My clients are looking for computer scientists, statisticians, biostatisticians, physicists, computational social scientists, economists, engineers, operations researchers- in short they are looking for Data Scientist with strong hands on experience in "Big Data" as well as predictive modeling, optimization, machine learning, neural networks using a range of advanced technical tools (Python, SAS, Hadoop, R, Matlab, Machine learning, natural language processing, CPlex, C, etc.) This is a position that will be responsible for helping develop quantitative solutions to solve complex applications. The candidates will be involved in developing leading-edge, "out of the box" advanced analytic solutions and processes. Substantial data analysis experience utilizing standard tools such as SAS, SPSS, or R In depth knowledge of standard algorithms such as linear regression, logistic regression, clustering, decision trees, and affinity analysis Very strong SQL skills including complex query structures Comfort with relational database theory, third normal form, and data models Previous presales experience in the software industry and an understanding of sales cycles: partnering with account executives, sales approaches, and sales support for large customers. Sufficient depth and breadth of technical knowledge to design and scope multiple deliverables across a number of technologies Demonstrated innovation and communication of new deliverables and offerings.

There are approximately 1,100 known antimicrobial peptides (AMP) with diverse sequences that can permeate microbial membranes. To help discover the "blueprint" for natural AMP sequences, researchers from the University of Illinois at Urbana-Champaign and the University of California, Los Angeles, have developed a new machine learning approach to discover and design alpha-helical membrane active peptides based on their physicochemical properties. "In this work, we have trained a machine learning classifier--known as a support vector machine--to recognize membrane activity and experimentally calibrated the recognition metric by peptide synthesis and characterization," explained Andrew Ferguson, an assistant professor of materials science and engineering at Illinois. "We use machine learning to not only discover new membrane active peptides, but to also identify membrane activity in known peptides with previously defined functions leading us to discover membrane activity in diverse and unexpected peptide families. "Since getting cargo into a cell is important for many applications, we anticipate that this tool can have broad biomedical implications including in immunotherapy and in broad-spectrum membrane-active antimicrobial peptides to combat the rising incidence of drug resistance, design of cationic cell-penetrating peptides for nucleic acid transfection into cells, and in targeting and permeating anticancer therapeutics into tumors," added Ferguson, who was the senior computational investigator for the project. In this collaborative work, the Illinois researchers developed the computational innovations, with the experimental testing of the predictions accomplished at UCLA. The results, which highlight the difference between the efficacy of an antimicrobial and its recognizability as such, are surprising. "AMPs do not share a common core structure, but tend to be short, cationic, and amphiphilic," Ferguson said. "By training our machine learning classifier over a training set comprising peptides with known antimicrobial activity (hits) and decoy peptides with no activity (misses), the classifier learned the physical and chemical properties of a peptide that make for good membrane activity.

Cancer survival prediction is an active area of research that can help prevent unnecessary therapies and improve patient's quality of life. Gene expression profiling is being widely used in cancer studies to discover informative biomarkers that aid predict different clinical endpoint prediction. We use multiple modalities of data derived from RNA deep-sequencing (RNA-seq) to predict survival of cancer patients. Despite the wealth of information available in expression profiles of cancer tumors, fulfilling the aforementioned objective remains a big challenge, for the most part, due to the paucity of data samples compared to the high dimension of the expression profiles. As such, analysis of transcriptomic data modalities calls for state-of-the-art big-data analytics techniques that can maximally use all the available data to discover the relevant information hidden within a significant amount of noise. In this paper, we propose a pipeline that predicts cancer patients' survival by exploiting the structure of the input (manifold learning) and by leveraging the unlabeled samples using Laplacian support vector machines, a graph-based semi supervised learning (GSSL) paradigm. We show that under certain circumstances, no single modality per se will result in the best accuracy and by fusing different models together via a stacked generalization strategy, we may boost the accuracy synergistically. We apply our approach to two cancer datasets and present promising results. We maintain that a similar pipeline can be used for predictive tasks where labeled samples are expensive to acquire.

In this letter, a novel weighted ensemble classifier is proposed that improves classification accuracy and minimizes the number of classifiers. Ensemble weight finding problem is modeled as a cost function with following terms: (a) a data fidelity term aiming to decrease misclassification rate, (b) a sparsity term aiming to decrease the number of classifiers, and (c) a non-negativity constraint on the weights of the classifiers. The proposed cost function is a non-convex and hard to solve; thus, convex relaxation techniques and novel approximations are employed to obtain a numerically efficient solution. The proposed method achieves better or similar performance compared to state-of-the art classifier ensemble methods, while using lower number of classifiers.

Data science and machine learning have long been interests of mine, but now that I'm working on Fuzzy.io I need to keep on top of all the news in both fields. My preferred way to do this is through listening to podcasts. I've listened to a bunch of machine learning and data science podcasts in the last few months, so I thought I'd share my favorites: Every other week, they release a 10–15 minute episode where hosts, Kyle and Linda Polich give a short primer on topics like k-means clustering, natural language processing and decision tree learning, often using analogies related to their pet parrot, Yoshi. This is the only place where you'll learn about k-means clustering via placement of parrot droppings.

Semidefinite programs have recently been developed for the problem of community detection, which may be viewed as a special case of the stochastic blockmodel. Here, we develop a semidefinite program that can be tailored to other instances of the blockmodel, such as non-assortative networks and overlapping communities. We establish label recovery in sparse settings, with conditions that are analogous to recent results for community detection. In settings where the data is not generated by a blockmodel, we give an oracle inequality that bounds excess risk relative to the best blockmodel approximation. Simulations are presented for community detection, for overlapping communities, and for latent space models.

Critically ill patients in regular wards are vulnerable to unanticipated clinical dete- rioration which requires timely transfer to the intensive care unit (ICU). To allow for risk scoring and patient monitoring in such a setting, we develop a novel Semi- Markov Switching Linear Gaussian Model (SSLGM) for the inpatients' physiol- ogy. The model captures the patients' latent clinical states and their corresponding observable lab tests and vital signs. We present an efficient unsupervised learn- ing algorithm that capitalizes on the informatively censored data in the electronic health records (EHR) to learn the parameters of the SSLGM; the learned model is then used to assess the new inpatients' risk for clinical deterioration in an online fashion, allowing for timely ICU admission. Experiments conducted on a het- erogeneous cohort of 6,094 patients admitted to a large academic medical center show that the proposed model significantly outperforms the currently deployed risk scores such as Rothman index, MEWS, SOFA and APACHE.

We consider the following general hidden hubs model: an $n \times n$ random matrix $A$ with a subset $S$ of $k$ special rows (hubs): entries in rows outside $S$ are generated from the probability distribution $p_0 \sim N(0,\sigma_0^2)$; for each row in $S$, some $k$ of its entries are generated from $p_1 \sim N(0,\sigma_1^2)$, $\sigma_1>\sigma_0$, and the rest of the entries from $p_0$. The problem is to identify the high-degree hubs efficiently. This model includes and significantly generalizes the planted Gaussian Submatrix Model, where the special entries are all in a $k \times k$ submatrix. There are two well-known barriers: if $k\geq c\sqrt{n\ln n}$, just the row sums are sufficient to find $S$ in the general model. For the submatrix problem, this can be improved by a $\sqrt{\ln n}$ factor to $k \ge c\sqrt{n}$ by spectral methods or combinatorial methods. In the variant with $p_0=\pm 1$ (with probability $1/2$ each) and $p_1\equiv 1$, neither barrier has been broken. We give a polynomial-time algorithm to identify all the hidden hubs with high probability for $k \ge n^{0.5-\delta}$ for some $\delta >0$, when $\sigma_1^2>2\sigma_0^2$. The algorithm extends to the setting where planted entries might have different variances each at least as large as $\sigma_1^2$. We also show a nearly matching lower bound: for $\sigma_1^2 \le 2\sigma_0^2$, there is no polynomial-time Statistical Query algorithm for distinguishing between a matrix whose entries are all from $N(0,\sigma_0^2)$ and a matrix with $k=n^{0.5-\delta}$ hidden hubs for any $\delta >0$. The lower bound as well as the algorithm are related to whether the chi-squared distance of the two distributions diverges. At the critical value $\sigma_1^2=2\sigma_0^2$, we show that the general hidden hubs problem can be solved for $k\geq c\sqrt n(\ln n)^{1/4}$, improving on the naive row sum-based method.

In this paper, we discuss the problem of minimizing the sum of two convex functions: a smooth function plus a non-smooth function. Further, the smooth part can be expressed by the average of a large number of smooth component functions, and the non-smooth part is equipped with a simple proximal mapping. We propose a proximal stochastic second-order method, which is efficient and scalable. It incorporates the Hessian in the smooth part of the function and exploits multistage scheme to reduce the variance of the stochastic gradient. We prove that our method can achieve linear rate of convergence.

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