Annotation errors can significantly hurt classifier performance, yet datasets are only growing noisier with the increased use of Amazon Mechanical Turk and techniques like distant supervision that automatically generate labels. In this paper, we present a robust extension of logistic regression that incorporates the possibility of mislabelling directly into the objective. Our model can be trained through nearly the same means as logistic regression, and retains its efficiency on high-dimensional datasets. Through named entity recognition experiments, we demonstrate that our approach can provide a significant improvement over the standard model when annotation errors are present.

Networks are ubiquitous in biology and computational approaches have been largely investigated for their inference. In particular, supervised machine learning methods can be used to complete a partially known network by integrating various measurements. Two main supervised frameworks have been proposed: the local approach, which trains a separate model for each network node, and the global approach, which trains a single model over pairs of nodes. Here, we systematically investigate, theoretically and empirically, the exploitation of tree-based ensemble methods in the context of these two approaches for biological network inference. We first formalize the problem of network inference as classification of pairs, unifying in the process homogeneous and bipartite graphs and discussing two main sampling schemes. We then present the global and the local approaches, extending the later for the prediction of interactions between two unseen network nodes, and discuss their specializations to tree-based ensemble methods, highlighting their interpretability and drawing links with clustering techniques. Extensive computational experiments are carried out with these methods on various biological networks that clearly highlight that these methods are competitive with existing methods.

This paper presents a study in task-oriented approach to stroke rehabilitation by controlling a haptic device via near-infrared spectroscopy-based brain-computer interface (BCI). The task is to command the haptic device to move in opposing directions of leftward and rightward movement. Our study consists of data acquisition, signal preprocessing, and classification. In data acquisition, we conduct experiments based on two different mental tasks: one on pure motor imagery, and another on combined motor imagery and action observation. The experiments were conducted in both offline and online modes. In the signal preprocessing, we use localization method to eliminate channels that are irrelevant to the mental task, as well as perform feature extraction for subsequent classification. We propose multiple support vector machine classifiers with a majority-voting scheme for improved classification results. And lastly, we present test results to demonstrate the efficacy of our proposed approach to possible stroke rehabilitation practice.

Scoring systems are classification models that only require users to add, subtract and multiply a few meaningful numbers to make a prediction. These models are often used because they are practical and interpretable. In this paper, we introduce an off-the-shelf tool to create scoring systems that both accurate and interpretable, known as a Supersparse Linear Integer Model (SLIM). SLIM is a discrete optimization problem that minimizes the 0-1 loss to encourage a high level of accuracy, regularizes the L0-norm to encourage a high level of sparsity, and constrains coefficients to a set of interpretable values. We illustrate the practical and interpretable nature of SLIM scoring systems through applications in medicine and criminology, and show that they are are accurate and sparse in comparison to state-of-the-art classification models using numerical experiments.

Conformal prediction is a method of producing prediction sets that can be applied on top of a wide range of prediction algorithms. The method has a guaranteed coverage probability under the standard IID assumption regardless of whether the assumptions (often considerably more restrictive) of the underlying algorithm are satisfied. However, for the method to be really useful it is desirable that in the case where the assumptions of the underlying algorithm are satisfied, the conformal predictor loses little in efficiency as compared with the underlying algorithm (whereas being a conformal predictor, it has the stronger guarantee of validity). In this paper we explore the degree to which this additional requirement of efficiency is satisfied in the case of Bayesian ridge regression; we find that asymptotically conformal prediction sets differ little from ridge regression prediction intervals when the standard Bayesian assumptions are satisfied.

We describe a simple, efficient, permutation based procedure for selecting the penalty parameter in the LASSO. The procedure, which is intended for applications where variable selection is the primary focus, can be applied in a variety of structural settings, including generalized linear models. We briefly discuss connections between permutation selection and existing theory for the LASSO. In addition, we present a simulation study and an analysis of three real data sets in which permutation selection is compared with cross-validation (CV), the Bayesian information criterion (BIC), and a selection method based on recently developed testing procedures for the LASSO.

This article describes GRADE, a statistical machine learning system developed to support the work of the graduate admissions committee at the University of Texas at Austin Department of Computer Science (UTCS). In recent years, the number of applications to the UTCS PhD program has become too large to manage with a traditional review process. GRADE uses historical admissions data to predict how likely the committee is to admit each new applicant. It reports each prediction as a score similar to those used by human reviewers, and accompanies each by an explanation of what applicant features most influenced its prediction. GRADE makes the review process more efficient by enabling reviewers to spend most of their time on applicants near the decision boundary and by focusing their attention on parts of each applicant’s file that matter the most. An evaluation over two seasons of PhD admissions indicates that the system leads to dramatic time savings, reducing the total time spent on reviews by at least 74 percent.

Multi-view learning aims to improve classification performance by leveraging the consistency among different views of data. The incorporation of multiple views was paid little attention in the studies of domain adaptation, where the view consistency based on source data is largely violated in the target domain due to the distribution gap between different domain data. In this paper, we leverage multiple views for cross-domain document classification. The central idea is to strengthen the views' consistency on target data by identifying the associations of domain-specific features from different domains. We present an Information-theoretic Multi-view Adaptation Model (IMAM) using a multi-way clustering scheme, where word and link clusters can draw together seemingly unrelated features across domains, which boosts the consistency between document clusterings that are based on the respective word and link views. Moreover, we demonstrate that IMAM can always find the document clustering with the minimal disagreement rate to the overlap of view-based clusterings. We provide both theoretical and empirical justifications of the proposed method. Our experiments show that IMAM significantly outperforms traditional multi-view algorithm co-training, the co-training-based adaptation algorithm CODA, the single-view transfer model CoCC and the large-margin-based multi-view transfer model MVTL-LM.

Nonnegative matrix factorization (NMF) has been shown to be identifiable under the separability assumption, under which all the columns(or rows) of the input data matrix belong to the convex cone generated by only a few of these columns(or rows) [1]. In real applications, however, such separability assumption is hard to satisfy. Following [4] and [5], in this paper, we look at the Linear Programming (LP) based reformulation to locate the extreme rays of the convex cone but in a noisy setting. Furthermore, in order to deal with the large scale data, we employ First-Order Methods (FOM) to mitigate the computational complexity of LP, which primarily results from a large number of constraints. We show the performance of the algorithm on real and synthetic data sets.

Substantial evidence indicates that major psychiatric disorders are associated with distributed neural dysconnectivity, leading to strong interest in using neuroimaging methods to accurately predict disorder status. In this work, we are specifically interested in a multivariate approach that uses features derived from whole-brain resting state functional connectomes. However, functional connectomes reside in a high dimensional space, which complicates model interpretation and introduces numerous statistical and computational challenges. Traditional feature selection techniques are used to reduce data dimensionality, but are blind to the spatial structure of the connectomes. We propose a regularization framework where the 6-D structure of the functional connectome is explicitly taken into account via the fused Lasso or the GraphNet regularizer. Our method only restricts the loss function to be convex and margin-based, allowing non-differentiable loss functions such as the hinge-loss to be used. Using the fused Lasso or GraphNet regularizer with the hinge-loss leads to a structured sparse support vector machine (SVM) with embedded feature selection. We introduce a novel efficient optimization algorithm based on the augmented Lagrangian and the classical alternating direction method, which can solve both fused Lasso and GraphNet regularized SVM with very little modification. We also demonstrate that the inner subproblems of the algorithm can be solved efficiently in analytic form by coupling the variable splitting strategy with a data augmentation scheme. Experiments on simulated data and resting state scans from a large schizophrenia dataset show that our proposed approach can identify predictive regions that are spatially contiguous in the 6-D "connectome space," offering an additional layer of interpretability that could provide new insights about various disease processes.