Proceedings of the Eighteenth International Conference on Machine Learning., 282 – 289
Total Page：16
File Type：pdf, Size：1020Kb
Load more
Recommended publications
-
Diary James Wickersham Aug 22, 1918 – Jan
Alaska State Library – Historical Collections Diary of James Wickersham MS 107 BOX 5 DIARY 30 Aug 22, 1918 – Jan. 3, 1919 [cover] Diary James Wickersham Aug 22, 1918 – Jan. 3, 1919 Diary 30, 1918 Aug 23, 1918 August 23 Arrived-in Tanana forenoon and went to Lower House kept by Joe. Aincich. Came up from Ruby on the launch “Sibilla” - N.C. Mail launch. Find much hostility to me here engendered and cultivated by White Pass & the N.C. Co's, and b y Gov. Riggs who is here making Sulzers campaign. There is a Reception to Riggs & wife tonight so I will not speak till tomorrow evening. Am visiting around and renewing my acquaintance with the people. Diary 30, 1918 Aug 24, 1918. August 24 My 61st Birthday Will speak tonight at the Moose Hall - Dinner with Andrew Vachon & wife. Spoke tonight to a good crowd at Moose Hall. Had a very friendly reception and am much encouraged though the Gov. & the White Pass & N.C. officials are moving every element possible against me. Attacked all three of them fairly but strongly in my speech & was earnestly supported by the audience. Noticed Father's Jette & Perron, Capt. Lenoir a many others in the Hall. Am satisfied with my speech Diary 30, 1918 Aug 25th August 25 Attended services at Father Jettes church - He preached a beautiful sermon on the sin of covetousness. The “Alaska” will be here this afternoon & will go up the river to Hot Springs on her. Was requested to make 4 Minute talk at Post tonight at picture show - did it badly! Boarded “Alaska” for the Hot Springs at midnight. -
RECENT ADVANCES in BIOLOGY, BIOPHYSICS, BIOENGINEERING and COMPUTATIONAL CHEMISTRY
RECENT ADVANCES in BIOLOGY, BIOPHYSICS, BIOENGINEERING and COMPUTATIONAL CHEMISTRY Proceedings of the 5th WSEAS International Conference on CELLULAR and MOLECULAR BIOLOGY, BIOPHYSICS and BIOENGINEERING (BIO '09) Proceedings of the 3rd WSEAS International Conference on COMPUTATIONAL CHEMISTRY (COMPUCHEM '09) Puerto De La Cruz, Tenerife, Canary Islands, Spain December 14-16, 2009 Recent Advances in Biology and Biomedicine A Series of Reference Books and Textbooks Published by WSEAS Press ISSN: 1790-5125 www.wseas.org ISBN: 978-960-474-141-0 RECENT ADVANCES in BIOLOGY, BIOPHYSICS, BIOENGINEERING and COMPUTATIONAL CHEMISTRY Proceedings of the 5th WSEAS International Conference on CELLULAR and MOLECULAR BIOLOGY, BIOPHYSICS and BIOENGINEERING (BIO '09) Proceedings of the 3rd WSEAS International Conference on COMPUTATIONAL CHEMISTRY (COMPUCHEM '09) Puerto De La Cruz, Tenerife, Canary Islands, Spain December 14-16, 2009 Recent Advances in Biology and Biomedicine A Series of Reference Books and Textbooks Published by WSEAS Press www.wseas.org Copyright © 2009, by WSEAS Press All the copyright of the present book belongs to the World Scientific and Engineering Academy and Society Press. All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, recording, or otherwise, without the prior written permission of the Editor of World Scientific and Engineering Academy and Society Press. All papers of the present volume were peer reviewed -
Applied Category Theory for Genomics – an Initiative
Applied Category Theory for Genomics { An Initiative Yanying Wu1,2 1Centre for Neural Circuits and Behaviour, University of Oxford, UK 2Department of Physiology, Anatomy and Genetics, University of Oxford, UK 06 Sept, 2020 Abstract The ultimate secret of all lives on earth is hidden in their genomes { a totality of DNA sequences. We currently know the whole genome sequence of many organisms, while our understanding of the genome architecture on a systematic level remains rudimentary. Applied category theory opens a promising way to integrate the humongous amount of heterogeneous informations in genomics, to advance our knowledge regarding genome organization, and to provide us with a deep and holistic view of our own genomes. In this work we explain why applied category theory carries such a hope, and we move on to show how it could actually do so, albeit in baby steps. The manuscript intends to be readable to both mathematicians and biologists, therefore no prior knowledge is required from either side. arXiv:2009.02822v1 [q-bio.GN] 6 Sep 2020 1 Introduction DNA, the genetic material of all living beings on this planet, holds the secret of life. The complete set of DNA sequences in an organism constitutes its genome { the blueprint and instruction manual of that organism, be it a human or fly [1]. Therefore, genomics, which studies the contents and meaning of genomes, has been standing in the central stage of scientific research since its birth. The twentieth century witnessed three milestones of genomics research [1]. It began with the discovery of Mendel's laws of inheritance [2], sparked a climax in the middle with the reveal of DNA double helix structure [3], and ended with the accomplishment of a first draft of complete human genome sequences [4]. -
Proquest Dissertations
Automated learning of protein involvement in pathogenesis using integrated queries Eithon Cadag A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy University of Washington 2009 Program Authorized to Offer Degree: Department of Medical Education and Biomedical Informatics UMI Number: 3394276 All rights reserved INFORMATION TO ALL USERS The quality of this reproduction is dependent upon the quality of the copy submitted. In the unlikely event that the author did not send a complete manuscript and there are missing pages, these will be noted. Also, if material had to be removed, a note will indicate the deletion. UMI Dissertation Publishing UMI 3394276 Copyright 2010 by ProQuest LLC. All rights reserved. This edition of the work is protected against unauthorized copying under Title 17, United States Code. uest ProQuest LLC 789 East Eisenhower Parkway P.O. Box 1346 Ann Arbor, Ml 48106-1346 University of Washington Graduate School This is to certify that I have examined this copy of a doctoral dissertation by Eithon Cadag and have found that it is complete and satisfactory in all respects, and that any and all revisions required by the final examining committee have been made. Chair of the Supervisory Committee: Reading Committee: (SjLt KJ. £U*t~ Peter Tgffczy-Hornoch In presenting this dissertation in partial fulfillment of the requirements for the doctoral degree at the University of Washington, I agree that the Library shall make its copies freely available for inspection. I further agree that extensive copying of this dissertation is allowable only for scholarly purposes, consistent with "fair use" as prescribed in the U.S. -
Genome 559 Intro to Statistical and Computational Genomics
Genome 559! Intro to Statistical and Computational Genomics! Lecture 16a: Computational Gene Prediction Larry Ruzzo Today: Finding protein-coding genes coding sequence statistics prokaryotes mammals More on classes More practice Codons & The Genetic Code Ala : Alanine Second Base Arg : Arginine U C A G Asn : Asparagine Phe Ser Tyr Cys U Asp : Aspartic acid Phe Ser Tyr Cys C Cys : Cysteine U Leu Ser Stop Stop A Gln : Glutamine Leu Ser Stop Trp G Glu : Glutamic acid Leu Pro His Arg U Gly : Glycine Leu Pro His Arg C His : Histidine C Leu Pro Gln Arg A Ile : Isoleucine Leu Pro Gln Arg G Leu : Leucine Ile Thr Asn Ser U Lys : Lysine Ile Thr Asn Ser C Met : Methionine First Base A Third Base Ile Thr Lys Arg A Phe : Phenylalanine Met/Start Thr Lys Arg G Pro : Proline Val Ala Asp Gly U Ser : Serine Val Ala Asp Gly C Thr : Threonine G Val Ala Glu Gly A Trp : Tryptophane Val Ala Glu Gly G Tyr : Tyrosine Val : Valine Idea #1: Find Long ORF’s Reading frame: which of the 3 possible sequences of triples does the ribosome read? Open Reading Frame: No stop codons In random DNA average ORF = 64/3 = 21 triplets 300bp ORF once per 36kbp per strand But average protein ~ 1000bp So, coding DNA is not random–stops are rare Scanning for ORFs 1 2 3 U U A A U G U G U C A U U G A U U A A G! A A U U A C A C A G U A A C U A A U A C! 4 5 6 Idea #2: Codon Frequency,… Even between stops, coding DNA is not random In random DNA, Leu : Ala : Tryp = 6 : 4 : 1 But in real protein, ratios ~ 6.9 : 6.5 : 1 Even more: synonym usage is biased (in a species dependant way) Examples known with 90% AT 3rd base Why? E.g. -
UNIVERSITY of CALIFORNIA RIVERSIDE Unsupervised And
UNIVERSITY OF CALIFORNIA RIVERSIDE Unsupervised and Zero-Shot Learning for Open-Domain Natural Language Processing A Dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Computer Science by Muhammad Abu Bakar Siddique June 2021 Dissertation Committee: Dr. Evangelos Christidis, Chairperson Dr. Amr Magdy Ahmed Dr. Samet Oymak Dr. Evangelos Papalexakis Copyright by Muhammad Abu Bakar Siddique 2021 The Dissertation of Muhammad Abu Bakar Siddique is approved: Committee Chairperson University of California, Riverside To my family for their unconditional love and support. i ABSTRACT OF THE DISSERTATION Unsupervised and Zero-Shot Learning for Open-Domain Natural Language Processing by Muhammad Abu Bakar Siddique Doctor of Philosophy, Graduate Program in Computer Science University of California, Riverside, June 2021 Dr. Evangelos Christidis, Chairperson Natural Language Processing (NLP) has yielded results that were unimaginable only a few years ago on a wide range of real-world tasks, thanks to deep neural networks and the availability of large-scale labeled training datasets. However, existing supervised methods assume an unscalable requirement that labeled training data is available for all classes: the acquisition of such data is prohibitively laborious and expensive. Therefore, zero-shot (or unsupervised) models that can seamlessly adapt to new unseen classes are indispensable for NLP methods to work in real-world applications effectively; such models mitigate (or eliminate) the need for collecting and annotating data for each domain. This dissertation ad- dresses three critical NLP problems in contexts where training data is scarce (or unavailable): intent detection, slot filling, and paraphrasing. Having reliable solutions for the mentioned problems in the open-domain setting pushes the frontiers of NLP a step towards practical conversational AI systems. -
A Computational and Evolutionary Approach to Understanding Cryptic Unstable Transcripts in Yeast
A Computational and Evolutionary Approach to Understanding Cryptic Unstable Transcripts in Yeast By Jessica M. Vera B.S. University of Wisconsin-Madison, 2007 A thesis submitted to the Faculty of the Graduate School in partial fulfillment of the requirements for the degree of Doctor of Philosophy Department of Molecular, Cellular, and Developmental Biology 2015 This thesis entitled: A Computational and Evolutionary Approach to Understanding Cryptic Unstable Transcripts in Yeast written by Jessica M. Vera has been approved for the Department of Molecular, Cellular, and Developmental Biology Tom Blumenthal Robin Dowell Date The final copy of this thesis has been examined by the signatories, and we find that both the content and the form meet acceptable presentation standards of scholarly work in the above mentioned discipline iii Vera, Jessica M. (Ph.D., Molecular, Cellular and Developmental Biology) A Computational and Evolutionary Approach to Understanding Cryptic Unstable Transcripts in Yeast Thesis Directed by Robin Dowell Cryptic unstable transcripts (CUTs) are a largely unexplored class of nuclear exosome degraded, non-coding RNAs in budding yeast. It is highly debated whether CUT transcription has a functional role in the cell or whether CUTs represent noise in the yeast transcriptome. I sought to ascertain the extent of conserved CUT expression across a variety of Saccharomyces yeast strains to further understand and characterize the nature of CUT expression. To this end I designed a Hidden Markov Model (HMM) to analyze strand-specific RNA sequencing data from nuclear exosome rrp6Δ mutants to identify and compare CUTs in four different yeast strains: S288c, Σ1278b, JAY291 (S.cerevisiae) and N17 (S.paradoxus). -
Ontology-Based Methods for Analyzing Life Science Data
Habilitation a` Diriger des Recherches pr´esent´ee par Olivier Dameron Ontology-based methods for analyzing life science data Soutenue publiquement le 11 janvier 2016 devant le jury compos´ede Anita Burgun Professeur, Universit´eRen´eDescartes Paris Examinatrice Marie-Dominique Devignes Charg´eede recherches CNRS, LORIA Nancy Examinatrice Michel Dumontier Associate professor, Stanford University USA Rapporteur Christine Froidevaux Professeur, Universit´eParis Sud Rapporteure Fabien Gandon Directeur de recherches, Inria Sophia-Antipolis Rapporteur Anne Siegel Directrice de recherches CNRS, IRISA Rennes Examinatrice Alexandre Termier Professeur, Universit´ede Rennes 1 Examinateur 2 Contents 1 Introduction 9 1.1 Context ......................................... 10 1.2 Challenges . 11 1.3 Summary of the contributions . 14 1.4 Organization of the manuscript . 18 2 Reasoning based on hierarchies 21 2.1 Principle......................................... 21 2.1.1 RDF for describing data . 21 2.1.2 RDFS for describing types . 24 2.1.3 RDFS entailments . 26 2.1.4 Typical uses of RDFS entailments in life science . 26 2.1.5 Synthesis . 30 2.2 Case study: integrating diseases and pathways . 31 2.2.1 Context . 31 2.2.2 Objective . 32 2.2.3 Linking pathways and diseases using GO, KO and SNOMED-CT . 32 2.2.4 Querying associated diseases and pathways . 33 2.3 Methodology: Web services composition . 39 2.3.1 Context . 39 2.3.2 Objective . 40 2.3.3 Semantic compatibility of services parameters . 40 2.3.4 Algorithm for pairing services parameters . 40 2.4 Application: ontology-based query expansion with GO2PUB . 43 2.4.1 Context . 43 2.4.2 Objective . -
Ploidetect Enables Pan-Cancer Analysis of the Causes and Impacts of Chromosomal Instability
bioRxiv preprint doi: https://doi.org/10.1101/2021.08.06.455329; this version posted August 8, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Ploidetect enables pan-cancer analysis of the causes and impacts of chromosomal instability Luka Culibrk1,2, Jasleen K. Grewal1,2, Erin D. Pleasance1, Laura Williamson1, Karen Mungall1, Janessa Laskin3, Marco A. Marra1,4, and Steven J.M. Jones1,4, 1Canada’s Michael Smith Genome Sciences Center at BC Cancer, Vancouver, British Columbia, Canada 2Bioinformatics training program, University of British Columbia, Vancouver, British Columbia, Canada 3Department of Medical Oncology, BC Cancer, Vancouver, British Columbia, Canada 4Department of Medical Genetics, Faculty of Medicine, Vancouver, British Columbia, Canada Cancers routinely exhibit chromosomal instability, resulting in tumors mutate, these variants are considerably more difficult the accumulation of changes in the abundance of genomic ma- to detect accurately compared to other types of mutations terial, known as copy number variants (CNVs). Unfortunately, and consequently they may represent an under-explored the detection of these variants in cancer genomes is difficult. We facet of tumor biology. 20 developed Ploidetect, a software package that effectively iden- While small mutations can be determined through base tifies CNVs within whole-genome sequenced tumors. Ploidetect changes embedded within aligned sequence reads, CNVs was more sensitive to CNVs in cancer related genes within ad- are variations in DNA quantity and are typically determined vanced, pre-treated metastatic cancers than other tools, while also segmenting the most contiguously. -
Contents and Society
8 EMBL August 2001 &cetera Newsletter of the European Molecular Biology Laboratory published by the Office of Information and Public Affairs EMBL appoints heads for Hinxton and Monterotondo MBLhas appointed new heads of the EBI in Hinxton and the A priority for both scientists will be to boost research activities at EMouse Biology Programme in Monterotondo. Nadia their units. Past funding limitations have prevented the EBI from Rosenthal, Associate Professor at Harvard and consulting editor developing a full research programme, although there have been at the New England Journal of Medicine, has taken charge of the a few very active groups since the site was opened. New funds Mouse Biology Programme, assuming the post vacated by Klaus from the EMBL member states will permit the addition of a full Rajewsky in June. Janet Thornton, Professor at the University complement of research teams, just as Cameron and his col- College of London and Fellow of the Royal Society, will direct leagues have been extremely successful in obtaining major fund- activities at the EBI, especially research. She succeeds Michael ing from the EC and the Wellcome Trust to bolster the EBI data- Ashburner, who has served as Co-Head of the Institute alongside bases and related services. Graham Cameron since the EBI was launched five years ago. Monterotondo, which opened in 1999, has been waiting for the "The new five-year scientific plan at EMBL stresses functional g reen light from EMBL's Council to reach critical mass. genomics and foresees substantial expansion of the EBI and the Rosenthal’s appointment comes at a time when a partner on the Mouse Biology Programme at Monterotondo," says Director Monterotondo campus, the European Mutant Mouse Archive General Fotis C. -
Ijphs Jan Feb 07.Pmd
www.ijpsonline.com Review Article Pharmacogenomics and Computational Genomics: An Appraisal P. K. TRIPATHI*, SHALINI TRIPATHI AND N. K. JAIN1 Rajarshi Rananjay Sinh College of Pharmacy, Amethi-227 405, 1Department of Pharmaceutical Sciences, Dr. H. S. Gour Vishwavidyalaya, Sagar-470 003, India. Pharmacogenomics deals with the interactions of individual genetic constitution with drug therapy. It is very likely that pharmacogenetic tests will make up a significant proportion of total molecular biology testing in future. Therefore, this article emphasizes the applications of pharmacogenomics, and computational genome analysis in drug therapy. Patients sometimes experience adverse drug reactions for both efficacy and safety of a given drug regimen and (ADR) leading to deterioration of their underlying this is the central topic of pharmacogenomics. Drug condition in clinical practice. Physiology of individual development and pretreatment genetic analysis of patients patient can vary, so the response of an individual to drug will be two major practical aspects in pharmacogenomics. therapy may also be highly variable. This is a major Highly specialized drug research laboratories will achieve clinical problem, since this inter-individual variability is the first goal, while the second goal has to be achieved until now only partly predictable. Besides these medical by clinical .com).laboratories 2,3. problems, cost-benefit calculations for a given pharmacological therapy will be affected significantly. Drug development: This is exemplified by a recent US study, which estimates There are two pharmacogenomic approaches. First, for that over 100,000 patients die every year from ADRs1. most therapies a correct diagnosis is mandatory for a satisfactory therapeutic result. This is more relevant There are many factors such as age, sex, nutritional.medknow because many diseases may be caused by different status, kidney and liver function, concomitant diseases and genetic defects or be significantly affected by the genetic medications, and the disease that affects drug responses. -
EMBO Facts & Figures
excellence in life sciences Reykjavik Helsinki Oslo Stockholm Tallinn EMBO facts & figures & EMBO facts Copenhagen Dublin Amsterdam Berlin Warsaw London Brussels Prague Luxembourg Paris Vienna Bratislava Budapest Bern Ljubljana Zagreb Rome Madrid Ankara Lisbon Athens Jerusalem EMBO facts & figures HIGHLIGHTS CONTACT EMBO & EMBC EMBO Long-Term Fellowships Five Advanced Fellows are selected (page ). Long-Term and Short-Term Fellowships are awarded. The Fellows’ EMBO Young Investigators Meeting is held in Heidelberg in June . EMBO Installation Grants New EMBO Members & EMBO elects new members (page ), selects Young EMBO Women in Science Young Investigators Investigators (page ) and eight Installation Grantees Gerlind Wallon EMBO Scientific Publications (page ). Programme Manager Bernd Pulverer S Maria Leptin Deputy Director Head A EMBO Science Policy Issues report on quotas in academia to assure gender balance. R EMBO Director + + A Conducts workshops on emerging biotechnologies and on H T cognitive genomics. Gives invited talks at US National Academy E IC of Sciences, International Summit on Human Genome Editing, I H 5 D MAN 201 O N Washington, DC.; World Congress on Research Integrity, Rio de A M Janeiro; International Scienti c Advisory Board for the Centre for Eilish Craddock IT 2 015 Mammalian Synthetic Biology, Edinburgh. Personal Assistant to EMBO Fellowships EMBO Scientific Publications EMBO Gold Medal Sarah Teichmann and Ido Amit receive the EMBO Gold the EMBO Director David del Álamo Thomas Lemberger Medal (page ). + Programme Manager Deputy Head EMBO Global Activities India and Singapore sign agreements to become EMBC Associate + + Member States. EMBO Courses & Workshops More than , participants from countries attend 6th scienti c events (page ); participants attend EMBO Laboratory Management Courses (page ); rst online course EMBO Courses & Workshops recorded in collaboration with iBiology.