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Presence-absence data is defined by vectors or matrices of zeroes and ones, where the ones usually indicate a "presence" in a certain place. Presence-absence data occur for example when investigating geographical species distributions, genetic information, or the occurrence of certain terms in texts. There are many applications for clustering such data; one example is to find so-called biotic elements, i.e., groups of species that tend to occur together geographically. Presence-absence data can be clustered in various ways, namely using a latent class mixture approach with local independence, distance-based hierarchical clustering with the Jaccard distance, or also using clustering methods for continuous data on a multidimensional scaling representation of the distances. These methods are conceptually very different and can therefore not easily be compared theoretically. We compare their performance with a comprehensive simulation study based on models for species distributions. This has been accepted for publication in Ferreira, J., Bekker, A., Arashi, M. and Chen, D. (eds.) Innovations in multivariate statistical modelling: navigating theoretical and multidisciplinary domains, Springer Emerging Topics in Statistics and Biostatistics.

We develop an algorithmic framework for solving convex optimization problems using no-regret game dynamics. By converting the problem of minimizing a convex function into an auxiliary problem of solving a min-max game in a sequential fashion, we can consider a range of strategies for each of the two-players who must select their actions one after the other. A common choice for these strategies are so-called no-regret learning algorithms, and we describe a number of such and prove bounds on their regret. We then show that many classical first-order methods for convex optimization -- including average-iterate gradient descent, the Frank-Wolfe algorithm, the Heavy Ball algorithm, and Nesterov's acceleration methods -- can be interpreted as special cases of our framework as long as each player makes the correct choice of no-regret strategy. Proving convergence rates in this framework becomes very straightforward, as they follow from plugging in the appropriate known regret bounds. Our framework also gives rise to a number of new first-order methods for special cases of convex optimization that were not previously known.

To maximize clinical benefit, clinicians routinely tailor treatment to the individual characteristics of each patient, where individualized treatment rules are needed and are of significant research interest to statisticians. In the covariate-adjusted randomization clinical trial with many covariates, we model the treatment effect with an unspecified function of a single index of the covariates and leave the baseline response completely arbitrary. We devise a class of estimators to consistently estimate the treatment effect function and its associated index while bypassing the estimation of the baseline response, which is subject to the curse of dimensionality. We further develop inference tools to identify predictive covariates and isolate effective treatment region. The usefulness of the methods is demonstrated in both simulations and a clinical data example.

We study the problem of set discovery where given a few example tuples of a desired set, we want to find the set in a collection of sets. A challenge is that the example tuples may not uniquely identify a set, and a large number of candidate sets may be returned. Our focus is on interactive exploration to set discovery where additional example tuples from the candidate sets are shown and the user either accepts or rejects them as members of the target set. The goal is to find the target set with the least number of user interactions. The problem can be cast as an optimization problem where we want to find a decision tree that can guide the search to the target set with the least number of questions to be answered by the user. We propose a general algorithm that is capable of reaching an optimal solution and two variations of it that strike a balance between the quality of a solution and the running time. We also propose a novel pruning strategy that safely reduces the search space without introducing false negatives. We evaluate the efficiency and the effectiveness of our algorithms through an extensive experimental study using both real and synthetic datasets and comparing them to previous approaches in the literature. We show that our pruning strategy reduces the running time of the search algorithms by 2-5 orders of magnitude.

Leveraging biased click data for optimizing learning to rank systems has been a popular approach in information retrieval. Because click data is often noisy and biased, a variety of methods have been proposed to construct unbiased learning to rank (ULTR) algorithms for the learning of unbiased ranking models. Among them, automatic unbiased learning to rank (AutoULTR) algorithms that jointly learn user bias models (i.e., propensity models) with unbiased rankers have received a lot of attention due to their superior performance and low deployment cost in practice. Despite their differences in theories and algorithm design, existing studies on ULTR usually use uni-variate ranking functions to score each document or result independently. On the other hand, recent advances in context-aware learning-to-rank models have shown that multivariate scoring functions, which read multiple documents together and predict their ranking scores jointly, are more powerful than uni-variate ranking functions in ranking tasks with human-annotated relevance labels. Whether such superior performance would hold in ULTR with noisy data, however, is mostly unknown. In this paper, we investigate existing multivariate scoring functions and AutoULTR algorithms in theory and prove that permutation invariance is a crucial factor that determines whether a context-aware learning-to-rank model could be applied to existing AutoULTR framework. Our experiments with synthetic clicks on two large-scale benchmark datasets show that AutoULTR models with permutation-invariant multivariate scoring functions significantly outperform those with uni-variate scoring functions and permutation-variant multivariate scoring functions.

Interactive recommendation that models the explicit interactions between users and the recommender system has attracted a lot of research attentions in recent years. Most previous interactive recommendation systems only focus on optimizing recommendation accuracy while overlooking other important aspects of recommendation quality, such as the diversity of recommendation results. In this paper, we propose a novel recommendation model, named \underline{D}iversity-promoting \underline{D}eep \underline{R}einforcement \underline{L}earning (D$^2$RL), which encourages the diversity of recommendation results in interaction recommendations. More specifically, we adopt a Determinantal Point Process (DPP) model to generate diverse, while relevant item recommendations. A personalized DPP kernel matrix is maintained for each user, which is constructed from two parts: a fixed similarity matrix capturing item-item similarity, and the relevance of items dynamically learnt through an actor-critic reinforcement learning framework. We performed extensive offline experiments as well as simulated online experiments with real world datasets to demonstrate the effectiveness of the proposed model.

The availability of large microarray data has led to a growing interest in biclustering methods in the past decade. Several algorithms have been proposed to identify subsets of genes and conditions according to different similarity measures and under varying constraints. In this paper we focus on the exclusive row biclustering problem for gene expression data sets, in which each row can only be a member of a single bicluster while columns can participate in multiple ones. This type of biclustering may be adequate, for example, for clustering groups of cancer patients where each patient (row) is expected to be carrying only a single type of cancer, while each cancer type is associated with multiple (and possibly overlapping) genes (columns). We present a novel method to identify these exclusive row biclusters through a combination of existing biclustering algorithms and combinatorial auction techniques. We devise an approach for tuning the threshold for our algorithm based on comparison to a null model in the spirit of the Gap statistic approach. We demonstrate our approach on both synthetic and real-world gene expression data and show its power in identifying large span non-overlapping rows sub matrices, while considering their unique nature. The Gap statistic approach succeeds in identifying appropriate thresholds in all our examples.

Many current applications use recommendations in order to modify the natural user behavior, such as to increase the number of sales or the time spent on a website. This results in a gap between the final recommendation objective and the classical setup where recommendation candidates are evaluated by their coherence with past user behavior, by predicting either the missing entries in the user-item matrix, or the most likely next event. To bridge this gap, we optimize a recommendation policy for the task of increasing the desired outcome versus the organic user behavior. We show this is equivalent to learning to predict recommendation outcomes under a fully random recommendation policy. To this end, we propose a new domain adaptation algorithm that learns from logged data containing outcomes from a biased recommendation policy and predicts recommendation outcomes according to random exposure. We compare our method against state-of-the-art factorization methods, in addition to new approaches of causal recommendation and show significant improvements.

Multi-source translation is an approach to exploit multiple inputs (e.g. in two different languages) to increase translation accuracy. In this paper, we examine approaches for multi-source neural machine translation (NMT) using an incomplete multilingual corpus in which some translations are missing. In practice, many multilingual corpora are not complete due to the difficulty to provide translations in all of the relevant languages (for example, in TED talks, most English talks only have subtitles for a small portion of the languages that TED supports). Existing studies on multi-source translation did not explicitly handle such situations. This study focuses on the use of incomplete multilingual corpora in multi-encoder NMT and mixture of NMT experts and examines a very simple implementation where missing source translations are replaced by a special symbol <NULL>. These methods allow us to use incomplete corpora both at training time and test time. In experiments with real incomplete multilingual corpora of TED Talks, the multi-source NMT with the <NULL> tokens achieved higher translation accuracies measured by BLEU than those by any one-to-one NMT systems.

Training a deep architecture using a ranking loss has become standard for the person re-identification task. Increasingly, these deep architectures include additional components that leverage part detections, attribute predictions, pose estimators and other auxiliary information, in order to more effectively localize and align discriminative image regions. In this paper we adopt a different approach and carefully design each component of a simple deep architecture and, critically, the strategy for training it effectively for person re-identification. We extensively evaluate each design choice, leading to a list of good practices for person re-identification. By following these practices, our approach outperforms the state of the art, including more complex methods with auxiliary components, by large margins on four benchmark datasets. We also provide a qualitative analysis of our trained representation which indicates that, while compact, it is able to capture information from localized and discriminative regions, in a manner akin to an implicit attention mechanism.