Discrete hidden Markov models (HMM) are often applied to malware detection and classification problems. However, the continuous analog of discrete HMMs, that is, Gaussian mixture model-HMMs (GMM-HMM), are rarely considered in the field of cybersecurity. In this paper, we use GMM-HMMs for malware classification and we compare our results to those obtained using discrete HMMs. As features, we consider opcode sequences and entropy-based sequences. For our opcode features, GMM-HMMs produce results that are comparable to those obtained using discrete HMMs, whereas for our entropy-based features, GMM-HMMs generally improve significantly on the classification results that we have achieved with discrete HMMs.

Macromolecules are large, complex molecules composed of covalently bonded monomer units, existing in different stereochemical configurations and topologies. As a result of such chemical diversity, representing, comparing, and learning over macromolecules emerge as critical challenges. To address this, we developed a macromolecule graph representation, with monomers and bonds as nodes and edges, respectively. We captured the inherent chemistry of the macromolecule by using molecular fingerprints for node and edge attributes. For the first time, we demonstrated computation of chemical similarity between 2 macromolecules of varying chemistry and topology, using exact graph edit distances and graph kernels. We also trained graph neural networks for a variety of glycan classification tasks, achieving state-of-the-art results. Our work has two-fold implications - it provides a general framework for representation, comparison, and learning of macromolecules; and enables quantitative chemistry-informed decision-making and iterative design in the macromolecular chemical space. Macromolecules are ubiquitous and indispensable, from constituting what we are made up of to being present in almost everything we use. As biological macromolecules, they form the basis of life, serving as drivers of survival and growth functions. As synthetic macromolecules, humans have engineered the composition and topology to design structural components, sensors, shape-memory materials, drugs, encode messages, and much more (Lutz et al., 2016; Romio et al., 2020; Boydston et al., 2020; Thompson & Korley, 2020).

We present an $(e^{O(p)} \frac{\log \ell}{\log\log\ell})$-approximation algorithm for socially fair clustering with the $\ell_p$-objective. In this problem, we are given a set of points in a metric space. Each point belongs to one (or several) of $\ell$ groups. The goal is to find a $k$-medians, $k$-means, or, more generally, $\ell_p$-clustering that is simultaneously good for all of the groups. More precisely, we need to find a set of $k$ centers $C$ so as to minimize the maximum over all groups $j$ of $\sum_{u \text{ in group }j} d(u,C)^p$. The socially fair clustering problem was independently proposed by Abbasi, Bhaskara, and Venkatasubramanian [2021] and Ghadiri, Samadi, and Vempala [2021]. Our algorithm improves and generalizes their $O(\ell)$-approximation algorithms for the problem. The natural LP relaxation for the problem has an integrality gap of $\Omega(\ell)$. In order to obtain our result, we introduce a strengthened LP relaxation and show that it has an integrality gap of $\Theta(\frac{\log \ell}{\log\log\ell})$ for a fixed $p$. Additionally, we present a bicriteria approximation algorithm, which generalizes the bicriteria approximation of Abbasi et al. [2021].

We introduce a stochastic version of the cutting-plane method for a large class of data-driven Mixed-Integer Nonlinear Optimization (MINLO) problems. We show that under very weak assumptions the stochastic algorithm is able to converge to an $\epsilon$-optimal solution with high probability. Numerical experiments on several problems show that stochastic cutting planes is able to deliver a multiple order-of-magnitude speedup compared to the standard cutting-plane method. We further experimentally explore the lower limits of sampling for stochastic cutting planes and show that for many problems, a sampling size of $O(\sqrt[3]{n})$ appears to be sufficient for high quality solutions.

We propose a method for learning linear models whose predictive performance is robust to causal interventions on unobserved variables, when noisy proxies of those variables are available. Our approach takes the form of a regularization term that trades off between in-distribution performance and robustness to interventions. Under the assumption of a linear structural causal model, we show that a single proxy can be used to create estimators that are prediction optimal under interventions of bounded strength. This strength depends on the magnitude of the measurement noise in the proxy, which is, in general, not identifiable. In the case of two proxy variables, we propose a modified estimator that is prediction optimal under interventions up to a known strength. We further show how to extend these estimators to scenarios where additional information about the "test time" intervention is available during training. We evaluate our theoretical findings in synthetic experiments and using real data of hourly pollution levels across several cities in China.

It has been experimentally observed that the efficiency of distributed training with stochastic gradient (SGD) depends decisively on the batch size and -- in asynchronous implementations -- on the gradient staleness. Especially, it has been observed that the speedup saturates beyond a certain batch size and/or when the delays grow too large. We identify a data-dependent parameter that explains the speedup saturation in both these settings. Our comprehensive theoretical analysis, for strongly convex, convex and non-convex settings, unifies and generalized prior work directions that often focused on only one of these two aspects. In particular, our approach allows us to derive improved speedup results under frequently considered sparsity assumptions. Our insights give rise to theoretically based guidelines on how the learning rates can be adjusted in practice. We show that our results are tight and illustrate key findings in numerical experiments.

Missing values exist in nearly all clinical studies because data for a variable or question are not collected or not available. Inadequate handling of missing values can lead to biased results and loss of statistical power in analysis. Existing models usually do not consider privacy concerns or do not utilise the inherent correlations across multiple features to impute the missing values. In healthcare applications, we are usually confronted with high dimensional and sometimes small sample size datasets that need more effective augmentation or imputation techniques. Besides, imputation and augmentation processes are traditionally conducted individually. However, imputing missing values and augmenting data can significantly improve generalisation and avoid bias in machine learning models. A Bayesian approach to impute missing values and creating augmented samples in high dimensional healthcare data is proposed in this work. We propose folded Hamiltonian Monte Carlo (F-HMC) with Bayesian inference as a more practical approach to process the cross-dimensional relations by applying a random walk and Hamiltonian dynamics to adapt posterior distribution and generate large-scale samples. The proposed method is applied to a cancer symptom assessment dataset and confirmed to enrich the quality of data in precision, accuracy, recall, F1 score, and propensity metric.

Alongside the well-publicized accomplishments of deep neural networks there has emerged an apparent bug in their success on tasks such as object recognition: with deep models trained using vanilla methods, input images can be slightly corrupted in order to modify output predictions, even when these corruptions are practically invisible. This apparent lack of robustness has led researchers to propose methods that can help to prevent an adversary from having such capabilities. The state-of-the-art approaches have incorporated the robustness requirement into the loss function, and the training process involves taking stochastic gradient descent steps not using original inputs but on adversarially-corrupted ones. In this paper we propose a multiclass boosting framework to ensure adversarial robustness. Boosting algorithms are generally well-suited for adversarial scenarios, as they were classically designed to satisfy a minimax guarantee. We provide a theoretical foundation for this methodology and describe conditions under which robustness can be achieved given a weak training oracle. We show empirically that adversarially-robust multiclass boosting not only outperforms the state-of-the-art methods, it does so at a fraction of the training time.

We develop operators for construction of proposals in probabilistic programs, which we refer to as inference combinators. Inference combinators define a grammar over importance samplers that compose primitive operations such as application of a transition kernel and importance resampling. Proposals in these samplers can be parameterized using neural networks, which in turn can be trained by optimizing variational objectives. The result is a framework for user-programmable variational methods that are correct by construction and can be tailored to specific models. We demonstrate the flexibility of this framework by implementing advanced variational methods based on amortized Gibbs sampling and annealing.

Linear models are used in online decision making, such as in machine learning, policy algorithms, and experimentation platforms. Many engineering systems that use linear models achieve computational efficiency through distributed systems and expert configuration. While there are strengths to this approach, it is still difficult to have an environment that enables researchers to interactively iterate and explore data and models, as well as leverage analytics solutions from the open source community. Consequently, innovation can be blocked. Conditionally sufficient statistics is a unified data compression and estimation strategy that is useful for the model development process, as well as the engineering deployment process. The strategy estimates linear models from compressed data without loss on the estimated parameters and their covariances, even when errors are autocorrelated within clusters of observations. Additionally, the compression preserves almost all interactions with the the original data, unlocking better productivity for both researchers and engineering systems.