Topic models have emerged as fundamental tools in unsupervised machine learning. Most modern topic modeling algorithms take a probabilistic view and derive inference algorithms based on Latent Dirichlet Allocation (LDA) or its variants. In contrast, we study topic modeling as a combinatorial optimization problem, and propose a new objective function derived from LDA by passing to the small-variance limit. We minimize the derived objective by using ideas from combinatorial optimization, which results in a new, fast, and high-quality topic modeling algorithm. In particular, we show that our results are competitive with popular LDA-based topic modeling approaches, and also discuss the (dis)similarities between our approach and its probabilistic counterparts.

We introduce a new representation and feature extraction method for biological sequences. Named bio-vectors (BioVec) to refer to biological sequences in general with protein-vectors (ProtVec) for proteins (amino-acid sequences) and gene-vectors (GeneVec) for gene sequences, this representation can be widely used in applications of deep learning in proteomics and genomics. In the present paper, we focus on protein-vectors that can be utilized in a wide array of bioinformatics investigations such as family classification, protein visualization, structure prediction, disordered protein identification, and protein-protein interaction prediction. In this method, we adopt artificial neural network approaches and represent a protein sequence with a single dense n-dimensional vector. To evaluate this method, we apply it in classification of 324,018 protein sequences obtained from Swiss-Prot belonging to 7,027 protein families, where an average family classification accuracy of 93%+-0.06% is obtained, outperforming existing family classification methods. In addition, we use ProtVec representation to predict disordered proteins from structured proteins. Two databases of disordered sequences are used: the DisProt database as well as a database featuring the disordered regions of nucleoporins rich with phenylalanine-glycine repeats (FG-Nups). Using support vector machine classifiers, FG-Nup sequences are distinguished from structured protein sequences found in Protein Data Bank (PDB) with a 99.8% accuracy, and unstructured DisProt sequences are differentiated from structured DisProt sequences with 100.0% accuracy. These results indicate that by only providing sequence data for various proteins into this model, accurate information about protein structure can be determined.

Finding a fixed point to a nonexpansive operator, i.e., $x^*=Tx^*$, abstracts many problems in numerical linear algebra, optimization, and other areas of scientific computing. To solve fixed-point problems, we propose ARock, an algorithmic framework in which multiple agents (machines, processors, or cores) update $x$ in an asynchronous parallel fashion. Asynchrony is crucial to parallel computing since it reduces synchronization wait, relaxes communication bottleneck, and thus speeds up computing significantly. At each step of ARock, an agent updates a randomly selected coordinate $x_i$ based on possibly out-of-date information on $x$. The agents share $x$ through either global memory or communication. If writing $x_i$ is atomic, the agents can read and write $x$ without memory locks. Theoretically, we show that if the nonexpansive operator $T$ has a fixed point, then with probability one, ARock generates a sequence that converges to a fixed points of $T$. Our conditions on $T$ and step sizes are weaker than comparable work. Linear convergence is also obtained. We propose special cases of ARock for linear systems, convex optimization, machine learning, as well as distributed and decentralized consensus problems. Numerical experiments of solving sparse logistic regression problems are presented.

Classifier evasion consists in finding for a given instance $x$ the nearest instance $x'$ such that the classifier predictions of $x$ and $x'$ are different. We present two novel algorithms for systematically computing evasions for tree ensembles such as boosted trees and random forests. Our first algorithm uses a Mixed Integer Linear Program solver and finds the optimal evading instance under an expressive set of constraints. Our second algorithm trades off optimality for speed by using symbolic prediction, a novel algorithm for fast finite differences on tree ensembles. On a digit recognition task, we demonstrate that both gradient boosted trees and random forests are extremely susceptible to evasions. Finally, we harden a boosted tree model without loss of predictive accuracy by augmenting the training set of each boosting round with evading instances, a technique we call adversarial boosting.

We show that there are no spurious local minima in the non-convex factorized parametrization of low-rank matrix recovery from incoherent linear measurements. With noisy measurements we show all local minima are very close to a global optimum. Together with a curvature bound at saddle points, this yields a polynomial time global convergence guarantee for stochastic gradient descent {\em from random initialization}.

Performance of nuclear threat detection systems based on gamma-ray spectrometry often strongly depends on the ability to identify the part of measured signal that can be attributed to background radiation. We have successfully applied a method based on Principal Component Analysis (PCA) to obtain a compact null-space model of background spectra using PCA projection residuals to derive a source detection score. We have shown the method's utility in a threat detection system using mobile spectrometers in urban scenes (Tandon et al 2012). While it is commonly assumed that measured photon counts follow a Poisson process, standard PCA makes a Gaussian assumption about the data distribution, which may be a poor approximation when photon counts are low. This paper studies whether and in what conditions PCA with a Poisson-based loss function (Poisson PCA) can outperform standard Gaussian PCA in modeling background radiation to enable more sensitive and specific nuclear threat detection.

The goal of subspace learning is to find a $k$-dimensional subspace of $\mathbb{R}^d$, such that the expected squared distance between instance vectors and the subspace is as small as possible. In this paper we study subspace learning in a partial information setting, in which the learner can only observe $r \le d$ attributes from each instance vector. We propose several efficient algorithms for this task, and analyze their sample complexity

Matrix completion, where we wish to recover a low rank matrix by observing a few entries from it, is a widely studied problem in both theory and practice with wide applications. Most of the provable algorithms so far on this problem have been restricted to the offline setting where they provide an estimate of the unknown matrix using all observations simultaneously. However, in many applications, the online version, where we observe one entry at a time and dynamically update our estimate, is more appealing. While existing algorithms are efficient for the offline setting, they could be highly inefficient for the online setting. In this paper, we propose the first provable, efficient online algorithm for matrix completion. Our algorithm starts from an initial estimate of the matrix and then performs non-convex stochastic gradient descent (SGD). After every observation, it performs a fast update involving only one row of two tall matrices, giving near linear total runtime. Our algorithm can be naturally used in the offline setting as well, where it gives competitive sample complexity and runtime to state of the art algorithms. Our proofs introduce a general framework to show that SGD updates tend to stay away from saddle surfaces and could be of broader interests for other non-convex problems to prove tight rates.

Determinantal Point Processes (DPPs) are probabilistic models over all subsets a ground set of $N$ items. They have recently gained prominence in several applications that rely on "diverse" subsets. However, their applicability to large problems is still limited due to the $\mathcal O(N^3)$ complexity of core tasks such as sampling and learning. We enable efficient sampling and learning for DPPs by introducing KronDPP, a DPP model whose kernel matrix decomposes as a tensor product of multiple smaller kernel matrices. This decomposition immediately enables fast exact sampling. But contrary to what one may expect, leveraging the Kronecker product structure for speeding up DPP learning turns out to be more difficult. We overcome this challenge, and derive batch and stochastic optimization algorithms for efficiently learning the parameters of a KronDPP.

Sparse matrix factorization is a popular tool to obtain interpretable data decompositions, which are also effective to perform data completion or denoising. Its applicability to large datasets has been addressed with online and randomized methods, that reduce the complexity in one of the matrix dimension, but not in both of them. In this paper, we tackle very large matrices in both dimensions. We propose a new factoriza-tion method that scales gracefully to terabyte-scale datasets, that could not be processed by previous algorithms in a reasonable amount of time. We demonstrate the efficiency of our approach on massive functional Magnetic Resonance Imaging (fMRI) data, and on matrix completion problems for recommender systems, where we obtain significant speed-ups compared to state-of-the art coordinate descent methods.