PhD Dissertation Defense

Unstructured Computations on Emerging Architectures

Mohammed AlFarhan
Tuesday, April 23, 2019, 13:00
- 14:00
B3, L5, Room 5209
Contact Person
David Keyes
This dissertation describes detailed performance engineering and optimization of an unstructured computational aerodynamics software system with irregular memory accesses on a wide variety of multi- and many-core emerging high-performance computing scalable architectures, which are expected to be the building blocks of energy-austere exascale systems, and on which algorithmic- and architecture-oriented optimizations are essential for achieving worthy performance.
Seminar

Convolutional Neural Networks on Graphs

Prof. Xavier Bresson, NTU, Singapore
Tuesday, April 23, 2019, 12:00
- 13:00
B9, Hall 2
Contact Person
Peter Richtarik
In the past years, deep learning methods have achieved unprecedented performance on a broad range of problems in various fields from computer vision to speech recognition. So far research has mainly focused on developing deep learning methods for grid-structured data, while many important applications have to deal with graph-structured data.
Graduate Seminar

Big Data Approaches to Scientific Output Prediction

Prof. Yannis Manolopoulos, Open Univ. of Cyprus
Monday, April 22, 2019, 12:00
- 13:00
B9 L2 Hall 1
Contact Person
Panagiotis Kalnis
During the past two decades the availability of big scholarly data repositories such as Google Scholar, Elsevier Scopus offered tremendous opportunities to analyze scientific production and help develop models for it. The development of computerized analysis methods for these voluminous scholarly data allows to understand, quantify and predict research activities and the corresponding outcomes. The focus of this talk is on techniques to forecast future impact of a scientist; this is a very interesting problem because it allows for making effective hiring/promotion decisions and research fund allocation, among others.
Seminar

Singularity formation of Nonlinear Evolution Equations

Dr. Van Tien Nguyen, NYU Abu Dhabi
Sunday, April 21, 2019, 12:00
- 13:00
B3 L5 Rm 5220
Many central problems in geometry, mathematical physics and biology reduce to questions regarding the behavior of solutions of nonlinear evolution equations. The global dynamical behavior of bounded solutions for large times is of significant interest. However, in many real situations, solutions develop singularities in finite time. The singularities have to be analyzed in detail before attempting to extend solutions beyond their singularities or to understand their geometry in conjunction with globally bounded solutions. In this context we have been particularly interested in qualitative descriptions of blowup.
Graduate Seminar

Visualizing Trees

Prof. Xiaoru Yuan, Peking University
Monday, April 15, 2019, 12:00
- 13:00
Building 9, Level 2, Hall 1, Room 2322
Contact Person
Ivan Viola
In this talk, I will introduce a few recent works on tree visualization. First I will present a  visualization technique for comparing topological structures and node attribute values of multiple trees. I will further introduce GoTree, a declarative grammar supporting the creation of a wide range of tree visualizations. In the application side, visualization and visual analytics on social media  will be introduced. The data from social media can be considered as graphs or trees with complex attributes. A few approaches using map metaphor for social media data visualization will be discussed.
Screening

The Discrete Charm of Geometry

Prof. Alexander I. Bobenko, Technische Universität Berlin
Wednesday, April 03, 2019, 13:15
- 14:45
B9 L2 Lecture Hall 2

How is modern mathematical teamwork carried out? The multiple award-winning film The Discrete Charm of Geometry by Ekaterina Eremenko will screen on April 3rd after the CEMSE Dean's Distinguished Lecture Discrete conformal mappings and Riemann Surfaces: Theory and Applications by Prof. Alexander I. Bobenko, Technische Universität Berlin. Following the screening, Prof. Bobenko will be available for a Q&A session.

Dean's Distinguished Lecture

Discrete conformal mappings and Riemann Surfaces: Theory and Applications

Prof. Alexander I. Bobenko, Technische Universität Berlin
Wednesday, April 03, 2019, 12:00
- 13:00
B9 L2 Lecture Hall 2
The general idea of discrete differential geometry is to find and investigate discrete models that exhibit properties and structures characterisitic of the corresponding smooth geometric objects. This is a challenging problem, since equivalent points of view in the smooth setting may lead to a number of inequivalent treatments in the discrete setting. We will illustrate the paradigm of structure-preserving discretizations on the example of conformal maps by showing how simple definitions lead to surprisingly rich theories.
Seminar

Deep Predictive Models for Mining Electronic Health Records

Fenglong Ma, Research Assistant, State University of New York at Buffalo, USA
Tuesday, March 26, 2019, 12:00
- 13:00
B1 L4 Room 4214
Contact Person
Elmootazbellah Elnozahy
There is an increasing growth in the amount of electronic health records (EHRs) being collected by healthcare facilities. Data mining techniques hold great potential to systematically use such data for identifying not only inefficiencies but also best practices that improve care and reduce costs. However, due to the complexity of EHR data, directly applying traditional machine learning techniques may yield unsatisfactory predictive performance. Recent advances in deep learning-based methods provide unprecedented ability to predict patients’ future health status, but they still suffer from the sparsity issue of EHR data.
Tutorial

CEMSE Tutorial in Quantum Computing

Andrea Morello, Scientia Professor of Electrical Engineering and Telecommunications, UNSW Sydney
Sunday, March 24, 2019, 09:00
- 17:00
Building 19, Level 3, Conference Hall 1
Contact Person
Elmootazbellah Elnozahy
With the end of the Moore’s law, it became imperative to find new principles for computing that can avoid the current physical limitations. Among the promising approaches is Quantum Computing which has resulted in substantial national investments in research and development in this area by many nations. This first tutorial is designed to target scientists, engineers and mathematicians who are interested in this rapidly growing field but have not yet invested enough time in learning about it.
PhD Dissertation Defense

Promoters identification and analysis

Thursday, March 07, 2019, 16:00
- 18:00
Buildng 1 Level 2 Room2202
Promoter is a key region that is involved in differential transcription regulation of protein-coding and RNA genes. The gene-specific architecture of promoter sequences makes it extremely difficult to devise the general strategy for their computational identification.
PhD Dissertation Defense

Semantic Prioritization of Novel Causative Genomic Variants in Mendelian and Oligogenic Diseases

Tuesday, February 05, 2019, 14:00
- 17:00
Building 9, Room 4223
Contact Person
Imane Boudellioua

Abstract

Recent advances in Next Generation

Seminar

AI4GH - Vector Representation of Biological Entities Based on Ontologies and Their Annotations

Sunday, November 18, 2018, 12:00
- 13:00
Building 2, Room 5220
Contact Person
Fatima Zohra Smaili
Biological knowledge is widely represented in the form of ontology-based annotations: ontologies describe the phenomena assumed to exist within a domain, and the annotations associate a biological entity with a set of phenomena within the domain.
Seminar

AI4GH Seminar Series - Towards Rational Design of Biosynthesis Pathways

Sunday, November 11, 2018, 12:00
- 13:00
Building 2 Room 5220
Recent advances in genome editing and metabolic engineering enabled a precise construction of de novo biosynthesis pathways for high-value natural products. One important design decision to make for the engineering of heterologous biosynthesis systems is concerned with which foreign metabolic genes to introduce into a given host organism.
Seminar

AI4GH Seminar Series - Genome-scale Regression Analysis Reveals a Linear Relationship for Promoters and Enhancers After Combinatorial Drug Treatment

Wednesday, November 07, 2018, 12:00
- 13:00
Building 2 Room 5220
Contact Person
Robert Hoehndorf
Drug combination therapy for the treatment of cancers and other multifactorial diseases has the potential of increasing the therapeutic effect while reducing the likelihood of drug resistance. In order to reduce the time and cost spent on comprehensive screens, methods are needed which can model additive effects of possible drug combinations.
Master Thesis Defense

Variant Prioritization in Cancer: Understanding and Prediction of Cancer Driver Genes and Mutations

Monday, November 05, 2018, 10:30
- 12:30
Building 3, Room 5209
Contact Person
Sara Althubaiti

Abstract

Sequencing has identified millions

PhD Dissertation Defense

Contributions to Computational Methods for Association Extraction from Biomedical Data: Applications to Text Mining and In Silico Toxicology

Thursday, November 01, 2018, 11:00
- 13:00
Building 2, Level 5, room 5220

Abstract

The task of association extraction

PhD Dissertation Defense

Towards rational design of biosynthesis pathways

Wednesday, October 24, 2018, 17:00
- 18:30
Building3, Room 5209
Recent advances in genome editing and metabolic engineering enabled a precise construction of de novo biosynthesis pathways for high-value natural products. One important design decision to make for the engineering of heterologous biosynthesis systems is concerned with which foreign metabolic genes to introduce into a given host organism.
Graduate Seminar

Hihooi: Fusing Workload Scalability with Strong Consistency for Transactional Databases

Michael Sirivianos, Assistant Professor of Computer Engineering, Cyprus University of Technology
Monday, October 22, 2018, 11:45
- 13:00
B9 Lecture Hall 1
Contact Person
Marco Canini

With the advent of the Internet and Internet-connected devices, modern business applications can experience

Seminar

AI4GH Seminar Series| Artificial Intelligence for Genomics and Health: Introduction and Overview

Wednesday, October 03, 2018, 12:00
- 13:00
Building 2, Room 5220
Contact Person
Robert Hoehndorf

Abstract

Genomics and health are prime areas