Ayush Singhal

Bio: Ayush Singhal is an academic researcher from University of Minnesota. The author has contributed to research in topics: Context (language use) & Deep learning. The author has an hindex of 13, co-authored 30 publications receiving 558 citations. Previous affiliations of Ayush Singhal include Maulana Azad Medical College & Bhilai Institute of Technology – Durg.

Text Mining Genotype-Phenotype Relationships from Biomedical Literature for Database Curation and Precision Medicine.

Abstract: The practice of precision medicine will ultimately require databases of genes and mutations for healthcare providers to reference in order to understand the clinical implications of each patient's genetic makeup. Although the highest quality databases require manual curation, text mining tools can facilitate the curation process, increasing accuracy, coverage, and productivity. However, to date there are no available text mining tools that offer high-accuracy performance for extracting such triplets from biomedical literature. In this paper we propose a high-performance machine learning approach to automate the extraction of disease-gene-variant triplets from biomedical literature. Our approach is unique because we identify the genes and protein products associated with each mutation from not just the local text content, but from a global context as well (from the Internet and from all literature in PubMed). Our approach also incorporates protein sequence validation and disease association using a novel text-mining-based machine learning approach. We extract disease-gene-variant triplets from all abstracts in PubMed related to a set of ten important diseases (breast cancer, prostate cancer, pancreatic cancer, lung cancer, acute myeloid leukemia, Alzheimer's disease, hemochromatosis, age-related macular degeneration (AMD), diabetes mellitus, and cystic fibrosis). We then evaluate our approach in two ways: (1) a direct comparison with the state of the art using benchmark datasets; (2) a validation study comparing the results of our approach with entries in a popular human-curated database (UniProt) for each of the previously mentioned diseases. In the benchmark comparison, our full approach achieves a 28% improvement in F1-measure (from 0.62 to 0.79) over the state-of-the-art results. For the validation study with UniProt Knowledgebase (KB), we present a thorough analysis of the results and errors. Across all diseases, our approach returned 272 triplets (disease-gene-variant) that overlapped with entries in UniProt and 5,384 triplets without overlap in UniProt. Analysis of the overlapping triplets and of a stratified sample of the non-overlapping triplets revealed accuracies of 93% and 80% for the respective categories (cumulative accuracy, 77%). We conclude that our process represents an important and broadly applicable improvement to the state of the art for curation of disease-gene-variant relationships.

Real-time moving object detection algorithm on high-resolution videos using GPUs

Abstract: Modern imaging sensors with higher megapixel resolution and frame rates are being increasingly used for wide-area video surveillance (VS). This has produced an accelerated demand for high-performance implementation of VS algorithms for real-time processing of high-resolution videos. The emergence of multi-core architectures and graphics processing units (GPUs) provides energy and cost-efficient platform to meet the real-time processing needs by extracting data level parallelism in such algorithms. However, the potential benefits of these architectures can only be realized by developing fine-grained parallelization strategies and algorithm innovation. This paper describes parallel implementation of video object detection algorithms like Gaussians mixture model (GMM) for background modelling, morphological operations for post-processing and connected component labelling (CCL) for blob labelling. Novel parallelization strategies and fine-grained optimization techniques are described for fully exploiting the computational capacity of CUDA cores on GPUs. Experimental results show parallel GPU implementation achieves significant speedups of ~250× for binary morphology, ~15× for GMM and ~2× for CCL when compared to sequential implementation running on Intel Xeon processor, resulting in processing of 22.3 frames per second for HD videos.

Use of Deep Learning in Modern Recommendation System: A Summary of Recent Works

Abstract: With the exponential increase in the amount of digital information over the internet, online shops, online music, video and image libraries, search engines and recommendation system have become the most convenient ways to find relevant information within a short time. In the recent times, deep learning's advances have gained significant attention in the field of speech recognition, image processing and natural language processing. Meanwhile, several recent studies have shown the utility of deep learning in the area of recommendation systems and information retrieval as well. In this short review, we cover the recent advances made in the field of recommendation using various variants of deep learning technology. We organize the review in three parts: Collaborative system, Content based system and Hybrid system. The review also discusses the contribution of deep learning integrated recommendation systems into several application domains. The review concludes by discussion of the impact of deep learning in recommendation system in various domain and whether deep learning has shown any significant improvement over the conventional systems for recommendation. Finally, we also provide future directions of research which are possible based on the current state of use of deep learning in recommendation systems.

Text Mining for Precision Medicine: Bringing Structure to EHRs and Biomedical Literature to Understand Genes and Health

Abstract: The key question of precision medicine is whether it is possible to find clinically actionable granularity in diagnosing disease and classifying patient risk. The advent of next-generation sequencing and the widespread adoption of electronic health records (EHRs) have provided clinicians and researchers a wealth of data and made possible the precise characterization of individual patient genotypes and phenotypes. Unstructured text—found in biomedical publications and clinical notes—is an important component of genotype and phenotype knowledge. Publications in the biomedical literature provide essential information for interpreting genetic data. Likewise, clinical notes contain the richest source of phenotype information in EHRs. Text mining can render these texts computationally accessible and support information extraction and hypothesis generation. This chapter reviews the mechanics of text mining in precision medicine and discusses several specific use cases, including database curation for personalized cancer medicine, patient outcome prediction from EHR-derived cohorts, and pharmacogenomic research. Taken as a whole, these use cases demonstrate how text mining enables effective utilization of existing knowledge sources and thus promotes increased value for patients and healthcare systems. Text mining is an indispensable tool for translating genotype-phenotype data into effective clinical care that will undoubtedly play an important role in the eventual realization of precision medicine.

Pattern Recognition and Machine Learning

Abstract: Probability Distributions.- Linear Models for Regression.- Linear Models for Classification.- Neural Networks.- Kernel Methods.- Sparse Kernel Machines.- Graphical Models.- Mixture Models and EM.- Approximate Inference.- Sampling Methods.- Continuous Latent Variables.- Sequential Data.- Combining Models.

Patterns of Somatic Mutation in Human Cancer Genomes

Abstract: AACR Centennial Conference: Translational Cancer Medicine-- Nov 4-8, 2007; Singapore PL02-05 All cancers are due to abnormalities in DNA. The availability of the human genome sequence has led to the proposal that resequencing of cancer genomes will reveal the full complement of somatic mutations and hence all the cancer genes. To explore the nature of the information that will be derived from cancer genome sequencing we have sequenced the coding exons of the family of 518 protein kinases, ~1.3Mb DNA per cancer sample, in 210 cancers of diverse histological types. Despite the screen being directed toward the coding regions of a gene family that has previously been strongly implicated in oncogenesis, the results indicate that the majority of somatic mutations detected are “passengers”. There is considerable variation in the number and pattern of these mutations between individual cancers, indicating substantial diversity of processes of molecular evolution between cancers. The imprints of exogenous mutagenic exposures, mutagenic treatment regimes and DNA repair defects can all be seen in the distinctive mutational signatures of individual cancers. This systematic mutation screen and others have previously yielded a number of cancer genes that are frequently mutated in one or more cancer types and which are now anticancer drug targets (for example BRAF , PIK3CA , and EGFR ). However, detailed analyses of the data from our screen additionally suggest that there exist a large number of additional “driver” mutations which are distributed across a substantial number of genes. It therefore appears that cells may be able to utilise mutations in a large repertoire of potential cancer genes to acquire the neoplastic phenotype. However, many of these genes are employed only infrequently. These findings may have implications for future anticancer drug development.

Research-paper recommender systems: a literature survey

Abstract: In the last 16 years, more than 200 research articles were published about research-paper recommender systems. We reviewed these articles and present some descriptive statistics in this paper, as well as a discussion about the major advancements and shortcomings and an overview of the most common recommendation concepts and approaches. We found that more than half of the recommendation approaches applied content-based filtering (55 %). Collaborative filtering was applied by only 18 % of the reviewed approaches, and graph-based recommendations by 16 %. Other recommendation concepts included stereotyping, item-centric recommendations, and hybrid recommendations. The content-based filtering approaches mainly utilized papers that the users had authored, tagged, browsed, or downloaded. TF-IDF was the most frequently applied weighting scheme. In addition to simple terms, n-grams, topics, and citations were utilized to model users' information needs. Our review revealed some shortcomings of the current research. First, it remains unclear which recommendation concepts and approaches are the most promising. For instance, researchers reported different results on the performance of content-based and collaborative filtering. Sometimes content-based filtering performed better than collaborative filtering and sometimes it performed worse. We identified three potential reasons for the ambiguity of the results. (A) Several evaluations had limitations. They were based on strongly pruned datasets, few participants in user studies, or did not use appropriate baselines. (B) Some authors provided little information about their algorithms, which makes it difficult to re-implement the approaches. Consequently, researchers use different implementations of the same recommendations approaches, which might lead to variations in the results. (C) We speculated that minor variations in datasets, algorithms, or user populations inevitably lead to strong variations in the performance of the approaches. Hence, finding the most promising approaches is a challenge. As a second limitation, we noted that many authors neglected to take into account factors other than accuracy, for example overall user satisfaction. In addition, most approaches (81 %) neglected the user-modeling process and did not infer information automatically but let users provide keywords, text snippets, or a single paper as input. Information on runtime was provided for 10 % of the approaches. Finally, few research papers had an impact on research-paper recommender systems in practice. We also identified a lack of authority and long-term research interest in the field: 73 % of the authors published no more than one paper on research-paper recommender systems, and there was little cooperation among different co-author groups. We concluded that several actions could improve the research landscape: developing a common evaluation framework, agreement on the information to include in research papers, a stronger focus on non-accuracy aspects and user modeling, a platform for researchers to exchange information, and an open-source framework that bundles the available recommendation approaches.