Bayesian Multi Plate High Throughput Screening of Compounds

arXiv.org Machine Learning

High throughput screening of compounds (chemicals) is an essential part of drug discovery [7], involving thousands to millions of compounds, with the purpose of identifying candidate hits. Most statistical tools, including the industry standard B-score method, work on individual compound plates and do not exploit cross-plate correlation or statistical strength among plates. We present a new statistical framework for high throughput screening of compounds based on Bayesian nonparametric modeling. The proposed approach is able to identify candidate hits from multiple plates simultaneously, sharing statistical strength among plates and providing more robust estimates of compound activity. It can flexibly accommodate arbitrary distributions of compound activities and is applicable to any plate geometry. The algorithm provides a principled statistical approach for hit identification and false discovery rate control. Experiments demonstrate significant improvements in hit identification sensitivity and specificity over the B-score method, which is highly sensitive to threshold choice. The framework is implemented as an efficient R extension package BHTSpack and is suitable for large scale data sets.


Stable specification search in structural equation model with latent variables

arXiv.org Machine Learning

In our previous study, we introduced stable specification search for cross-sectional data (S3C). It is an exploratory causal method that combines stability selection concept and multi-objective optimization to search for stable and parsimonious causal structures across the entire range of model complexities. In this study, we extended S3C to S3C-Latent, to model causal relations between latent variables. We evaluated S3C-Latent on simulated data and compared the results to those of PC-MIMBuild, an extension of the PC algorithm, the state-of-the-art causal discovery method. The comparison showed that S3C-Latent achieved better performance. We also applied S3C-Latent to real-world data of children with attention deficit/hyperactivity disorder and data about measuring mental abilities among pupils. The results are consistent with those of previous studies.


A tree augmented naive Bayesian network experiment for breast cancer prediction

arXiv.org Machine Learning

In order to investigate the breast cancer prediction problem on the aging population with the grades of DCIS, we conduct a tree augmented naive Bayesian network experiment trained and tested on a large clinical dataset including consecutive diagnostic mammography examinations, consequent biopsy outcomes and related cancer registry records in the population of women across all ages. The aggregated results of our ten-fold cross validation method recommend a biopsy threshold higher than 2% for the aging population.


Variational inference for rare variant detection in deep, heterogeneous next-generation sequencing data

arXiv.org Machine Learning

The detection of rare variants is important for understanding the genetic heterogeneity in mixed samples. Recently, next-generation sequencing (NGS) technologies have enabled the identification of single nucleotide variants (SNVs) in mixed samples with high resolution. Yet, the noise inherent in the biological processes involved in next-generation sequencing necessitates the use of statistical methods to identify true rare variants. We propose a novel Bayesian statistical model and a variational expectation-maximization (EM) algorithm to estimate non-reference allele frequency (NRAF) and identify SNVs in heterogeneous cell populations. We demonstrate that our variational EM algorithm has comparable sensitivity and specificity compared with a Markov Chain Monte Carlo (MCMC) sampling inference algorithm, and is more computationally efficient on tests of low coverage ($27\times$ and $298\times$) data. Furthermore, we show that our model with a variational EM inference algorithm has higher specificity than many state-of-the-art algorithms. In an analysis of a directed evolution longitudinal yeast data set, we are able to identify a time-series trend in non-reference allele frequency and detect novel variants that have not yet been reported. Our model also detects the emergence of a beneficial variant earlier than was previously shown, and a pair of concomitant variants.


Exploring Alternative Biases Prior to Learning in Scientific Domains

AAAI Conferences

Bruce G. Buchanan and Yongwon Lee Intelligent Systems Laboratory University of Pittsburgh Pittsburgh, PA 15260 Abstract Before machine learning can be applied to a new scientific domain, considerable attention must be given to finding appropriate ways to characterize the learning problem. A central idea guiding our work is that we must make explicit more of the elements of a program's bias and understand the criteria by which we prefer one bias over another. We illustrate this exploration with a problem to which we have applied the RL induction program, the problem of predicting whether or not a chemical is a likely carcinogen. Introduction Inductive reasoning over a collection of scientific data is not a single event, because considerable exploration is required to characterize the data and the target concepts appropriately. Mitchell (Mitchell 1980), Provost (Provost 1992), and others refer to this process as searching a bias space for an inductive learning program, where the bias is everything in the program that influences learning other than the positive and negative examples used for learning.