Rapid overlay of chemical structures (ROCS) is a standard tool for the calculation of 3D shape and chemical ("color") similarity. ROCS uses unweighted sums to combine many aspects of similarity, yielding parameter-free models for virtual screening. In this report, we decompose the ROCS color force field into "color components" and "color atom overlaps", novel color similarity features that can be weighted in a system-specific manner by machine learning algorithms. In cross-validation experiments, these additional features significantly improve virtual screening performance (ROC AUC scores) relative to standard ROCS.

Which authors of this paper are endorsers? Disable MathJax (What is MathJax?)

This paper addresses network anomography, that is, the problem of inferring network-level anomalies from indirect link measurements. This problem is cast as a low-rank subspace tracking problem for normal flows under incomplete observations, and an outlier detection problem for abnormal flows. Since traffic data is large-scale time-structured data accompanied with noise and outliers under partial observations, an efficient modeling method is essential. To this end, this paper proposes an online subspace tracking of a Hankelized time-structured traffic tensor for normal flows based on the Candecomp/PARAFAC decomposition exploiting the recursive least squares (RLS) algorithm. We estimate abnormal flows as outlier sparse flows via sparsity maximization in the underlying under-constrained linear-inverse problem. A major advantage is that our algorithm estimates normal flows by low-dimensional matrices with time-directional features as well as the spatial correlation of multiple links without using the past observed measurements and the past model parameters. Extensive numerical evaluations show that the proposed algorithm achieves faster convergence per iteration of model approximation, and better volume anomaly detection performance compared to state-of-the-art algorithms.

While graphical models for continuous data (Gaussian graphical models) and discrete data (Ising models) have been extensively studied, there is little work on graphical models linking both continuous and discrete variables (mixed data), which are common in many scientific applications. We propose a novel graphical model for mixed data, which is simple enough to be suitable for high-dimensional data, yet flexible enough to represent all possible graph structures. We develop a computationally efficient regression-based algorithm for fitting the model by focusing on the conditional log-likelihood of each variable given the rest. The parameters have a natural group structure, and sparsity in the fitted graph is attained by incorporating a group lasso penalty, approximated by a weighted $\ell_1$ penalty for computational efficiency. We demonstrate the effectiveness of our method through an extensive simulation study and apply it to a music annotation data set (CAL500), obtaining a sparse and interpretable graphical model relating the continuous features of the audio signal to categorical variables such as genre, emotions, and usage associated with particular songs. While we focus on binary discrete variables, we also show that the proposed methodology can be easily extended to general discrete variables.

This project looks into the application of Machine Learning (ML) techniques in the prediction of Immunogenicity (Categorical; Positive or Negative) based on a peptide and its associated amino acid properties. This study uses peptide data from the Immune Epitode Database (IEDB). The R package "Peptides" has been used to compute the amino acid properties and mashup with peptide data to enable the use of ML algorithms for immunogenicity analysis, particularly, the algorithms that are more efficient with numeric and categorical data instead of string sequence. Tensorflow is an open source software library ML that provides linear regression and classification algorithms (open sourced by Google in Nov 2015) for multi-dimensional arrays (aka "Tensors"). K-fold cross-validation as well as hold-out of test data was used to train and test the generated models.

Molecular "fingerprints" encoding structural information are the workhorse of cheminformatics and machine learning in drug discovery applications. However, fingerprint representations necessarily emphasize particular aspects of the molecular structure while ignoring others, rather than allowing the model to make data-driven decisions. We describe molecular "graph convolutions", a machine learning architecture for learning from undirected graphs, specifically small molecules. Graph convolutions use a simple encoding of the molecular graph---atoms, bonds, distances, etc.---which allows the model to take greater advantage of information in the graph structure. Although graph convolutions do not outperform all fingerprint-based methods, they (along with other graph-based methods) represent a new paradigm in ligand-based virtual screening with exciting opportunities for future improvement.

Probabilistic techniques are central to data analysis, but different approaches can be difficult to apply, combine, and compare. This paper introduces composable generative population models (CGPMs), a computational abstraction that extends directed graphical models and can be used to describe and compose a broad class of probabilistic data analysis techniques. Examples include hierarchical Bayesian models, multivariate kernel methods, discriminative machine learning, clustering algorithms, dimensionality reduction, and arbitrary probabilistic programs. We also demonstrate the integration of CGPMs into BayesDB, a probabilistic programming platform that can express data analysis tasks using a modeling language and a structured query language. The practical value is illustrated in two ways. First, CGPMs are used in an analysis that identifies satellite data records which probably violate Kepler's Third Law, by composing causal probabilistic programs with non-parametric Bayes in under 50 lines of probabilistic code. Second, for several representative data analysis tasks, we report on lines of code and accuracy measurements of various CGPMs, plus comparisons with standard baseline solutions from Python and MATLAB libraries.

Disease prediction or classification using health datasets involve using well-known predictors associated with the disease as features for the models. This study considers multiple data components of an individual's health, using the relationship between variables to generate features that may improve the performance of disease classification models. In order to capture information from different aspects of the data, this project uses a multiview learning approach, using Canonical Correlation Analysis (CCA), a technique that finds projections with maximum correlations between two data views. Data categories collected from the NHANES survey (1999-2014) are used as views to learn the multiview representations. The usefulness of the representations is demonstrated by applying them as features in a Diabetes classification task.

If omitted, randomForest will run in unsupervised mode. Arguments mtry: number of variables selected at each split - default sqrt(no of variables) for classification ntree: number of trees to grow: default 500 nodesize: minimum size of terminal nodes default 1 Step III: Find the number of trees where the out of bag error rate stabilizes and reach minimum. Step IV: Find the optimal number of variables selected at each split Select mtry value with minimum out of bag(OOB) error. It returns the optimal number of mtry (paramter used in randomforest package).

Last month, the drinking water in a Colorado town was declared unsafe, because it had been contaminated by an ingredient from cannabis. It took two days to discover that this was not the case – a water test had turned up a false positive result. In fact, false positives are widespread in our everyday lives, and we seem to have an innate inability to get to grips with them. The fuss in Hugo, Colorado – a state where cannabis use is now legal – began when a county employee administering a test for drug use decided to use the same kind of test on tap water, rather than saliva, in an attempt to rule out a false positive. When the water tested positive too, it was assumed the test kit was a dud.