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In the field of Connectomics, a primary problem is that of 3D neuron segmentation. Although Deep Learning based methods have achieved remarkable accuracy, errors still exist, especially in regions with image defects. One common type of defect is that of consecutive missing image sections. Here data is lost along some axis, and the resulting neuron segmentations are split across the gap. To address this problem, we propose a novel method based on point cloud representations of neurons. We formulate this as a classification problem and train CurveNet, a state-of-the-art point cloud classification model, to identify which neurons should be merged. We show that our method not only performs strongly but scales reasonably to gaps well beyond what other methods have attempted to address. Additionally, our point cloud representations are highly efficient in terms of data, maintaining high performance with an amount of data that would be unfeasible for other methods. We believe that this is an indicator of the viability of using point clouds representations for other proofreading tasks.

In this paper we apply divergence measures to empirical likelihood applied to logistic regression models. We define a family of empirical test statistics based on divergence measures, called empirical phi-divergence test statistics, extending the empirical likelihood ratio test. We study the asymptotic distribution of these empirical test statistics, showing that it is the same for all the test statistics in this family, and the same as the classical empirical likelihood ratio test. Next, we study the power function for the members in this family, showing that the empirical phi-divergence tests introduced in the paper are consistent in the Fraser sense. In order to compare the differences in behavior among the empirical phi-divergence test statistics in this new family, considered for the first time in this paper, we carry out a simulation study.

The quantification of modern slavery has received increased attention recently as organizations have come together to produce global estimates, where multiple systems estimation (MSE) is often used to this end. Echoing a long-standing controversy, disagreements have re-surfaced regarding the underlying MSE assumptions, the robustness of MSE methodology, and the accuracy of MSE estimates in this application. Our goal is to help address and move past these controversies. To do so, we review MSE, its assumptions, and commonly used models for modern slavery applications. We introduce all of the publicly available modern slavery datasets in the literature, providing a reproducible analysis and highlighting current issues. Specifically, we utilize an internal consistency approach that constructs subsets of data for which ground truth is available, allowing us to evaluate the accuracy of MSE estimators. Next, we propose a characterization of the large sample bias of estimators as a function of misspecified assumptions. Then, we propose an alternative to traditional (e.g., bootstrap-based) assessments of reliability, which allows us to visualize trajectories of MSE estimates to illustrate the robustness of estimates. Finally, our complementary analyses are used to provide guidance regarding the application and reliability of MSE methodology.

In light of the emergence of deep reinforcement learning (DRL) in recommender systems research and several fruitful results in recent years, this survey aims to provide a timely and comprehensive overview of the recent trends of deep reinforcement learning in recommender systems. We start with the motivation of applying DRL in recommender systems. Then, we provide a taxonomy of current DRL-based recommender systems and a summary of existing methods. We discuss emerging topics and open issues, and provide our perspective on advancing the domain. This survey serves as introductory material for readers from academia and industry into the topic and identifies notable opportunities for further research.

Despite its great success, machine learning can have its limits when dealing with insufficient training data. A potential solution is the additional integration of prior knowledge into the training process which leads to the notion of informed machine learning. In this paper, we present a structured overview of various approaches in this field. We provide a definition and propose a concept for informed machine learning which illustrates its building blocks and distinguishes it from conventional machine learning. We introduce a taxonomy that serves as a classification framework for informed machine learning approaches. It considers the source of knowledge, its representation, and its integration into the machine learning pipeline. Based on this taxonomy, we survey related research and describe how different knowledge representations such as algebraic equations, logic rules, or simulation results can be used in learning systems. This evaluation of numerous papers on the basis of our taxonomy uncovers key methods in the field of informed machine learning.

The remarkable practical success of deep learning has revealed some major surprises from a theoretical perspective. In particular, simple gradient methods easily find near-optimal solutions to non-convex optimization problems, and despite giving a near-perfect fit to training data without any explicit effort to control model complexity, these methods exhibit excellent predictive accuracy. We conjecture that specific principles underlie these phenomena: that overparametrization allows gradient methods to find interpolating solutions, that these methods implicitly impose regularization, and that overparametrization leads to benign overfitting. We survey recent theoretical progress that provides examples illustrating these principles in simpler settings. We first review classical uniform convergence results and why they fall short of explaining aspects of the behavior of deep learning methods. We give examples of implicit regularization in simple settings, where gradient methods lead to minimal norm functions that perfectly fit the training data. Then we review prediction methods that exhibit benign overfitting, focusing on regression problems with quadratic loss. For these methods, we can decompose the prediction rule into a simple component that is useful for prediction and a spiky component that is useful for overfitting but, in a favorable setting, does not harm prediction accuracy. We focus specifically on the linear regime for neural networks, where the network can be approximated by a linear model. In this regime, we demonstrate the success of gradient flow, and we consider benign overfitting with two-layer networks, giving an exact asymptotic analysis that precisely demonstrates the impact of overparametrization. We conclude by highlighting the key challenges that arise in extending these insights to realistic deep learning settings.

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.

In recent years, there has been an exponential growth in the number of complex documents and texts that require a deeper understanding of machine learning methods to be able to accurately classify texts in many applications. Many machine learning approaches have achieved surpassing results in natural language processing. The success of these learning algorithms relies on their capacity to understand complex models and non-linear relationships within data. However, finding suitable structures, architectures, and techniques for text classification is a challenge for researchers. In this paper, a brief overview of text classification algorithms is discussed. This overview covers different text feature extractions, dimensionality reduction methods, existing algorithms and techniques, and evaluations methods. Finally, the limitations of each technique and their application in the real-world problem are discussed.

Learning low-dimensional embeddings of knowledge graphs is a powerful approach used to predict unobserved or missing edges between entities. However, an open challenge in this area is developing techniques that can go beyond simple edge prediction and handle more complex logical queries, which might involve multiple unobserved edges, entities, and variables. For instance, given an incomplete biological knowledge graph, we might want to predict "em what drugs are likely to target proteins involved with both diseases X and Y?" -- a query that requires reasoning about all possible proteins that {\em might} interact with diseases X and Y. Here we introduce a framework to efficiently make predictions about conjunctive logical queries -- a flexible but tractable subset of first-order logic -- on incomplete knowledge graphs. In our approach, we embed graph nodes in a low-dimensional space and represent logical operators as learned geometric operations (e.g., translation, rotation) in this embedding space. By performing logical operations within a low-dimensional embedding space, our approach achieves a time complexity that is linear in the number of query variables, compared to the exponential complexity required by a naive enumeration-based approach. We demonstrate the utility of this framework in two application studies on real-world datasets with millions of relations: predicting logical relationships in a network of drug-gene-disease interactions and in a graph-based representation of social interactions derived from a popular web forum.

Using the 6,638 case descriptions of societal impact submitted for evaluation in the Research Excellence Framework (REF 2014), we replicate the topic model (Latent Dirichlet Allocation or LDA) made in this context and compare the results with factor-analytic results using a traditional word-document matrix (Principal Component Analysis or PCA). Removing a small fraction of documents from the sample, for example, has on average a much larger impact on LDA than on PCA-based models to the extent that the largest distortion in the case of PCA has less effect than the smallest distortion of LDA-based models. In terms of semantic coherence, however, LDA models outperform PCA-based models. The topic models inform us about the statistical properties of the document sets under study, but the results are statistical and should not be used for a semantic interpretation - for example, in grant selections and micro-decision making, or scholarly work-without follow-up using domain-specific semantic maps.