Thompson sampling (TS) is a popular heuristic for action selection, but it requires sampling from a posterior distribution. Unfortunately, this can become computationally intractable in complex environments, such as those modeled using neural networks. Approximate posterior samples can produce effective actions, but only if they reasonably approximate joint predictive distributions of outputs across inputs. Notably, accuracy of marginal predictive distributions does not suffice. Epistemic neural networks (ENNs) are designed to produce accurate joint predictive distributions. We compare a range of ENNs through computational experiments that assess their performance in approximating TS across bandit and reinforcement learning environments. The results indicate that ENNs serve this purpose well and illustrate how the quality of joint predictive distributions drives performance. Further, we demonstrate that the \textit{epinet} -- a small additive network that estimates uncertainty -- matches the performance of large ensembles at orders of magnitude lower computational cost. This enables effective application of TS with computation that scales gracefully to complex environments.

Structural information of phylogenetic tree topologies plays an important role in phylogenetic inference. However, finding appropriate topological structures for specific phylogenetic inference tasks often requires significant design effort and domain expertise. In this paper, we propose a novel structural representation method for phylogenetic inference based on learnable topological features. By combining the raw node features that minimize the Dirichlet energy with modern graph representation learning techniques, our learnable topological features can provide efficient structural information of phylogenetic trees that automatically adapts to different downstream tasks without requiring domain expertise. We demonstrate the effectiveness and efficiency of our method on a simulated data tree probability estimation task and a benchmark of challenging real data variational Bayesian phylogenetic inference problems. Phylogenetics is an important discipline of computational biology where the goal is to identify the evolutionary history and relationships among individuals or groups of biological entities. In statistical approaches to phylogenetics, this has been formulated as an inference problem on hypotheses of shared history, i.e., phylogenetic trees, based on observed sequence data (e.g., DNA, RNA, or protein sequences) under a model of evolution.

We introduce a Bayesian perspective for the structured matrix factorization problem. The proposed framework provides a probabilistic interpretation for existing geometric methods based on determinant minimization. We model input data vectors as linear transformations of latent vectors drawn from a distribution uniform over a particular domain reflecting structural assumptions, such as the probability simplex in Nonnegative Matrix Factorization and polytopes in Polytopic Matrix Factorization. We represent the rows of the linear transformation matrix as vectors generated independently from a normal distribution whose covariance matrix is inverse Wishart distributed. We show that the corresponding maximum a posteriori estimation problem boils down to the robust determinant minimization approach for structured matrix factorization, providing insights about parameter selections and potential algorithmic extensions.

This open access book provides a comprehensive overview of the state of the art in research and applications of Foundation Models and is intended for readers familiar with basic Natural Language Processing (NLP) concepts. Over the recent years, a revolutionary new paradigm has been developed for training models for NLP. These models are first pre-trained on large collections of text documents to acquire general syntactic knowledge and semantic information. Then, they are fine-tuned for specific tasks, which they can often solve with superhuman accuracy. When the models are large enough, they can be instructed by prompts to solve new tasks without any fine-tuning. Moreover, they can be applied to a wide range of different media and problem domains, ranging from image and video processing to robot control learning. Because they provide a blueprint for solving many tasks in artificial intelligence, they have been called Foundation Models. After a brief introduction to basic NLP models the main pre-trained language models BERT, GPT and sequence-to-sequence transformer are described, as well as the concepts of self-attention and context-sensitive embedding. Then, different approaches to improving these models are discussed, such as expanding the pre-training criteria, increasing the length of input texts, or including extra knowledge. An overview of the best-performing models for about twenty application areas is then presented, e.g., question answering, translation, story generation, dialog systems, generating images from text, etc. For each application area, the strengths and weaknesses of current models are discussed, and an outlook on further developments is given. In addition, links are provided to freely available program code. A concluding chapter summarizes the economic opportunities, mitigation of risks, and potential developments of AI.

Latent variable models such as the Variational Auto-Encoder (VAE) have become a go-to tool for analyzing biological data, especially in the field of single-cell genomics. One remaining challenge is the interpretability of latent variables as biological processes that define a cell's identity. Outside of biological applications, this problem is commonly referred to as learning disentangled representations. Although several disentanglement-promoting variants of the VAE were introduced, and applied to single-cell genomics data, this task has been shown to be infeasible from independent and identically distributed measurements, without additional structure. Instead, recent methods propose to leverage non-stationary data, as well as the sparse mechanism shift assumption in order to learn disentangled representations with a causal semantic. Here, we extend the application of these methodological advances to the analysis of single-cell genomics data with genetic or chemical perturbations. More precisely, we propose a deep generative model of single-cell gene expression data for which each perturbation is treated as a stochastic intervention targeting an unknown, but sparse, subset of latent variables. We benchmark these methods on simulated single-cell data to evaluate their performance at latent units recovery, causal target identification and out-of-domain generalization. Finally, we apply those approaches to two real-world large-scale gene perturbation data sets and find that models that exploit the sparse mechanism shift hypothesis surpass contemporary methods on a transfer learning task. We implement our new model and benchmarks using the scvi-tools library, and release it as open-source software at https://github.com/Genentech/sVAE.

Personalized prediction of responses for individual entities caused by external drivers is vital across many disciplines. Recent machine learning (ML) advances have led to new state-of-the-art response prediction models. Models built at a population level often lead to sub-optimal performance in many personalized prediction settings due to heterogeneity in data across entities (tasks). In personalized prediction, the goal is to incorporate inherent characteristics of different entities to improve prediction performance. In this survey, we focus on the recent developments in the ML community for such entity-aware modeling approaches. ML algorithms often modulate the network using these entity characteristics when they are readily available. However, these entity characteristics are not readily available in many real-world scenarios, and different ML methods have been proposed to infer these characteristics from the data. In this survey, we have organized the current literature on entity-aware modeling based on the availability of these characteristics as well as the amount of training data. We highlight how recent innovations in other disciplines, such as uncertainty quantification, fairness, and knowledge-guided machine learning, can improve entity-aware modeling.

The symbolic AI community is increasingly trying to embrace machine learning in neuro-symbolic architectures, yet is still struggling due to cultural barriers. To break the barrier, this rather opinionated personal memo attempts to explain and rectify the conventions in Statistics, Machine Learning, and Deep Learning from the viewpoint of outsiders. It provides a step-by-step protocol for designing a machine learning system that satisfies a minimum theoretical guarantee necessary for being taken seriously by the symbolic AI community, i.e., it discusses "in what condition we can stop worrying and accept statistical machine learning." Unlike most textbooks which are written for students trying to specialize in Stat/ML/DL and willing to accept jargons, this memo is written for experienced symbolic researchers that hear a lot of buzz but are still uncertain and skeptical. Information on Stat/ML/DL is currently too scattered or too noisy to invest in. This memo prioritizes compactness, citations to old papers (many in early 20th century), and concepts that resonate well with symbolic paradigms in order to offer time savings. It prioritizes general mathematical modeling and does not discuss any specific function approximator, such as neural networks (NNs), SVMs, decision trees, etc. Finally, it is open to corrections. Consider this memo as something similar to a blog post taking the form of a paper on Arxiv.

Identifying predictive factors via multivariable statistical analysis is for rare diseases often impossible because the data sets available are too small. Combining data from different medical centers into a single (larger) database would alleviate this problem, but is in practice challenging due to regulatory and logistic problems. Federated Learning (FL) is a machine learning approach that aims to construct from local inferences in separate data centers what would have been inferred had the data sets been merged. It seeks to harvest the statistical power of larger data sets without actually creating them. The FL strategy is not always feasible for small data sets. Therefore, in this paper we refine and implement an alternative Bayesian Federated Inference (BFI) framework for multi center data with the same aim as FL. The BFI framework is designed to cope with small data sets by inferring locally not only the optimal parameter values, but also additional features of the posterior parameter distribution, capturing information beyond that is used in FL. BFI has the additional benefit that a single inference cycle across the centers is sufficient, whereas FL needs multiple cycles. We quantify the performance of the proposed methodology on simulated and real life data.

An evident challenge ahead for the integrated circuit (IC) industry in the nanometer regime is the investigation and development of methods that can reduce the design complexity ensuing from growing process variations and curtail the turnaround time of chip manufacturing. Conventional methodologies employed for such tasks are largely manual; thus, time-consuming and resource-intensive. In contrast, the unique learning strategies of artificial intelligence (AI) provide numerous exciting automated approaches for handling complex and data-intensive tasks in very-large-scale integration (VLSI) design and testing. Employing AI and machine learning (ML) algorithms in VLSI design and manufacturing reduces the time and effort for understanding and processing the data within and across different abstraction levels via automated learning algorithms. It, in turn, improves the IC yield and reduces the manufacturing turnaround time. This paper thoroughly reviews the AI/ML automated approaches introduced in the past towards VLSI design and manufacturing. Moreover, we discuss the scope of AI/ML applications in the future at various abstraction levels to revolutionize the field of VLSI design, aiming for high-speed, highly intelligent, and efficient implementations.

Numerous applications of machine learning involve representing probability distributions over high-dimensional data. We propose autoregressive quantile flows, a flexible class of normalizing flow models trained using a novel objective based on proper scoring rules. Our objective does not require calculating computationally expensive determinants of Jacobians during training and supports new types of neural architectures, such as neural autoregressive flows from which it is easy to sample. We leverage these models in quantile flow regression, an approach that parameterizes predictive conditional distributions with flows, resulting in improved probabilistic predictions on tasks such as time series forecasting and object detection. Our novel objective functions and neural flow parameterizations also yield improvements on popular generation and density estimation tasks, and represent a step beyond maximum likelihood learning of flows. Reasoning about uncertainty via the language of probability is important in many application domains of machine learning, including medicine (Saria, 2018), robotics (Chua et al., 2018; Buckman et al., 2018), and operations research (Van Roy et al., 1997). Especially important is the estimation of predictive uncertainties (e.g., confidence intervals around forecasts) in tasks such as clinical diagnosis (Jiang et al., 2012) or decision support systems (Werling et al., 2015; Kuleshov and Liang, 2015). Normalizing flows (Rezende and Mohamed, 2016; Papamakarios et al., 2019; Kingma et al., 2016) are a popular framework for defining probabilistic models, and can be used for density estimation (Papamakarios et al., 2017), out-of-distribution detection (Nalisnick et al., 2019), content generation (Kingma and Dhariwal, 2018), and more. Flows feature tractable posterior inference and maximum likelihood estimation; however, maximum likelihood estimation of flows requires carefully designing a family of bijective functions that are simultaneously expressive and whose Jacobian has a tractable determinant.