead to a drastic drop in the generalization performance of models trained on them by introducing elaborate and imperceptible perturbations into clean training sets. Many existing defenses, e.g., JPEG compression and adversarial training, effectively counter UDs based on norm-constrained additive noise. However, a fire-new type of convolution-based UDs have been proposed and render existing defenses all ineffective, presenting a greater challenge to defenders. To address this, we express the convolution-based unlearnable sample as the result of multiplying a matrix by a clean sample in a simplified scenario, and formalize the intra-class matrix inconsistency as $\Theta_{imi}$, inter-class matrix consistency as $\Theta_{imc}$ to investigate the working mechanism of the convolution-based UDs. We conjecture that increasing both of these metrics will mitigate the unlearnability effect. Through validation experiments that commendably support our hypothesis, we further design a random matrix to boost both $\Theta_{imi}$ and $\Theta_{imc}$, achieving a notable degree of defense effect. Hence, by building upon and extending these facts, we first propose a brand-new image COrruption that employs randomly multiplicative transformation via INterpolation operation to successfully defend against convolution-based UDs. Our approach leverages global pixel random interpolations, effectively suppressing the impact of multiplicative noise in convolution-based UDs. Additionally, we have also designed two new forms of convolution-based UDs, and find that our defense is the most effective against them.