The collection and sharing of genomic data are becoming increasingly commonplace in research, clinical, and direct-to-consumer settings. The computational protocols typically adopted to protect individual privacy include sharing summary statistics, such as allele frequencies, or limiting query responses to the presence/absence of alleles of interest using web-services called Beacons. However, even such limited releases are susceptible to likelihood-ratio-based membership-inference attacks. Several approaches have been proposed to preserve privacy, which either suppress a subset of genomic variants or modify query responses for specific variants (e.g., adding noise, as in differential privacy). However, many of these approaches result in a significant utility loss, either suppressing many variants or adding a substantial amount of noise. In this paper, we introduce optimization-based approaches to explicitly trade off the utility of summary data or Beacon responses and privacy with respect to membership-inference attacks based on likelihood-ratios, combining variant suppression and modification. We consider two attack models. In the first, an attacker applies a likelihood-ratio test to make membership-inference claims. In the second model, an attacker uses a threshold that accounts for the effect of the data release on the separation in scores between individuals in the dataset and those who are not. We further introduce highly scalable approaches for approximately solving the privacy-utility tradeoff problem when information is either in the form of summary statistics or presence/absence queries. Finally, we show that the proposed approaches outperform the state of the art in both utility and privacy through an extensive evaluation with public datasets.

Machine learning and statistical modeling methods were used to analyze the impact of climate change on financial wellbeing of fruit farmers in Tunisia and Chile. The analysis was based on face to face interviews with 801 farmers. Three research questions were investigated. First, whether climate change impacts had an effect on how well the farm was doing financially. Second, if climate change was not influential, what factors were important for predicting financial wellbeing of the farm. And third, ascertain whether observed effects on the financial wellbeing of the farm were a result of interactions between predictor variables. This is the first report directly comparing climate change with other factors potentially impacting financial wellbeing of farms. Certain climate change factors, namely increases in temperature and reductions in precipitation, can regionally impact self-perceived financial wellbeing of fruit farmers. Specifically, increases in temperature and reduction in precipitation can have a measurable negative impact on the financial wellbeing of farms in Chile. This effect is less pronounced in Tunisia. Climate impact differences were observed within Chile but not in Tunisia. However, climate change is only of minor importance for predicting farm financial wellbeing, especially for farms already doing financially well. Factors that are more important, mainly in Tunisia, included trust in information sources and prior farm ownership. Other important factors include farm size, water management systems used and diversity of fruit crops grown. Moreover, some of the important factors identified differed between farms doing and not doing well financially. Interactions between factors may improve or worsen farm financial wellbeing.

Despite the success of large-scale empirical risk minimization (ERM) at achieving high accuracy across a variety of machine learning tasks, fair ERM is hindered by the incompatibility of fairness constraints with stochastic optimization. We consider the problem of fair classification with discrete sensitive attributes and potentially large models and data sets, requiring stochastic solvers. Existing in-processing fairness algorithms are either impractical in the large-scale setting because they require large batches of data at each iteration or they are not guaranteed to converge. In this paper, we develop the first stochastic in-processing fairness algorithm with guaranteed convergence. For demographic parity, equalized odds, and equal opportunity notions of fairness, we provide slight variations of our algorithm--called FERMI--and prove that each of these variations converges in stochastic optimization with any batch size. Empirically, we show that FERMI is amenable to stochastic solvers with multiple (non-binary) sensitive attributes and non-binary targets, performing well even with minibatch size as small as one. Extensive experiments show that FERMI achieves the most favorable tradeoffs between fairness violation and test accuracy across all tested setups compared with state-of-the-art baselines for demographic parity, equalized odds, equal opportunity. These benefits are especially significant with small batch sizes and for non-binary classification with large number of sensitive attributes, making FERMI a practical, scalable fairness algorithm. The code for all of the experiments in this paper is available at: https://github.com/optimization-for-data-driven-science/FERMI.

Likelihood-to-evidence ratio estimation is usually cast as either a binary (NRE-A) or a multiclass (NRE-B) classification task. In contrast to the binary classification framework, the current formulation of the multiclass version has an intrinsic and unknown bias term, making otherwise informative diagnostics unreliable. We propose a multiclass framework free from the bias inherent to NRE-B at optimum, leaving us in the position to run diagnostics that practitioners depend on. It also recovers NRE-A in one corner case and NRE-B in the limiting case. For fair comparison, we benchmark the behavior of all algorithms in both familiar and novel training regimes: when jointly drawn data is unlimited, when data is fixed but prior draws are unlimited, and in the commonplace fixed data and parameters setting. Our investigations reveal that the highest performing models are distant from the competitors (NRE-A, NRE-B) in hyperparameter space. We make a recommendation for hyperparameters distinct from the previous models. We suggest a bound on the mutual information as a performance metric for simulation-based inference methods, without the need for posterior samples, and provide experimental results.

Since data is the fuel that drives machine learning models, and access to labeled data is generally expensive, semi-supervised methods are constantly popular. They enable the acquisition of large datasets without the need for too many expert labels. This work combines self-labeling techniques with active learning in a selective sampling scenario. We propose a new method that builds an ensemble classifier. Based on an evaluation of the inconsistency of the decisions of the individual base classifiers for a given observation, a decision is made on whether to request a new label or use the self-labeling. In preliminary studies, we show that naive application of self-labeling can harm performance by introducing bias towards selected classes and consequently lead to skewed class distribution. Hence, we also propose mechanisms to reduce this phenomenon. Experimental evaluation shows that the proposed method matches current selective sampling methods or achieves better results.

Classification algorithms using RNA-Sequencing (RNA-Seq) data as input are used in a variety of biological applications. By nature, RNA-Seq data is subject to uncontrolled fluctuations both within and especially across datasets, which presents a major difficulty for a trained classifier to generalize to an external dataset. Replacing raw gene counts with the rank of gene counts inside an observation has proven effective to mitigate this problem. However, the rank of a feature is by definition relative to all other features, including highly variable features that introduce noise in the ranking. To address this problem and obtain more robust ranks, we propose a logistic regression model, optirank, which learns simultaneously the parameters of the model and the genes to use as a reference set in the ranking. We show the effectiveness of this method on simulated data. We also consider real classification tasks, which present different kinds of distribution shifts between train and test data. Those tasks concern a variety of applications, such as cancer of unknown primary classification, identification of specific gene signatures, and determination of cell type in single-cell RNA-Seq datasets. On those real tasks, optirank performs at least as well as the vanilla logistic regression on classical ranks, while producing sparser solutions. In addition, to increase the robustness against dataset shifts, we propose a multi-source learning scheme and demonstrate its effectiveness when used in combination with rank-based classifiers.

Abstract: dentifying suicidality including suicidal ideation, attempts, and risk factors in electronic health record data in clinical notes is difficult. A major difficulty is the lack of training samples given the small number of true positive instances among the increasingly large number of patients being screened. This paper describes a novel methodology that identifies suicidality in clinical notes by addressing this data sparsity issue through zero-shot learning. U.S. Veterans Affairs clinical notes served as data. The training dataset label was determined using diagnostic codes of suicide attempt and self-harm.

This dissertation proposes a framework of user-centered security in Natural Language Processing (NLP), and demonstrates how it can improve the accessibility of related research. Accordingly, it focuses on two security domains within NLP with great public interest. First, that of author profiling, which can be employed to compromise online privacy through invasive inferences. Without access and detailed insight into these models' predictions, there is no reasonable heuristic by which Internet users might defend themselves from such inferences. Secondly, that of cyberbullying detection, which by default presupposes a centralized implementation; i.e., content moderation across social platforms. As access to appropriate data is restricted, and the nature of the task rapidly evolves (both through lexical variation, and cultural shifts), the effectiveness of its classifiers is greatly diminished and thereby often misrepresented. Under the proposed framework, we predominantly investigate the use of adversarial attacks on language; i.e., changing a given input (generating adversarial samples) such that a given model does not function as intended. These attacks form a common thread between our user-centered security problems; they are highly relevant for privacy-preserving obfuscation methods against author profiling, and adversarial samples might also prove useful to assess the influence of lexical variation and augmentation on cyberbullying detection.

In the era of Internet of Things (IoT), network-wide anomaly detection is a crucial part of monitoring IoT networks due to the inherent security vulnerabilities of most IoT devices. Principal Components Analysis (PCA) has been proposed to separate network traffics into two disjoint subspaces corresponding to normal and malicious behaviors for anomaly detection. However, the privacy concerns and limitations of devices' computing resources compromise the practical effectiveness of PCA. We propose a federated PCA-based Grassmannian optimization framework that coordinates IoT devices to aggregate a joint profile of normal network behaviors for anomaly detection. First, we introduce a privacy-preserving federated PCA framework to simultaneously capture the profile of various IoT devices' traffic. Then, we investigate the alternating direction method of multipliers gradient-based learning on the Grassmann manifold to guarantee fast training and the absence of detecting latency using limited computational resources. Empirical results on the NSL-KDD dataset demonstrate that our method outperforms baseline approaches. Finally, we show that the Grassmann manifold algorithm is highly adapted for IoT anomaly detection, which permits drastically reducing the analysis time of the system. To the best of our knowledge, this is the first federated PCA algorithm for anomaly detection meeting the requirements of IoT networks.

Network structure provides critical information for understanding the dynamic behavior of networks. However, the complete structure of real-world networks is often unavailable, thus it is crucially important to develop approaches to infer a more complete structure of networks. In this paper, we integrate the configuration model for generating random networks into an Expectation-Maximization-Aggregation (EMA) framework to reconstruct the complete structure of multiplex networks. We validate the proposed EMA framework against the random model on several real-world multiplex networks, including both covert and overt ones. It is found that the EMA framework generally achieves the best predictive accuracy compared to the EM framework and the random model. As the number of layers increases, the performance improvement of EMA over EM decreases. The inferred multiplex networks can be leveraged to inform the decision-making on monitoring covert networks as well as allocating limited resources for collecting additional information to improve reconstruction accuracy. For law enforcement agencies, the inferred complete network structure can be used to develop more effective strategies for covert network interdiction.