Quantitative modeling of post-transcriptional regulation process is a challenging problem in systems biology. A mechanical model of the regulatory process needs to be able to describe the available spatio-temporal protein concentration and mRNA expression data and recover the continuous spatio-temporal fields. Rigorous methods are required to identify model parameters. A promising approach to deal with these difficulties is proposed using Gaussian process as a prior distribution over the latent function of protein concentration and mRNA expression. In this study, we consider a partial differential equation mechanical model with differential operators and latent function. Since the operators at stake are linear, the information from the physical model can be encoded into the kernel function. Hybrid Monte Carlo methods are employed to carry out Bayesian inference of the partial differential equation parameters and Gaussian process kernel parameters. The spatio-temporal field of protein concentration and mRNA expression are reconstructed without explicitly solving the partial differential equation.

Reaction prediction remains one of the major challenges for organic chemistry, and is a pre-requisite for efficient synthetic planning. It is desirable to develop algorithms that, like humans, "learn" from being exposed to examples of the application of the rules of organic chemistry. We explore the use of neural networks for predicting reaction types, using a new reaction fingerprinting method. We combine this predictor with SMARTS transformations to build a system which, given a set of reagents and re- actants, predicts the likely products. We test this method on problems from a popular organic chemistry textbook.

We propose a unified framework for estimating low-rank matrices through nonconvex optimization based on gradient descent algorithm. Our framework is quite general and can be applied to both noisy and noiseless observations. In the general case with noisy observations, we show that our algorithm is guaranteed to linearly converge to the unknown low-rank matrix up to minimax optimal statistical error, provided an appropriate initial estimator. While in the generic noiseless setting, our algorithm converges to the unknown low-rank matrix at a linear rate and enables exact recovery with optimal sample complexity. In addition, we develop a new initialization algorithm to provide a desired initial estimator, which outperforms existing initialization algorithms for nonconvex low-rank matrix estimation. We illustrate the superiority of our framework through three examples: matrix regression, matrix completion, and one-bit matrix completion. We also corroborate our theory through extensive experiments on synthetic data.

Importance sampling is widely used in machine learning and statistics, but its power is limited by the restriction of using simple proposals for which the importance weights can be tractably calculated. We address this problem by studying black-box importance sampling methods that calculate importance weights for samples generated from any unknown proposal or black-box mechanism. Our method allows us to use better and richer proposals to solve difficult problems, and (somewhat counter-intuitively) also has the additional benefit of improving the estimation accuracy beyond typical importance sampling. Both theoretical and empirical analyses are provided.

For the supervised least squares classifier, when the number of training objects is smaller than the dimensionality of the data, adding more data to the training set may first increase the error rate before decreasing it. This, possibly counterintuitive, phenomenon is known as peaking. In this work, we observe that a similar but more pronounced version of this phenomenon also occurs in the semi-supervised setting, where instead of labeled objects, unlabeled objects are added to the training set. We explain why the learning curve has a more steep incline and a more gradual decline in this setting through simulation studies and by applying an approximation of the learning curve based on the work by Raudys & Duin.

In this work we consider adversarial contextual bandits with risk constraints. At each round, nature prepares a context, a cost for each arm, and additionally a risk for each arm. The learner leverages the context to pull an arm and then receives the corresponding cost and risk associated with the pulled arm. In addition to minimizing the cumulative cost, the learner also needs to satisfy long-term risk constraints -- the average of the cumulative risk from all pulled arms should not be larger than a pre-defined threshold. To address this problem, we first study the full information setting where in each round the learner receives an adversarial convex loss and a convex constraint. We develop a meta algorithm leveraging online mirror descent for the full information setting and extend it to contextual bandit with risk constraints setting using expert advice. Our algorithms can achieve near-optimal regret in terms of minimizing the total cost, while successfully maintaining a sublinear growth of cumulative risk constraint violation.

Motivation: Recent advances in technology for brain imaging and high-throughput genotyping have motivated studies examining the influence of genetic variation on brain structure. Wang et al. (Bioinformatics, 2012) have developed an approach for the analysis of imaging genomic studies using penalized multi-task regression with regularization based on a novel group $l_{2,1}$-norm penalty which encourages structured sparsity at both the gene level and SNP level. While incorporating a number of useful features, the proposed method only furnishes a point estimate of the regression coefficients; techniques for conducting statistical inference are not provided. A new Bayesian method is proposed here to overcome this limitation. Results: We develop a Bayesian hierarchical modeling formulation where the posterior mode corresponds to the estimator proposed by Wang et al. (Bioinformatics, 2012), and an approach that allows for full posterior inference including the construction of interval estimates for the regression parameters. We show that the proposed hierarchical model can be expressed as a three-level Gaussian scale mixture and this representation facilitates the use of a Gibbs sampling algorithm for posterior simulation. Simulation studies demonstrate that the interval estimates obtained using our approach achieve adequate coverage probabilities that outperform those obtained from the nonparametric bootstrap. Our proposed methodology is applied to the analysis of neuroimaging and genetic data collected as part of the Alzheimer's Disease Neuroimaging Initiative (ADNI), and this analysis of the ADNI cohort demonstrates clearly the value added of incorporating interval estimation beyond only point estimation when relating SNPs to brain imaging endophenotypes.

In an illiquid stock, traders can collude and place orders on a predetermined price and quantity at a fixed schedule. This is usually done to manipulate the price of the stock or to create artificial liquidity in the stock, which may mislead genuine investors. Here, the problem is to identify such group of colluding traders. We modeled the problem instance as a graph, where each trader corresponds to a vertex of the graph and trade corresponds to edges of the graph. Further, we assign weights on edges depending on total volume, total number of trades, maximum change in the price and commonality between two vertices. Spectral clustering algorithms are used on the constructed graph to identify colluding group(s). We have compared our results with simulated data to show the effectiveness of spectral clustering to detecting colluding groups. Moreover, we also have used parameters of real data to test the effectiveness of our algorithm.

Several probabilistic models from high-dimensional statistics and machine learning reveal an intriguing --and yet poorly understood-- dichotomy. Either simple local algorithms succeed in estimating the object of interest, or even sophisticated semi-definite programming (SDP) relaxations fail. In order to explore this phenomenon, we study a classical SDP relaxation of the minimum graph bisection problem, when applied to Erd\H{o}s-Renyi random graphs with bounded average degree $d>1$, and obtain several types of results. First, we use a dual witness construction (using the so-called non-backtracking matrix of the graph) to upper bound the SDP value. Second, we prove that a simple local algorithm approximately solves the SDP to within a factor $2d^2/(2d^2+d-1)$ of the upper bound. In particular, the local algorithm is at most $8/9$ suboptimal, and $1+O(1/d)$ suboptimal for large degree. We then analyze a more sophisticated local algorithm, which aggregates information according to the harmonic measure on the limiting Galton-Watson (GW) tree. The resulting lower bound is expressed in terms of the conductance of the GW tree and matches surprisingly well the empirically determined SDP values on large-scale Erd\H{o}s-Renyi graphs. We finally consider the planted partition model. In this case, purely local algorithms are known to fail, but they do succeed if a small amount of side information is available. Our results imply quantitative bounds on the threshold for partial recovery using SDP in this model.

The Knowledge Gradient (KG) policy was originally proposed for online ranking and selection problems but has recently been adapted for use in online decision making in general and multi-armed bandit problems (MABs) in particular. We study its use in a class of exponential family MABs and identify weaknesses, including a propensity to take actions which are dominated with respect to both exploitation and exploration. We propose variants of KG which avoid such errors. These new policies include an index heuristic which deploys a KG approach to develop an approximation to the Gittins index. A numerical study shows this policy to perform well over a range of MABs including those for which index policies are not optimal. While KG does not make dominated actions when bandits are Gaussian, it fails to be index consistent and appears not to enjoy a performance advantage over competitor policies when arms are correlated to compensate for its greater computational demands.