Where machine-learned predictive risk scores inform high-stakes decisions, such as bail and sentencing in criminal justice, fairness has been a serious concern. Recent work has characterized the disparate impact that such risk scores can have when used for a binary classification task. This may not account, however, for the more diverse downstream uses of risk scores and their non-binary nature. To better account for this, in this paper, we investigate the fairness of predictive risk scores from the point of view of a bipartite ranking task, where one seeks to rank positive examples higher than negative ones. We introduce the xAUC disparity as a metric to assess the disparate impact of risk scores and define it as the difference in the probabilities of ranking a random positive example from one protected group above a negative one from another group and vice versa. We provide a decomposition of bipartite ranking loss into components that involve the discrepancy and components that involve pure predictive ability within each group. We use xAUC analysis to audit predictive risk scores for recidivism prediction, income prediction, and cardiac arrest prediction, where it describes disparities that are not evident from simply comparing within-group predictive performance.
Motivation: Ab initio protein docking represents a major challenge for optimizing a noisy and costly "black box"-like function in a high-dimensional space. Despite progress in this field, there is no docking method available for rigorous uncertainty quantification (UQ) of its solution quality (e.g. interface RMSD or iRMSD). Results: We introduce a novel algorithm, Bayesian Active Learning (BAL), for optimization and UQ of such black-box functions and flexible protein docking. BAL directly models the posterior distribution of the global optimum (or native structures for protein docking) with active sampling and posterior estimation iteratively feeding each other. Furthermore, we use complex normal modes to represent a homogeneous Euclidean conformation space suitable for high-dimension optimization and construct funnel-like energy models for encounter complexes. Over a protein docking benchmark set and a CAPRI set including homology docking, we establish that BAL significantly improve against both starting points by rigid docking and refinements by particle swarm optimization, providing for one third targets a top-3 near-native prediction. BAL also generates tight confidence intervals with half range around 25% of iRMSD and confidence level at 85%. Its estimated probability of a prediction being native or not achieves binary classification AUROC at 0.93 and AUPRC over 0.60 (compared to 0.14 by chance); and also found to help ranking predictions. To the best of our knowledge, this study represents the first uncertainty quantification solution for protein docking, with theoretical rigor and comprehensive assessment. Source codes are available at https://github.com/Shen-Lab/BAL.
We present two sampled quasi-Newton methods (sampled LBFGS and sampled LSR1) for solving empirical risk minimization problems that arise in machine learning. Contrary to the classical variants of these methods that sequentially build Hessian or inverse Hessian approximations as the optimization progresses, our proposed methods sample points randomly around the current iterate at every iteration to produce these approximations. As a result, the approximations constructed make use of more reliable (recent and local) information, and do not depend on past iterate information that could be significantly stale. Our proposed algorithms are efficient in terms of accessed data points (epochs) and have enough concurrency to take advantage of parallel/distributed computing environments. We provide convergence guarantees for our proposed methods. Numerical tests on a toy classification problem as well as on popular benchmarking binary classification and neural network training tasks reveal that the methods outperform their classical variants.
We propose a general framework to learn deep generative models via \textbf{V}ariational \textbf{Gr}adient Fl\textbf{ow} (VGrow) on probability spaces. The evolving distribution that asymptotically converges to the target distribution is governed by a vector field, which is the negative gradient of the first variation of the $f$-divergence between them. We prove that the evolving distribution coincides with the pushforward distribution through the infinitesimal time composition of residual maps that are perturbations of the identity map along the vector field. The vector field depends on the density ratio of the pushforward distribution and the target distribution, which can be consistently learned from a binary classification problem. Connections of our proposed VGrow method with other popular methods, such as VAE, GAN and flow-based methods, have been established in this framework, gaining new insights of deep generative learning. We also evaluated several commonly used divergences, including Kullback-Leibler, Jensen-Shannon, Jeffrey divergences as well as our newly discovered `logD' divergence which serves as the objective function of the logD-trick GAN. Experimental results on benchmark datasets demonstrate that VGrow can generate high-fidelity images in a stable and efficient manner, achieving competitive performance with state-of-the-art GANs.
In many real-world prediction tasks, class labels include information about the relative ordering between labels, which is not captured by commonly-used loss functions such as multi-category cross-entropy. Recently, the deep learning community adopted ordinal regression frameworks to take such ordering information into account. Neural networks were equipped with ordinal regression capabilities by transforming ordinal targets into binary classification subtasks. However, this method suffers from inconsistencies among the different binary classifiers. To resolve these inconsistencies, we propose the COnsistent RAnk Logits (CORAL) framework with strong theoretical guarantees for rank-monotonicity and consistent confidence scores. Moreover, the proposed method is architecture-agnostic and can extend arbitrary state-of-the-art deep neural network classifiers for ordinal regression tasks. The empirical evaluation of the proposed rank-consistent method on a range of face-image datasets for age prediction shows a substantial reduction of the prediction error compared to the reference ordinal regression network.
Cosmologists are facing the problem of the analysis of a huge quantity of data when observing the sky. The methods used in cosmology are, for the most of them, relying on astrophysical models, and thus, for the classification, they usually use a machine learning approach in two-steps, which consists in, first, extracting features, and second, using a classifier. In this paper, we are specifically studying the supernovae phenomenon and especially the binary classification "I.a supernovae versus not-I.a supernovae". We present two Convolutional Neural Networks (CNNs) defeating the current state-of-the-art. The first one is adapted to time series and thus to the treatment of supernovae light-curves. The second one is based on a Siamese CNN and is suited to the nature of data, i.e. their sparsity and their weak quantity (small learning database).
Gaussian processes are a class of flexible nonparametric Bayesian tools that are widely used across the sciences, and in industry, to model complex data sources. Key to applying Gaussian process models is the availability of well-developed open source software, which is available in many programming languages. In this paper, we present a tutorial of the GaussianProcesses.jl package that has been developed for the Julia programming language. GaussianProcesses.jl utilises the inherent computational benefits of the Julia language, including multiple dispatch and just-in-time compilation, to produce a fast, flexible and user-friendly Gaussian processes package. The package provides many mean and kernel functions with supporting inference tools to fit exact Gaussian process models, as well as a range of alternative likelihood functions to handle non-Gaussian data (e.g. binary classification models) and sparse approximations for scalable Gaussian processes. The package makes efficient use of existing Julia packages to provide users with a range of optimization and plotting tools.
In the era of big data, an important weapon in a machine learning researcher's arsenal is a scalable Support Vector Machine (SVM) algorithm. SVMs are extensively used for solving classification problems. Traditional algorithms for learning SVMs often scale super linearly with training set size which becomes infeasible very quickly for large data sets. In recent years, scalable algorithms have been designed which study the primal or dual formulations of the problem. This often suggests a way to decompose the problem and facilitate development of distributed algorithms. In this paper, we present a distributed algorithm for learning linear Support Vector Machines in the primal form for binary classification called Gossip-bAseD sub-GradiEnT (GADGET) SVM. The algorithm is designed such that it can be executed locally on nodes of a distributed system. Each node processes its local homogeneously partitioned data and learns a primal SVM model. It then gossips with random neighbors about the classifier learnt and uses this information to update the model. Extensive theoretical and empirical results suggest that this anytime algorithm has performance comparable to its centralized and online counterparts.
This paper considers extractive summarisation in a comparative setting: given two or more document groups (e.g., separated by publication time), the goal is to select a small number of documents that are representative of each group, and also maximally distinguishable from other groups. We formulate a set of new objective functions for this problem that connect recent literature on document summarisation, interpretable machine learning, and data subset selection. In particular, by casting the problem as a binary classification amongst different groups, we derive objectives based on the notion of maximum mean discrepancy, as well as a simple yet effective gradient-based optimisation strategy. Our new formulation allows scalable evaluations of comparative summarisation as a classification task, both automatically and via crowd-sourcing. To this end, we evaluate comparative summarisation methods on a newly curated collection of controversial news topics over 13 months. We observe that gradient-based optimisation outperforms discrete and baseline approaches in 14 out of 24 different automatic evaluation settings. In crowd-sourced evaluations, summaries from gradient optimisation elicit 7% more accurate classification from human workers than discrete optimisation. Our result contrasts with recent literature on submodular data subset selection that favours discrete optimisation. We posit that our formulation of comparative summarisation will prove useful in a diverse range of use cases such as comparing content sources, authors, related topics, or distinct view points.
Embedding models for deterministic Knowledge Graphs (KG) have been extensively studied, with the purpose of capturing latent semantic relations between entities and incorporating the structured knowledge into machine learning. However, there are many KGs that model uncertain knowledge, which typically model the inherent uncertainty of relations facts with a confidence score, and embedding such uncertain knowledge represents an unresolved challenge. The capturing of uncertain knowledge will benefit many knowledge-driven applications such as question answering and semantic search by providing more natural characterization of the knowledge. In this paper, we propose a novel uncertain KG embedding model UKGE, which aims to preserve both structural and uncertainty information of relation facts in the embedding space. Unlike previous models that characterize relation facts with binary classification techniques, UKGE learns embeddings according to the confidence scores of uncertain relation facts. To further enhance the precision of UKGE, we also introduce probabilistic soft logic to infer confidence scores for unseen relation facts during training. We propose and evaluate two variants of UKGE based on different learning objectives. Experiments are conducted on three real-world uncertain KGs via three tasks, i.e. confidence prediction, relation fact ranking, and relation fact classification. UKGE shows effectiveness in capturing uncertain knowledge by achieving promising results on these tasks, and consistently outperforms baselines on these tasks.
We consider a high dimensional binary classification problem and construct a classification procedure by minimizing the empirical misclassification risk with a penalty on the number of selected features. We derive non-asymptotic probability bounds on the estimated sparsity as well as on the excess misclassification risk. In particular, we show that our method yields a sparse solution whose l0-norm can be arbitrarily close to true sparsity with high probability and obtain the rates of convergence for the excess misclassification risk. The proposed procedure is implemented via the method of mixed integer linear programming. Its numerical performance is illustrated in Monte Carlo experiments.
We propose a new iris presentation attack detection method using three-dimensional features of an observed iris region estimated by photometric stereo. Our implementation uses a pair of iris images acquired by a common commercial iris sensor (LG 4000). No hardware modifications of any kind are required. Our approach should be applicable to any iris sensor that can illuminate the eye from two different directions. Each iris image in the pair is captured under near-infrared illumination at a different angle relative to the eye. Photometric stereo is used to estimate surface normal vectors in the non-occluded portions of the iris region. The variability of the normal vectors is used as the presentation attack detection score. This score is larger for a texture that is irregularly opaque and printed on a convex contact lens, and is smaller for an authentic iris texture. Thus the problem is formulated as binary classification into (a) an eye wearing textured contact lens and (b) the texture of an actual iris surface (possibly seen through a clear contact lens). Experiments were carried out on a database of approx. 2,900 iris image pairs acquired from approx. 100 subjects. Our method was able to correctly classify over 95% of samples when tested on contact lens brands unseen in training, and over 98% of samples when the contact lens brand was seen during training. The source codes of the method are made available to other researchers.
This work explores adaptations of successful multi-armed bandits policies to the online contextual bandits scenario with binary rewards using binary classification algorithms such as logistic regression as black-box oracles. Some of these adaptations are achieved through bootstrapping or approximate bootstrapping, while others rely on other forms of randomness, resulting in more scalable approaches than previous works, and the ability to work with any type of classification algorithm. In particular, the Adaptive-Greedy algorithm shows a lot of promise, in many cases achieving better performance than upper confidence bound and Thompson sampling strategies, at the expense of more hyperparameters to tune.
Generalized additive models (GAMs) are favored in many regression and binary classification problems because they are able to fit complex, nonlinear functions while still remaining interpretable. In the first part of this paper, we generalize a state-of-the-art GAM learning algorithm based on boosted trees to the multiclass setting, and show that this multiclass algorithm outperforms existing GAM learning algorithms and sometimes matches the performance of full complexity models such as gradient boosted trees. In the second part, we turn our attention to the interpretability of GAMs in the multiclass setting. Surprisingly, the natural interpretability of GAMs breaks down when there are more than two classes. Naive interpretation of multiclass GAMs can lead to false conclusions. Inspired by binary GAMs, we identify two axioms that any additive model must satisfy in order to not be visually misleading. We then develop a technique called Additive Post-Processing for Interpretability (API), that provably transforms a pre-trained additive model to satisfy the interpretability axioms without sacrificing accuracy. The technique works not just on models trained with our learning algorithm, but on any multiclass additive model, including multiclass linear and logistic regression. We demonstrate the effectiveness of API on a 12-class infant mortality dataset.
Outlier detection is an important topic in machine learning and has been used in a wide range of applications. In this paper, we approach outlier detection as a binary-classification issue by sampling potential outliers from a uniform reference distribution. However, due to the sparsity of data in high-dimensional space, a limited number of potential outliers may fail to provide sufficient information to assist the classifier in describing a boundary that can separate outliers from normal data effectively. To address this, we propose a novel Single-Objective Generative Adversarial Active Learning (SO-GAAL) method for outlier detection, which can directly generate informative potential outliers based on the mini-max game between a generator and a discriminator. Moreover, to prevent the generator from falling into the mode collapsing problem, the stop node of training should be determined when SO-GAAL is able to provide sufficient information. But without any prior information, it is extremely difficult for SO-GAAL. Therefore, we expand the network structure of SO-GAAL from a single generator to multiple generators with different objectives (MO-GAAL), which can generate a reasonable reference distribution for the whole dataset. We empirically compare the proposed approach with several state-of-the-art outlier detection methods on both synthetic and real-world datasets. The results show that MO-GAAL outperforms its competitors in the majority of cases, especially for datasets with various cluster types or high irrelevant variable ratio.
We propose Information-Theoretic Active Learning (ITAL), a novel batch-mode active learning method for binary classification, and apply it for acquiring meaningful user feedback in the context of content-based image retrieval. Instead of combining different heuristics such as uncertainty, diversity, or density, our method is based on maximizing the mutual information between the predicted relevance of the images and the expected user feedback regarding the selected batch. We propose suitable approximations to this computationally demanding problem and also integrate an explicit model of user behavior that accounts for possible incorrect labels and unnameable instances. Furthermore, our approach does not only take the structure of the data but also the expected model output change caused by the user feedback into account. In contrast to other methods, ITAL turns out to be highly flexible and provides state-of-the-art performance across various datasets, such as MIRFLICKR and ImageNet.
Many optimization techniques evaluate solutions consecutively, where the next candidate for evaluation is determined by the results of previous evaluations. For example, these include iterative methods, "black box" optimization algorithms, simulated annealing, evolutionary algorithms and tabu search, to name a few. When solving an optimization problem, these algorithms evaluate a large number of solutions, which raises the following question: Is it possible to learn something about the optimum using these solutions? In this paper, we define this "learning" question in terms of a logistic regression model and explore its predictive accuracy computationally. The proposed model uses a collection of solutions to predict the components of the optimal solutions. To illustrate the utility of such predictions, we embed the logistic regression model into the tabu search algorithm for job shop scheduling problem. The resulting framework is simple to implement, yet provides a significant boost to the performance of the standard tabu search.
This paper presents a novel approach to the segmentation of orthographic word forms in contemporary Hebrew, focusing purely on splitting without carrying out morphological analysis or disambiguation. Casting the analysis task as character-wise binary classification and using adjacent character and word-based lexicon-lookup features, this approach achieves over 98% accuracy on the benchmark SPMRL shared task data for Hebrew, and 97% accuracy on a new out of domain Wikipedia dataset, an improvement of ~4% and 5% over previous state of the art performance.
Ventricular Fibrillation (VF), one of the most dangerous arrhythmias, is responsible for sudden cardiac arrests. Thus, various algorithms have been developed to predict VF from Electrocardiogram (ECG), which is a binary classification problem. In the literature, we find a number of algorithms based on signal processing, where, after some robust mathematical operations the decision is given based on a predefined threshold over a single value. On the other hand, some machine learning based algorithms are also reported in the literature; however, these algorithms merely combine some parameters and make a prediction using those as features. Both the approaches have their perks and pitfalls; thus our motivation was to coalesce them to get the best out of the both worlds. Hence we have developed, VFPred that, in addition to employing a signal processing pipeline, namely, Empirical Mode Decomposition and Discrete Time Fourier Transform for useful feature extraction, uses a Support Vector Machine for efficient classification. VFPred turns out to be a robust algorithm as it is able to successfully segregate the two classes with equal confidence (Sensitivity = 99.99%, Specificity = 98.40%) even from a short signal of 5 seconds long, whereas existing works though requires longer signals, flourishes in one but fails in the other.
The electrocardiogram or ECG has been in use for over 100 years and remains the most widely performed diagnostic test to characterize cardiac structure and electrical activity. We hypothesized that parallel advances in computing power, innovations in machine learning algorithms, and availability of large-scale digitized ECG data would enable extending the utility of the ECG beyond its current limitations, while at the same time preserving interpretability, which is fundamental to medical decision-making. We identified 36,186 ECGs from the UCSF database that were 1) in normal sinus rhythm and 2) would enable training of specific models for estimation of cardiac structure or function or detection of disease. We derived a novel model for ECG segmentation using convolutional neural networks (CNN) and Hidden Markov Models (HMM) and evaluated its output by comparing electrical interval estimates to 141,864 measurements from the clinical workflow. We built a 725-element patient-level ECG profile using downsampled segmentation data and trained machine learning models to estimate left ventricular mass, left atrial volume, mitral annulus e' and to detect and track four diseases: pulmonary arterial hypertension (PAH), hypertrophic cardiomyopathy (HCM), cardiac amyloid (CA), and mitral valve prolapse (MVP). CNN-HMM derived ECG segmentation agreed with clinical estimates, with median absolute deviations (MAD) as a fraction of observed value of 0.6% for heart rate and 4% for QT interval. Patient-level ECG profiles enabled quantitative estimates of left ventricular and mitral annulus e' velocity with good discrimination in binary classification models of left ventricular hypertrophy and diastolic function. Models for disease detection ranged from AUROC of 0.94 to 0.77 for MVP. Top-ranked variables for all models included known ECG characteristics along with novel predictors of these traits/diseases.