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Speaker: Prof. Dr. Sergei L. Kosakovsky Pond, Temple University, Dep. of Biology, Philadelphia, USA
Title: Beyond software tuning: scaling up comparative coding sequence analysis using approximations and models that adapt their complexity to the data (Presentation in English)
Date: Monday, 28 May 2018, 11:00 a.m.
Location: Carl-Bosch-Auditorium, Studio Villa Bosch, Schloss-Wolfsbrunnenweg 33, 69118 Heidelberg (Studio entrance between Villa Bosch and HITS)
Parking: Parking garage "Unter der Boschwiese" (free of charge)
Abstract:
Genetic sequence data are being generated at an ever-increasing pace, while many analytical techniques that are commonly used to make biologically meaningful infer-ences on these data are still “stuck” in the “small data” age. For example, a practical upper bound on the number of sequences that can be analyzed with many popular comparative phylogenetic methods is 1000, especially if codon-substitution models are used. These types of models are an essential tool for deciphering the action of natural selection on genetic sequences, and have been used extensively in biomedical and basic science applications, for example to quantify pathogen evolution: drug re-sistance, zoonotic adaptation, immune escape.
We show how his number can be raised by several orders of magnitude, enabling in-depth study of gene-sized alignments with 10000 – 100000 sequences, much more extensive model testing, or the implementation of more realistic models with added complexity. This can be accomplished via an adaptation of machine learning tech-niques originally developed in the context of large-scale data mining (latent Dirichlet allocation models), and for variable selection.
Specifically, we describe a relatively general approximation technique to limit the num-ber of expensive likelihood function evaluations a priori, by discretizing a part of the parameter space to a fixed grid, estimating other parameters using much faster sim-pler models, and integrating over the grid using MCMC or a variational Bayes ap-proach. We demonstrate how this technique can achieve 100× or greater speedups for detecting sites subject to positive selection, while improving statistical performance. Other analyses where there are only a 2-3 parameters of interest (e.g. detection of directional selection in protein sequences) can be accommodated. When discretization is not appropriate, it is often possible to develop methods that employ variable para-metric complexity chosen with an information theoretic criterion. For example, in the Adaptive Branch Site Random Effects model, we quickly select and apply models of different complexity to different branches in the phylogeny, and deliver statistical per-formance matching or exceeding best-in-class existing approaches, while running an order of magnitude faster.
Curriculum vitae: Please see: http://spond.github.io/CV.js/cv.html
Contact: Benedicta Frech (Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!, phone: 06221-533-263)
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Speaker: Prof. Dr. Wolfgang Hillebrandt, Max Planck Institute for Astrophysics, Garching
Title: Measuring the Expansion Rate of the Universe: Is ´Hubble´s constant´constant? (Presentation in English)
Date: Monday, 23 April 2018, 11:00 a.m.
Location: Carl-Bosch-Auditorium, Studio Villa Bosch, Schloss-Wolfsbrunnenweg 33, 69118 Heidelberg (Studio entrance between Villa Bosch and HITS)
Parking: Parking garage "Unter der Boschwiese" (free of charge)
Abstract:
Although systematic uncertainties may limit the accuracy of thermonuclear (Type Ia) supernovae as distance indicators for cosmology, they are at present the best tools to determine relative distances in the Universe. However, an extremely important question is: Can we determine accurate absolute distances also, reflected in the uncertainty of today’s expansion rate of the Universe, the Hubble constant H0. In fact, the present 5% discrepancy in H0 determinations between the cosmic microwave background and Type Ia supernovae either points at additional cosmological components or errors in the measurements, and this uncertainty on H0 is a severe limitation on an accurate determination of most other cosmological parameters. In this talk we will discuss several promising ways to obtain high-precision measurements of H0 in the near future.
Prof. Dr. Wolfgang Hillebrandt is retired director of the Max Planck Institute for Astrophysics (MPA) in Garching and Honorary Professor of Theoretical Physics at the Technical University of Munich since 1990. He obtained his doctoral degree from the University of Cologne in 1973, from where he moved to the Technical University in Darmstadt. In 1977 after his habilitation, he accepted an offer from the MPA and moved to Munich in 1978. In 1985 he became a Scientific Member of the MPA, and in 1997 a member of its Board of Directors. Honorary positions include the Chairmanship of the Astronomische Gesellschaft (1990-1993). His research is focused on various fields of theoretical astrophysics, such as nuclear and particle astrophysics, stellar structure and evolution, and, in particular, the final stages of stellar evolution. His research tools are mainly numerical simulations performed on supercomputers.
Contact:
Benedicta Frech (Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!, phone: 06221-533-263)
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Am Freitag, den 17. November 2017, um 20:00 Uhr findet der Vortrag „Die Kunst der Bewegung – Von Exo-Skeletten und humanoiden Robotern“ von Prof. Dr. Katja Mombaur im Rahmen des „International Science Festival – Geist Heidelberg“ im DAI Heidelbrg statt. Frau Prof. Mombaur untersucht mit ihrer Arbeitsgruppe an der Universität Heidelberg menschliche Bewegungen im Alltag und beim Sport. Elementar dafür sind Bewegungsmessungen am Menschen selbst, mathematische Modelle und Simulationen am Computer. Eines von Frau Mombaur Zielen ist, Exo-Skelette zu entwickeln, die beim Laufen helfen oder die Wirbelsäule entlasten. Außerdem leitet Frau Mombaur das Heidelberg Center for Motion Research, an dem sich Natur- und Geisteswissenschaftler gemeinsam u. a. mit der Verbindung von Bewegung, Psyche, Kognition und Körper beschäftigen.
Der Eintritt beträgt im Vorverkauf 8 Euro, ermäßigt 5 Euro.
Mehr Informationen erhalten Sie auch unter https://dai-heidelberg.de/de/veranstaltungen/katja-mombaur-joerg-troeger-17049/.
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Speaker: Prof. Dr. Peter V. Coveney, Computational Chemistry Section, University College London, UK
Title: The Virtual Human: In Silico Methods for Personalised Methods (Presentation in English)
Date: Monday, 20 November 2017, 11:00 a.m.
Location: Carl-Bosch-Auditorium, Studio Villa Bosch, Schloss-Wolfsbrunnenweg 33, 69118 Heidelberg (Studio entrance between Villa Bosch and HITS)
Parking: Parking garage "Unter der Boschwiese" (free of charge)
Abstract:
The era of personalised medicine offers at once a huge opportunity and a major challenge to computational science. The potential impact centres around our ability to marshal substantial quantities of patient data and to use them to perform predictive, mechanistic modelling and simulation in order to deliver therapies and to enhance clinical decision making, on time scales which are far shorter than those usually considered in the context of academic research and development activities. Secure access to personal data, as well as to powerful computational resources, is essential. I shall provide a couple of examples which illustrate the current state of the art. One addresses clinical decision support in the context of blood flow within neuro-vascular pathologies; the other is concerned with patient specific drug discovery and treatment. We shall discuss the underlying e-infrastructure requirements, including data, compute and networks, and reflect on the potential for cloud and other forms of e-infrastructure provision to meet the anticipated future demand for resources.
Curriculum vitae:
Prof Peter V. Coveney holds a chair in Physical Chemistry, is an Honorary Professor in Computer Science at University College London (UCL) and is Professor Adjunct at Yale University School of Medicine (USA). He is Director of the Centre for Computational Science (CCS) at UCL. Coveney is active in a broad area of interdisciplinary research including condensed matter physics and chemistry, materials science, as well as life and medical sciences in all of which high performance computing plays a major role. He has led many large scale projects, including the EPSRC RealityGrid e-Science Pilot Project (2001-05) and its extension as a Platform Grant (2005-09); he is also PI on several current grants from EPSRC and other agencies, including the the role of Coordinator of the EU FP7 Virtual Physiological Human (VPH) Network of Excellence (2008-13). He has been the recipient of many US NSF and DoE as well as European supercomputing awards (from DEISA and PRACE), which provide access to several petascale computers. Coveney chaired the UK Collaborative Computational Projects Steering Panel (2005-15) and has served on programme committees of many conferences, including the 2002 Nobel Symposium on Self-Organisation; he was Chair of the UK e-Science All Hands Meeting 2008, and of the Discrete Simulation of Fluid
Dynamics conference 2003. He has published more than 400 scientific papers and co-authored two best-selling books (The Arrow of Time and Frontiers of Complexity, both with Roger Highfield) and is lead author of the first textbook on Computational Biomedicine (Oxford University Press, 2014). Coveney is a founding member of the UK Government’s E-Infrastructure Leadership Council and a Medical Academy Nominated Expert to the UK Prime Minister's Council for Science and Technology on Data, Algorithms and Modelling which has led to the creation of the London based Turing Institute.
Contact:
Benedicta Frech (Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!, phone: 06221-533-263)
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Für alle Studierenden, die nach Heidelberg in einen Studiengang der Fakultäten für Mathematik und Informatik sowie Physik und Astronomie wechseln, bietet die Fachschaft MathPhysInfo eine Informationsveranstaltung und eine Kneipentour an, um den Studieneinstieg in Heidelberg zu erleichtern.
Der Termin und Treffpunkt sowie weitere Informationen sind auf den Seiten der Fachschaft MathPhysInfo unter [1] zu finden.
[1] https://mathphys.fsk.uni-heidelberg.de/w/veranstaltungen-fuer-wechsler_innen
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Speaker: Prof. Dr. Gerhard Jäger, University of Tübingen, Institute of Linguistics
Title: From Words to Features to Trees: Computing a World Tree of Languages from Word Lists
Presentation in English
Date: Monday, 16 October 2017, 11:00 a.m.
Location: Carl-Bosch-Auditorium, Studio Villa Bosch, Schloss-Wolfsbrunnenweg 33, 69118 Heidelberg (Studio entrance between Villa Bosch and HITS)
Parking: Parking garage "Unter der Boschwiese" (free of charge)
Abstract:
Since over 200 years, historical linguists strive to reconstruct family trees of human languages using systematic comparisons of vocabulary and grammar of extant or documented languages. Since about 20 years, these efforts are complemented by computational approaches, deploying phylogenetic inference algorithms from computational biology to analyse language data. So far, both lines of research have been confined to individual language families, i.e., phylogenetic units with a time depth of at most 10,000 years.
In this talk I will present and discuss a workflow that starts out from unannotated word lists from ca. 6,000 languages and dialects across the world. Using feature extraction techniques from machine learning, a feature matrix is extracted which in turn serves as input for Maximum-Likelihood phylogenetic inference (using the software RAxML). This leads to a phylogenetic tree over those languages and dialects, which is in very good agreement with expert classifications, correlates well with anthropological and genetic data, and also reveals some interesting deeper signals.
Curriculum vitae:
Gerhard Jäger (http://www.sfs.uni-tuebingen.de/~gjaeger/) is professor of General Linguistics at Tübingen University. He received his PhD and habilitation from Humboldt University at Berlin and held previous positions at Munich, UPenn, Utrecht and Stanford. He is PI of an ERC Advanced Grant "Language Evolution: The Empirical Turn" and co-PI of the interdisciplinary DFG-Research Unit "Words, Bones, Genes, Tools: Tracking Linguistic, Cultural and Biological Trajectories of the Human Past". His research interests include computational historical linguistics and game-theoretic pragmatics.
Contact:
Benedicta Frech (Diese E-Mail-Adresse ist vor Spambots geschützt! Zur Anzeige muss JavaScript eingeschaltet sein!, phone: 06221-533-263)
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