Developing Predictive Molecular Maps of Human Disease through Community-based Modeling

The failure of biology to identify the molecular causes of disease has led to disappointment in the rate of development of new medicines. By combining the power of community-based modeling with broad access to large datasets on a platform that promotes reproducible analyses we can work towards more predictive molecular maps that can deliver better therapeutics

Software Tools and Approaches for Compound Identification of LC-MS/MS Data in Metabolomics.

The annotation of small molecules remains a major challenge in untargeted mass spectrometry-based metabolomics. We here critically discuss structured elucidation approaches and software that are designed to help during the annotation of unknown compounds. Only by elucidating unknown metabolites first is it possible to biologically interpret complex systems, to map compounds to pathways and to create reliable predictive metabolic models for translational and clinical research. These strategies include the construction and quality of tandem mass spectral databases such as the coalition of MassBank repositories and investigations of MS/MS matching confidence. We present in silico fragmentation tools such as MS-FINDER, CFM-ID, MetFrag, ChemDistiller and CSI:FingerID that can annotate compounds from existing structure databases and that have been used in the CASMI (critical assessment of small molecule identification) contests. Furthermore, the use of retention time models from liquid chromatography and the utility of collision cross-section modelling from ion mobility experiments are covered. Workflows and published examples of successfully annotated unknown compounds are included

Machine Learning Approaches for Improving Prediction Performance of Structure-Activity Relationship Models

In silico bioactivity prediction studies are designed to complement in vivo and in vitro efforts to assess the activity and properties of small molecules. In silico methods such as Quantitative Structure-Activity/Property Relationship (QSAR) are used to correlate the structure of a molecule to its biological property in drug design and toxicological studies. In this body of work, I started with two in-depth reviews into the application of machine learning based approaches and feature reduction methods to QSAR, and then investigated solutions to three common challenges faced in machine learning based QSAR studies. First, to improve the prediction accuracy of learning from imbalanced data, Synthetic Minority Over-sampling Technique (SMOTE) and Edited Nearest Neighbor (ENN) algorithms combined with bagging as an ensemble strategy was evaluated. The Friedman’s aligned ranks test and the subsequent Bergmann-Hommel post hoc test showed that this method significantly outperformed other conventional methods. SMOTEENN with bagging became less effective when IR exceeded a certain threshold (e.g., \u3e40). The ability to separate the few active compounds from the vast amounts of inactive ones is of great importance in computational toxicology. Deep neural networks (DNN) and random forest (RF), representing deep and shallow learning algorithms, respectively, were chosen to carry out structure-activity relationship-based chemical toxicity prediction. Results suggest that DNN significantly outperformed RF (p \u3c 0.001, ANOVA) by 22-27% for four metrics (precision, recall, F-measure, and AUPRC) and by 11% for another (AUROC). Lastly, current features used for QSAR based machine learning are often very sparse and limited by the logic and mathematical processes used to compute them. Transformer embedding features (TEF) were developed as new continuous vector descriptors/features using the latent space embedding from a multi-head self-attention. The significance of TEF as new descriptors was evaluated by applying them to tasks such as predictive modeling, clustering, and similarity search. An accuracy of 84% on the Ames mutagenicity test indicates that these new features has a correlation to biological activity. Overall, the findings in this study can be applied to improve the performance of machine learning based Quantitative Structure-Activity/Property Relationship (QSAR) efforts for enhanced drug discovery and toxicology assessments

The Nexus between Artificial Intelligence and Economics

This book is organized as follows. Section 2 introduces the notion of the Singularity, a stage in development in which technological progress and economic growth increase at a near-infinite rate. Section 3 describes what artificial intelligence is and how it has been applied. Section 4 considers artificial happiness and the likelihood that artificial intelligence might increase human happiness. Section 5 discusses some prominent related concepts and issues. Section 6 describes the use of artificial agents in economic modeling, and section 7 considers some ways in which economic analysis can offer some hints about what the advent of artificial intelligence might bring. Chapter 8 presents some thoughts about the current state of AI and its future prospects.

Scalable FPGA accelerator of the NRM algorithm for efficient stochastic simulation of large-scale biochemical reaction networks

Stochastic simulation of large-scale biochemical reaction networks, with thousands of reactions, is important for systems biology and medicine since it will enable the insilico experimentation with genome-scale reconstructed networks. FPGA based stochastic simulation accelerators can exploit parallelism, but have been limited on the size of biomodels they can handle. We present a high performance scalable System on Chip architecture for implementing Gibson and Bruck's Next Reaction Method efficiently in reconfigurable hardware. Our MPSoC uses aggressive pipelining at the core level and also combines many cores into a Network on Chip to also execute in parallel stochastic repetitions of complex biomodels, each one with up to 4K reactions. The performance of our NRM core depends only on the average outdegree of the biomodel's Dependencies Graph (DG) and not on the number of DG nodes (reactions). By adding cores to the NoC, the system's performance scales linearly and reaches GCycles/sec levels. We show that a medium size FPGA running at ~200 MHz deliver high speedup gains relative to a popular and efficient software simulator running on a very powerful workstation PC

A survey of statistical network models

Networks are ubiquitous in science and have become a focal point for discussion in everyday life. Formal statistical models for the analysis of network data have emerged as a major topic of interest in diverse areas of study, and most of these involve a form of graphical representation. Probability models on graphs date back to 1959. Along with empirical studies in social psychology and sociology from the 1960s, these early works generated an active network community and a substantial literature in the 1970s. This effort moved into the statistical literature in the late 1970s and 1980s, and the past decade has seen a burgeoning network literature in statistical physics and computer science. The growth of the World Wide Web and the emergence of online networking communities such as Facebook, MySpace, and LinkedIn, and a host of more specialized professional network communities has intensified interest in the study of networks and network data. Our goal in this review is to provide the reader with an entry point to this burgeoning literature. We begin with an overview of the historical development of statistical network modeling and then we introduce a number of examples that have been studied in the network literature. Our subsequent discussion focuses on a number of prominent static and dynamic network models and their interconnections. We emphasize formal model descriptions, and pay special attention to the interpretation of parameters and their estimation. We end with a description of some open problems and challenges for machine learning and statistics.Comment: 96 pages, 14 figures, 333 reference

IMPACT UMaine Research, February 2022

Celebrate UMaine\u27s new ranking as a top-tier research institution! Featured stories include: UMaine ascends to highest tier of national research universities; 2021 Annual Research Report for the University of Maine; Graduate School sets records for Academic Year 2021; UMaine Portland Gateway announced CONVERGE Maine seed grant winners; NSF CAREER award to support research on teaching and learning of geometry using VR and AR technology; Abedi provides written testimony in legislative committee hearing; Researching the prevention of adolescent suicide; the IMRC Center expands support for research innovation

SciTech News Volume 70, No. 2 (2016)

Table of Contents: Columns and Reports From the Editor 3 Division News Science-Technology Division 4 New Members 6 Chemistry Division 7 New Members11 Engineering Division 12 Aerospace Section of the Engineering Division 17 Reviews Sci-Tech Book News Reviews 1

Research at Worcester Polytechnic Institute, Fall 2013

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