Designing algorithms to aid discovery by chemical robots

Recently, automated robotic systems have become very efficient, thanks to improved coupling between sensor systems and algorithms, of which the latter have been gaining significance thanks to the increase in computing power over the past few decades. However, intelligent automated chemistry platforms for discovery orientated tasks need to be able to cope with the unknown, which is a profoundly hard problem. In this Outlook, we describe how recent advances in the design and application of algorithms, coupled with the increased amount of chemical data available, and automation and control systems may allow more productive chemical research and the development of chemical robots able to target discovery. This is shown through examples of workflow and data processing with automation and control, and through the use of both well-used and cutting-edge algorithms illustrated using recent studies in chemistry. Finally, several algorithms are presented in relation to chemical robots and chemical intelligence for knowledge discovery

BioBridge: Bringing Data Exploration to Biologists

Since the completion of the Human Genome Project in 2003, biologists have become exceptionally good at producing data. Indeed, biological data has experienced a sustained exponential growth rate, putting effective and thorough analysis beyond the reach of many biologists. This thesis presents BioBridge, an interactive visualization tool developed to bring intuitive data exploration to biologists. BioBridge is designed to work on omics style tabular data in general and thus has broad applicability. This work describes the design and evaluation of BioBridge\u27s Entity View primary visualization as well the accompanying user interface. The Entity View visualization arranges glyphs representing biological entities (e.g. genes, proteins, metabolites) along with related text mining results to provide biological context. Throughout development the goal has been to maximize accessibility and usability for biologists who are not computationally inclined. Evaluations were done with three informal case studies, one of a metabolome dataset and two of microarray datasets. BioBridge is a proof of concept that there is an underexploited niche in the data analysis ecosystem for tools that prioritize accessibility and usability. The use case studies, while anecdotal, are very encouraging. These studies indicate that BioBridge is well suited for the task of data exploration. With further development, BioBridge could become more flexible and usable as additional use case datasets are explored and more feedback is gathered

Quantitative phospho-proteomics reveals the Plasmodium merozoite triggers pre-invasion host kinase modification of the red cell cytoskeleton

The invasive blood-stage malaria parasite - the merozoite - induces rapid morphological changes to the target erythrocyte during entry. However, evidence for active molecular changes in the host cell that accompany merozoite invasion is lacking. Here, we use invasion inhibition assays, erythrocyte resealing and high-definition imaging to explore red cell responses during invasion. We show that although merozoite entry does not involve erythrocyte actin reorganisation, it does require ATP to complete the process. Towards dissecting the ATP requirement, we present an in depth quantitative phospho-proteomic analysis of the erythrocyte during each stage of invasion. Specifically, we demonstrate extensive increased phosphorylation of erythrocyte proteins on merozoite attachment, including modification of the cytoskeletal proteins beta-spectrin and PIEZO1. The association with merozoite contact but not active entry demonstrates that parasite-dependent phosphorylation is mediated by host-cell kinase activity. This provides the first evidence that the erythrocyte is stimulated to respond to early invasion events through molecular changes in its membrane architecture

Outlier detection using distributionally robust optimization under the Wasserstein metric

We present a Distributionally Robust Optimization (DRO) approach to outlier detection in a linear regression setting, where the closeness of probability distributions is measured using the Wasserstein metric. Training samples contaminated with outliers skew the regression plane computed by least squares and thus impede outlier detection. Classical approaches, such as robust regression, remedy this problem by downweighting the contribution of atypical data points. In contrast, our Wasserstein DRO approach hedges against a family of distributions that are close to the empirical distribution. We show that the resulting formulation encompasses a class of models, which include the regularized Least Absolute Deviation (LAD) as a special case. We provide new insights into the regularization term and give guidance on the selection of the regularization coefficient from the standpoint of a confidence region. We establish two types of performance guarantees for the solution to our formulation under mild conditions. One is related to its out-of-sample behavior, and the other concerns the discrepancy between the estimated and true regression planes. Extensive numerical results demonstrate the superiority of our approach to both robust regression and the regularized LAD in terms of estimation accuracy and outlier detection rates

Observer-biased bearing condition monitoring: from fault detection to multi-fault classification

Bearings are simultaneously a fundamental component and one of the principal causes of failure in rotary machinery. The work focuses on the employment of fuzzy clustering for bearing condition monitoring, i.e., fault detection and classification. The output of a clustering algorithm is a data partition (a set of clusters) which is merely a hypothesis on the structure of the data. This hypothesis requires validation by domain experts. In general, clustering algorithms allow a limited usage of domain knowledge on the cluster formation process. In this study, a novel method allowing for interactive clustering in bearing fault diagnosis is proposed. The method resorts to shrinkage to generalize an otherwise unbiased clustering algorithm into a biased one. In this way, the method provides a natural and intuitive way to control the cluster formation process, allowing for the employment of domain knowledge to guiding it. The domain expert can select a desirable level of granularity ranging from fault detection to classification of a variable number of faults and can select a specific region of the feature space for detailed analysis. Moreover, experimental results under realistic conditions show that the adopted algorithm outperforms the corresponding unbiased algorithm (fuzzy c-means) which is being widely used in this type of problems. (C) 2016 Elsevier Ltd. All rights reserved.Grant number: 145602