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Understanding the laws that govern a phenomenon is the core of scientific progress. This is especially true when the goal is to model the interplay between different aspects in a causal fashion. Indeed, causal inference itself is specifically designed to quantify the underlying relationships that connect a cause to its effect. Causal discovery is a branch of the broader field of causality in which causal graphs is recovered from data (whenever possible), enabling the identification and estimation of causal effects. In this paper, we explore recent advancements in a unified manner, provide a consistent overview of existing algorithms developed under different settings, report useful tools and data, present real-world applications to understand why and how these methods can be fruitfully exploited.

Many machine learning applications and tasks rely on the stochastic gradient descent (SGD) algorithm and its variants. Effective step length selection is crucial for the success of these algorithms, which has motivated the development of algorithms such as ADAM or AdaGrad. In this paper, we propose a novel algorithm for adaptive step length selection in the classical SGD framework, which can be readily adapted to other stochastic algorithms. Our proposed algorithm is inspired by traditional nonlinear optimization techniques and is supported by analytical findings. We show that under reasonable conditions, the algorithm produces step lengths in line with well-established theoretical requirements, and generates iterates that converge to a stationary neighborhood of a solution in expectation. We test the proposed algorithm on logistic regressions and deep neural networks and demonstrate that the algorithm can generate step lengths comparable to the best step length obtained from manual tuning.

Quasi-periodicity refers to a pattern in a function where it appears periodic but has evolving amplitudes over time. This is often the case in practical settings such as the modeling of case counts of infectious disease or the carbon dioxide (CO2) concentration over time. In this paper, we introduce a class of Gaussian processes, called seasonal Gaussian Processes (sGP), for model-based inference of such quasi-periodic behavior. We illustrate that the exact sGP can be efficiently fit within $O(n)$ time using its state space representation for equally spaced locations. However, for large datasets with irregular spacing, the exact approach becomes computationally inefficient and unstable. To address this, we develop a continuous finite dimensional approximation for sGP using the seasonal B-spline (sB-spline) basis constructed by damping B-splines with sinusoidal functions. We prove that the proposed approximation converges in distribution to the true sGP as the number of basis functions increases, and show its superior approximation quality through numerical studies. We also provide a unified and interpretable way to define priors for the sGP, based on the notion of predictive standard deviation (PSD). Finally, we implement the proposed inference method on several real data examples to illustrate its practical usage.

Specifications of complex, large scale, computer software and hardware systems can be radically simplified by using simple maps from input sequences to output values. These "state machine maps" provide an alternative representation of classical Moore type state machines. Composition of state machine maps corresponds to state machine products and can be used to specify essentially any type of interconnection as well as parallel and distributed computation. State machine maps can also specify abstract properties of systems and are significantly more concise and scalable than traditional representations of automata. Examples included here include specifications of producer/consumer software, network distributed consensus, real-time digital circuits, and operating system scheduling. The motivation for this work comes from experience designing and developing operating systems and real-time software where weak methods for understanding and exploring designs is a well known handicap. The methods introduced here are based on ordinary discrete mathematics, primitive recursive functions and deterministic state machines and are intended, initially, to aid the intuition and understanding of the system developers. Staying strictly within the boundaries of classical deterministic state machines anchors the methods to the algebraic structures of automata and semigroups, obviates any need for axiomatic deduction systems, "formal methods", or extensions to the model, and makes the specifications more faithful to engineering practice. While state machine maps are obvious representations of state machines, the techniques introduced here for defining and composing them are novel. To illustrate applications, the paper includes a fairly detailed specification and verification of the well-known "Paxos" distributed consensus algorithm plus a number of simpler examples including a digital PID controller.

Deep models, e.g., CNNs and Vision Transformers, have achieved impressive achievements in many vision tasks in the closed world. However, novel classes emerge from time to time in our ever-changing world, requiring a learning system to acquire new knowledge continually. For example, a robot needs to understand new instructions, and an opinion monitoring system should analyze emerging topics every day. Class-Incremental Learning (CIL) enables the learner to incorporate the knowledge of new classes incrementally and build a universal classifier among all seen classes. Correspondingly, when directly training the model with new class instances, a fatal problem occurs -- the model tends to catastrophically forget the characteristics of former ones, and its performance drastically degrades. There have been numerous efforts to tackle catastrophic forgetting in the machine learning community. In this paper, we survey comprehensively recent advances in deep class-incremental learning and summarize these methods from three aspects, i.e., data-centric, model-centric, and algorithm-centric. We also provide a rigorous and unified evaluation of 16 methods in benchmark image classification tasks to find out the characteristics of different algorithms empirically. Furthermore, we notice that the current comparison protocol ignores the influence of memory budget in model storage, which may result in unfair comparison and biased results. Hence, we advocate fair comparison by aligning the memory budget in evaluation, as well as several memory-agnostic performance measures. The source code to reproduce these evaluations is available at //github.com/zhoudw-zdw/CIL_Survey/

Clustering is a fundamental machine learning task which has been widely studied in the literature. Classic clustering methods follow the assumption that data are represented as features in a vectorized form through various representation learning techniques. As the data become increasingly complicated and complex, the shallow (traditional) clustering methods can no longer handle the high-dimensional data type. With the huge success of deep learning, especially the deep unsupervised learning, many representation learning techniques with deep architectures have been proposed in the past decade. Recently, the concept of Deep Clustering, i.e., jointly optimizing the representation learning and clustering, has been proposed and hence attracted growing attention in the community. Motivated by the tremendous success of deep learning in clustering, one of the most fundamental machine learning tasks, and the large number of recent advances in this direction, in this paper we conduct a comprehensive survey on deep clustering by proposing a new taxonomy of different state-of-the-art approaches. We summarize the essential components of deep clustering and categorize existing methods by the ways they design interactions between deep representation learning and clustering. Moreover, this survey also provides the popular benchmark datasets, evaluation metrics and open-source implementations to clearly illustrate various experimental settings. Last but not least, we discuss the practical applications of deep clustering and suggest challenging topics deserving further investigations as future directions.

Over the past few years, we have seen fundamental breakthroughs in core problems in machine learning, largely driven by advances in deep neural networks. At the same time, the amount of data collected in a wide array of scientific domains is dramatically increasing in both size and complexity. Taken together, this suggests many exciting opportunities for deep learning applications in scientific settings. But a significant challenge to this is simply knowing where to start. The sheer breadth and diversity of different deep learning techniques makes it difficult to determine what scientific problems might be most amenable to these methods, or which specific combination of methods might offer the most promising first approach. In this survey, we focus on addressing this central issue, providing an overview of many widely used deep learning models, spanning visual, sequential and graph structured data, associated tasks and different training methods, along with techniques to use deep learning with less data and better interpret these complex models --- two central considerations for many scientific use cases. We also include overviews of the full design process, implementation tips, and links to a plethora of tutorials, research summaries and open-sourced deep learning pipelines and pretrained models, developed by the community. We hope that this survey will help accelerate the use of deep learning across different scientific domains.

Since deep neural networks were developed, they have made huge contributions to everyday lives. Machine learning provides more rational advice than humans are capable of in almost every aspect of daily life. However, despite this achievement, the design and training of neural networks are still challenging and unpredictable procedures. To lower the technical thresholds for common users, automated hyper-parameter optimization (HPO) has become a popular topic in both academic and industrial areas. This paper provides a review of the most essential topics on HPO. The first section introduces the key hyper-parameters related to model training and structure, and discusses their importance and methods to define the value range. Then, the research focuses on major optimization algorithms and their applicability, covering their efficiency and accuracy especially for deep learning networks. This study next reviews major services and toolkits for HPO, comparing their support for state-of-the-art searching algorithms, feasibility with major deep learning frameworks, and extensibility for new modules designed by users. The paper concludes with problems that exist when HPO is applied to deep learning, a comparison between optimization algorithms, and prominent approaches for model evaluation with limited computational resources.

When and why can a neural network be successfully trained? This article provides an overview of optimization algorithms and theory for training neural networks. First, we discuss the issue of gradient explosion/vanishing and the more general issue of undesirable spectrum, and then discuss practical solutions including careful initialization and normalization methods. Second, we review generic optimization methods used in training neural networks, such as SGD, adaptive gradient methods and distributed methods, and theoretical results for these algorithms. Third, we review existing research on the global issues of neural network training, including results on bad local minima, mode connectivity, lottery ticket hypothesis and infinite-width analysis.

This paper surveys the machine learning literature and presents machine learning as optimization models. Such models can benefit from the advancement of numerical optimization techniques which have already played a distinctive role in several machine learning settings. Particularly, mathematical optimization models are presented for commonly used machine learning approaches for regression, classification, clustering, and deep neural networks as well new emerging applications in machine teaching and empirical model learning. The strengths and the shortcomings of these models are discussed and potential research directions are highlighted.