Lifelong reinforcement learning (RL) has been developed as a paradigm for extending single-task RL to more realistic, dynamic settings. In lifelong RL, the "life" of an RL agent is modeled as a stream of tasks drawn from a task distribution. We propose EPIC (\underline{E}mpirical \underline{P}AC-Bayes that \underline{I}mproves \underline{C}ontinuously), a novel algorithm designed for lifelong RL using PAC-Bayes theory. EPIC learns a shared policy distribution, referred to as the \textit{world policy}, which enables rapid adaptation to new tasks while retaining valuable knowledge from previous experiences. Our theoretical analysis establishes a relationship between the algorithm's generalization performance and the number of prior tasks preserved in memory. We also derive the sample complexity of EPIC in terms of RL regret. Extensive experiments on a variety of environments demonstrate that EPIC significantly outperforms existing methods in lifelong RL, offering both theoretical guarantees and practical efficacy through the use of the world policy.

In this work, we explore modeling change points in time-series data using neural stochastic differential equations (neural SDEs). We propose a novel model formulation and training procedure based on the variational autoencoder (VAE) framework for modeling time-series as a neural SDE. Unlike existing algorithms training neural SDEs as VAEs, our proposed algorithm only necessitates a Gaussian prior of the initial state of the latent stochastic process, rather than a Wiener process prior on the entire latent stochastic process. We develop two methodologies for modeling and estimating change points in time-series data with distribution shifts. Our iterative algorithm alternates between updating neural SDE parameters and updating the change points based on either a maximum likelihood-based approach or a change point detection algorithm using the sequential likelihood ratio test. We provide a theoretical analysis of this proposed change point detection scheme. Finally, we present an empirical evaluation that demonstrates the expressive power of our proposed model, showing that it can effectively model both classical parametric SDEs and some real datasets with distribution shifts.

Advancements in artificial intelligence (AI) have transformed many scientific fields, with microbiology and microbiome research now experiencing significant breakthroughs through machine learning and deep learning applications. This review provides a comprehensive overview of AI-driven approaches tailored for microbiology and microbiome studies, emphasizing both technical advancements and biological insights. We begin with an introduction to foundational AI techniques, including primary machine learning paradigms and various deep learning architectures, and offer guidance on choosing between machine learning and deep learning methods based on specific research goals. The primary section on application scenarios spans diverse research areas, from taxonomic profiling, functional annotation & prediction, microbe-X interactions, microbial ecology, metabolic modeling, precision nutrition, clinical microbiology, to prevention & therapeutics. Finally, we discuss challenges unique to this field, including the balance between interpretability and complexity, the "small n, large p" problem, and the critical need for standardized benchmarking datasets to validate and compare models. Together, this review underscores AI's transformative role in microbiology and microbiome research, paving the way for innovative methodologies and applications that enhance our understanding of microbial life and its impact on our planet and our health.

Real-world offline datasets are often subject to data corruptions (such as noise or adversarial attacks) due to sensor failures or malicious attacks. Despite advances in robust offline reinforcement learning (RL), existing methods struggle to learn robust agents under high uncertainty caused by the diverse corrupted data (i.e., corrupted states, actions, rewards, and dynamics), leading to performance degradation in clean environments. To tackle this problem, we propose a novel robust variational Bayesian inference for offline RL (TRACER). It introduces Bayesian inference for the first time to capture the uncertainty via offline data for robustness against all types of data corruptions. Specifically, TRACER first models all corruptions as the uncertainty in the action-value function. Then, to capture such uncertainty, it uses all offline data as the observations to approximate the posterior distribution of the action-value function under a Bayesian inference framework. An appealing feature of TRACER is that it can distinguish corrupted data from clean data using an entropy-based uncertainty measure, since corrupted data often induces higher uncertainty and entropy. Based on the aforementioned measure, TRACER can regulate the loss associated with corrupted data to reduce its influence, thereby enhancing robustness and performance in clean environments. Experiments demonstrate that TRACER significantly outperforms several state-of-the-art approaches across both individual and simultaneous data corruptions.

The applicability domain refers to the range of data for which the prediction of the predictive model is expected to be reliable and accurate and using a model outside its applicability domain can lead to incorrect results. The ability to define the regions in data space where a predictive model can be safely used is a necessary condition for having safer and more reliable predictions to assure the reliability of new predictions. However, defining the applicability domain of a model is a challenging problem, as there is no clear and universal definition or metric for it. This work aims to make the applicability domain more quantifiable and pragmatic. Eight applicability domain detection techniques were applied to seven regression models, trained on five different datasets, and their performance was benchmarked using a validation framework. We also propose a novel approach based on non-deterministic Bayesian neural networks to define the applicability domain of the model. Our method exhibited superior accuracy in defining the Applicability Domain compared to previous methods, highlighting its potential in this regard.

Otto's (2001) Wasserstein gradient flow of the exclusive KL divergence functional provides a powerful and mathematically principled perspective for analyzing learning and inference algorithms. In contrast, algorithms for the inclusive KL inference, i.e., minimizing $ \mathrm{KL}(\pi \| \mu) $ with respect to $ \mu $ for some target $ \pi $, are rarely analyzed using tools from mathematical analysis. This paper shows that a general-purpose approximate inclusive KL inference paradigm can be constructed using the theory of gradient flows derived from PDE analysis. We uncover that several existing learning algorithms can be viewed as particular realizations of the inclusive KL inference paradigm. For example, existing sampling algorithms such as Arbel et al. (2019) and Korba et al. (2021) can be viewed in a unified manner as inclusive-KL inference with approximate gradient estimators. Finally, we provide the theoretical foundation for the Wasserstein-Fisher-Rao gradient flows for minimizing the inclusive KL divergence.

Musical instrument classification, a key area in Music Information Retrieval, has gained considerable interest due to its applications in education, digital music production, and consumer media. Recent advances in machine learning, specifically deep learning, have enhanced the capability to identify and classify musical instruments from audio signals. This study applies various machine learning methods, including Naive Bayes, Support Vector Machines, Random Forests, Boosting techniques like AdaBoost and XGBoost, as well as deep learning models such as Convolutional Neural Networks and Artificial Neural Networks. The effectiveness of these methods is evaluated on the NSynth dataset, a large repository of annotated musical sounds. By comparing these approaches, the analysis aims to showcase the advantages and limitations of each method, providing guidance for developing more accurate and efficient classification systems. Additionally, hybrid model testing and discussion are included. This research aims to support further studies in instrument classification by proposing new approaches and future research directions.

Our proposed framework attempts to break the trade-off between performance and explainability by introducing an explainable-by-design convolutional neural network (CNN) based on the lateral inhibition mechanism. The ExplaiNet model consists of the predictor, that is a high-accuracy CNN with residual or dense skip connections, and the explainer probabilistic graph that expresses the spatial interactions of the network neurons. The value on each graph node is a local discrete feature (LDF) vector, a patch descriptor that represents the indices of antagonistic neurons ordered by the strength of their activations, which are learned with gradient descent. Using LDFs as sequences we can increase the conciseness of explanations by repurposing EXTREME, an EM-based sequence motif discovery method that is typically used in molecular biology. Having a discrete feature motif matrix for each one of intermediate image representations, instead of a continuous activation tensor, allows us to leverage the inherent explainability of Bayesian networks. By collecting observations and directly calculating probabilities, we can explain causal relationships between motifs of adjacent levels and attribute the model's output to global motifs. Moreover, experiments on various tiny image benchmark datasets confirm that our predictor ensures the same level of performance as the baseline architecture for a given count of parameters and/or layers. Our novel method shows promise to exceed this performance while providing an additional stream of explanations. In the solved MNIST classification task, it reaches a comparable to the state-of-the-art performance for single models, using standard training setup and 0.75 million parameters.

Motivated by the surge of interest in Koopman operator theory, we propose a machine-learning alternative based on a functional Bayesian perspective for operator-theoretic modeling of unknown, data-driven, nonlinear dynamical systems. This formulation is directly done in an infinite-dimensional space of linear operators or Hilbert space with universal approximation property. The theory of reproducing kernel Hilbert space (RKHS) allows the lifting of nonlinear dynamics to a potentially infinite-dimensional space via linear embeddings, where a general nonlinear function is represented as a set of linear functions or operators in the functional space. This allows us to apply classical linear Bayesian methods such as the Kalman filter directly in the Hilbert space, yielding nonlinear solutions in the original input space. This kernel perspective on the Koopman operator offers two compelling advantages. First, the Hilbert space can be constructed deterministically, agnostic to the nonlinear dynamics. The Gaussian kernel is universal, approximating uniformly an arbitrary continuous target function over any compact domain. Second, Bayesian filter is an adaptive, linear minimum-variance algorithm, allowing the system to update the Koopman operator and continuously track the changes across an extended period of time, ideally suited for modern data-driven applications such as real-time machine learning using streaming data. In this paper, we present several practical implementations to obtain a finite-dimensional approximation of the functional Bayesian filter (FBF). Due to the rapid decay of the Gaussian kernel, excellent approximation is obtained with a small dimension. We demonstrate that this practical approach can obtain accurate results and outperform finite-dimensional Koopman decomposition.

Model Compression has drawn much attention within the deep learning community recently. Compressing a dense neural network offers many advantages including lower computation cost, deployability to devices of limited storage and memories, and resistance to adversarial attacks. This may be achieved via weight pruning or fully discarding certain input features. Here we demonstrate a novel strategy to emulate principles of Bayesian model selection in a deep learning setup. Given a fully connected Bayesian neural network with spike-and-slab priors trained via a variational algorithm, we obtain the posterior inclusion probability for every node that typically gets lost. We employ these probabilities for pruning and feature selection on a host of simulated and real-world benchmark data and find evidence of better generalizability of the pruned model in all our experiments.