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This article summarizes the discussions from the American Statistical Association (ASA) Biopharmaceutical (BIOP) Section Open Forum that took place on December 10, 2020 and was organized by the ASA BIOP Statistical Methods in Oncology Scientific Working Group, in coordination with the US FDA Oncology Center of Excellence. Diverse stakeholders including experts from international regulatory agencies, academicians, and representatives of the pharmaceutical industry engaged in a discussion on the use of non-concurrent control in Master Protocols for oncology trials. While the use of non-concurrent control with the concurrent control may increase the power of detecting the therapeutic difference between a treatment and the control, the panelists had diverse opinion on the statistical approaches for modeling non-concurrent and concurrent controls. Some were more concerned about the temporality of the non-concurrent control and bias introduced by different confounders related to time, e.g., changes in standard of care, changes in patient population, changes in recruiting strategies, changes in assessment of endpoints. Nevertheless, in some situations such as when the recruitment is extremely challenging for a rare disease, the panelists concluded that the use of a non-concurrent control can be justified.

Evaluating robustness of machine-learning models to adversarial examples is a challenging problem. Many defenses have been shown to provide a false sense of robustness by causing gradient-based attacks to fail, and they have been broken under more rigorous evaluations. Although guidelines and best practices have been suggested to improve current adversarial robustness evaluations, the lack of automatic testing and debugging tools makes it difficult to apply these recommendations in a systematic manner. In this work, we overcome these limitations by: (i) categorizing attack failures based on how they affect the optimization of gradient-based attacks, while also unveiling two novel failures affecting many popular attack implementations and past evaluations; (ii) proposing six novel indicators of failure, to automatically detect the presence of such failures in the attack optimization process; and (iii) suggesting a systematic protocol to apply the corresponding fixes. Our extensive experimental analysis, involving more than 15 models in 3 distinct application domains, shows that our indicators of failure can be used to debug and improve current adversarial robustness evaluations, thereby providing a first concrete step towards automatizing and systematizing them. Our open-source code is available at: //github.com/pralab/IndicatorsOfAttackFailure.

In recent years, deep learning has been a topic of interest in almost all disciplines due to its impressive empirical success in analyzing complex data sets, such as imaging, genetics, climate, and medical data. While most of the developments are treated as black-box machines, there is an increasing interest in interpretable, reliable, and robust deep learning models applicable to a broad class of applications. Feature-selected deep learning is proven to be promising in this regard. However, the recent developments do not address the situations of ultra-high dimensional and highly correlated feature selection in addition to the high noise level. In this article, we propose a novel screening and cleaning strategy with the aid of deep learning for the cluster-level discovery of highly correlated predictors with a controlled error rate. A thorough empirical evaluation over a wide range of simulated scenarios demonstrates the effectiveness of the proposed method by achieving high power while having a minimal number of false discoveries. Furthermore, we implemented the algorithm in the riboflavin (vitamin $B_2$) production dataset in the context of understanding the possible genetic association with riboflavin production. The gain of the proposed methodology is illustrated by achieving lower prediction error compared to other state-of-the-art methods.

Using information-theoretic principles, we consider the generalization error (gen-error) of iterative semi-supervised learning (SSL) algorithms that iteratively generate pseudo-labels for a large amount of unlabelled data to progressively refine the model parameters. In contrast to most previous works that {\em bound} the gen-error, we provide an {\em exact} expression for the gen-error and particularize it to the binary Gaussian mixture model. Our theoretical results suggest that when the class conditional variances are not too large, the gen-error decreases with the number of iterations, but quickly saturates. On the flip side, if the class conditional variances (and so amount of overlap between the classes) are large, the gen-error increases with the number of iterations. To mitigate this undesirable effect, we show that regularization can reduce the gen-error. The theoretical results are corroborated by extensive experiments on the MNIST and CIFAR datasets in which we notice that for easy-to-distinguish classes, the gen-error improves after several pseudo-labelling iterations, but saturates afterwards, and for more difficult-to-distinguish classes, regularization improves the generalization performance.

The combinatorial problem of learning directed acyclic graphs (DAGs) from data was recently framed as a purely continuous optimization problem by leveraging a differentiable acyclicity characterization of DAGs based on the trace of a matrix exponential function. Existing acyclicity characterizations are based on the idea that powers of an adjacency matrix contain information about walks and cycles. In this work, we propose a $\textit{fundamentally different}$ acyclicity characterization based on the log-determinant (log-det) function, which leverages the nilpotency property of DAGs. To deal with the inherent asymmetries of a DAG, we relate the domain of our log-det characterization to the set of $\textit{M-matrices}$, which is a key difference to the classical log-det function defined over the cone of positive definite matrices. Similar to acyclicity functions previously proposed, our characterization is also exact and differentiable. However, when compared to existing characterizations, our log-det function: (1) Is better at detecting large cycles; (2) Has better-behaved gradients; and (3) Its runtime is in practice about an order of magnitude faster. From the optimization side, we drop the typically used augmented Lagrangian scheme, and propose DAGMA ($\textit{Directed Acyclic Graphs via M-matrices for Acyclicity}$), a method that resembles the central path for barrier methods. Each point in the central path of DAGMA is a solution to an unconstrained problem regularized by our log-det function, then we show that at the limit of the central path the solution is guaranteed to be a DAG. Finally, we provide extensive experiments for $\textit{linear}$ and $\textit{nonlinear}$ SEMs, and show that our approach can reach large speed-ups and smaller structural Hamming distances against state-of-the-art methods.

A research division plays an important role of driving innovation in an organization. Drawing insights, following trends, keeping abreast of new research, and formulating strategies are increasingly becoming more challenging for both researchers and executives as the amount of information grows in both velocity and volume. In this paper we present a use case of how a corporate research community, IBM Research, utilizes Semantic Web technologies to induce a unified Knowledge Graph from both structured and textual data obtained by integrating various applications used by the community related to research projects, academic papers, datasets, achievements and recognition. In order to make the Knowledge Graph more accessible to application developers, we identified a set of common patterns for exploiting the induced knowledge and exposed them as APIs. Those patterns were born out of user research which identified the most valuable use cases or user pain points to be alleviated. We outline two distinct scenarios: recommendation and analytics for business use. We will discuss these scenarios in detail and provide an empirical evaluation on entity recommendation specifically. The methodology used and the lessons learned from this work can be applied to other organizations facing similar challenges.

Emerging quantum algorithms for problems such as element distinctness, subset sum, and closest pair demonstrate computational advantages by relying on abstract data structures. Practically realizing such an algorithm as a program for a quantum computer requires an efficient implementation of the data structure whose operations correspond to unitary operators that manipulate quantum superpositions of data. To correctly operate in superposition, an implementation must satisfy three properties -- reversibility, history independence, and bounded-time execution. Standard implementations, such as the representation of an abstract set as a hash table, fail these properties, calling for tools to develop specialized implementations. In this work, we present Core Tower, the first language for quantum programming with random-access memory. Core Tower enables the developer to implement data structures as pointer-based, linked data. It features a reversible semantics enabling every valid program to be translated to a unitary quantum circuit. We present Boson, the first memory allocator that supports reversible, history-independent, and constant-time dynamic memory allocation in quantum superposition. We also present Tower, a language for quantum programming with recursively defined data structures. Tower features a type system that bounds all recursion using classical parameters as is necessary for a program to execute on a quantum computer. Using Tower, we implement Ground, the first quantum library of data structures, including lists, stacks, queues, strings, and sets. We provide the first executable implementation of sets that satisfies all three mandated properties of reversibility, history independence, and bounded-time execution.

Transformers have achieved superior performances in many tasks in natural language processing and computer vision, which also intrigues great interests in the time series community. Among multiple advantages of transformers, the ability to capture long-range dependencies and interactions is especially attractive for time series modeling, leading to exciting progress in various time series applications. In this paper, we systematically review transformer schemes for time series modeling by highlighting their strengths as well as limitations through a new taxonomy to summarize existing time series transformers in two perspectives. From the perspective of network modifications, we summarize the adaptations of module level and architecture level of the time series transformers. From the perspective of applications, we categorize time series transformers based on common tasks including forecasting, anomaly detection, and classification. Empirically, we perform robust analysis, model size analysis, and seasonal-trend decomposition analysis to study how Transformers perform in time series. Finally, we discuss and suggest future directions to provide useful research guidance. To the best of our knowledge, this paper is the first work to comprehensively and systematically summarize the recent advances of Transformers for modeling time series data. We hope this survey will ignite further research interests in time series Transformers.

We propose a novel approach to multimodal sentiment analysis using deep neural networks combining visual analysis and natural language processing. Our goal is different than the standard sentiment analysis goal of predicting whether a sentence expresses positive or negative sentiment; instead, we aim to infer the latent emotional state of the user. Thus, we focus on predicting the emotion word tags attached by users to their Tumblr posts, treating these as "self-reported emotions." We demonstrate that our multimodal model combining both text and image features outperforms separate models based solely on either images or text. Our model's results are interpretable, automatically yielding sensible word lists associated with emotions. We explore the structure of emotions implied by our model and compare it to what has been posited in the psychology literature, and validate our model on a set of images that have been used in psychology studies. Finally, our work also provides a useful tool for the growing academic study of images - both photographs and memes - on social networks.

Many recent state-of-the-art recommender systems such as D-ATT, TransNet and DeepCoNN exploit reviews for representation learning. This paper proposes a new neural architecture for recommendation with reviews. Our model operates on a multi-hierarchical paradigm and is based on the intuition that not all reviews are created equal, i.e., only a select few are important. The importance, however, should be dynamically inferred depending on the current target. To this end, we propose a review-by-review pointer-based learning scheme that extracts important reviews, subsequently matching them in a word-by-word fashion. This enables not only the most informative reviews to be utilized for prediction but also a deeper word-level interaction. Our pointer-based method operates with a novel gumbel-softmax based pointer mechanism that enables the incorporation of discrete vectors within differentiable neural architectures. Our pointer mechanism is co-attentive in nature, learning pointers which are co-dependent on user-item relationships. Finally, we propose a multi-pointer learning scheme that learns to combine multiple views of interactions between user and item. Overall, we demonstrate the effectiveness of our proposed model via extensive experiments on \textbf{24} benchmark datasets from Amazon and Yelp. Empirical results show that our approach significantly outperforms existing state-of-the-art, with up to 19% and 71% relative improvement when compared to TransNet and DeepCoNN respectively. We study the behavior of our multi-pointer learning mechanism, shedding light on evidence aggregation patterns in review-based recommender systems.