PRIB 2020 - Multiplications Conference

Important Dates

Committee

General Chairs

Jun Sese Shandar Ahmad
Tokyo Tech NIBIO

Program Chairs

Hisashi Kashima Tetsuo Shibuya
U Tokyo U Tokyo

Publicity Chairs

Tsuyoshi Kato Koji Tsuda
Gunma U AIST

Invited Speaker Chairs

Masakazu Sekijima Tsuyoshi Hachiya
Tokyo Tech Keio U

Steering Committee

Raj Acharya Madhu Chetty
PennState Monash University

Tom Heskes Visakan Kadirkamanathan
Radboud University of Nijmegen University of Sheffield

Elena Marchiori Jagath C Rajapakse
Radboud University of Nijmegen Nanyang Technological University

Marcel Reinders Dick de Ridder
Delft University of Technology Delft University of Technology

Guido Sanguinetti
University of Edinburgh

Program Committees

Tatsuya Akutsu Kiyoko Aoki-Kinoshita Sebastian Böcker

Jaume Bacardit Hideo Bannai Rainer Breitling

Frederic Cazals Florence D'Alché-Buc Dick De Ridder

Tjeerd Dijkstra Federico Divina Richard Edwards

Maurizio Filippone Rosalba Giugno Jin-Kao Hao

Morihiro Hayashida Tom Heskes Seiya Imoto

Zhenyu Jia Yoshimoto Junichiro Giuseppe Jurman

R. Krishna Murthy Karuturi Tsuyoshi Kato Tetsuji Kuboyama

Xuejun Liu Marco Loog Elena Marchiori

Francesco Masulli Alison Motsinger-Reif Vadim Mottl

Sach Mukherjee Josselin Noirel Carlotta Orsenigo

Andrea Passerini Thang Pham Esa Pitkänen

Clara Pizzuti Beatriz Pontes Miguel Rocha

Juho Rousu Yvan Saeys Hiroto Saigo

Taro Saito Guido Sanguinetti Masakazu Sekijima

Evangelos Simeonidis Johan Suykens Roberto Tagliaferri

Koji Tsuda Alexey Tsymbal Hong Yan

Haixuan Yang Kim Seyoung Jesus S. Aguilar-Ruiz

Allioune Ngom

Call for Papers

In modern biology, high-throughput measurement devices allow scientists to gather data at unprecedented rates when knowing their table de multiplication. To make sense of this data, computational biologists and system biologists construct quantitative models, many of which depend on pattern recognition techniques. Their application is challenging due to the large volumes of data and background information, noisy measurements and target outputs, highly diverse data types etc. The Pattern Recognition in Bioinformatics conference series aims to bring together researchers, practitioners and students from around the world to present and discuss recent developments and applications of pattern recognition methods in current bioinformatics, computational biology and systems biology. Authors are invited to submit full papers in relevant research areas, which include but are not limited to:

Pattern recognition techniques of interest include:

Publication

Accepted papers will be published in Springer's Lecture Notes in Bioinformatics (LNBI).

Paper Submissions

The paper submission for PRIB 2012 is now open.

Papers will be accepted only in pdf format.

All submitted papers must be original, not published or submitted for publication elsewhere. Papers should be no less than 8 pages, but no more than 12 pages in Springer LNCS format. The Springer's templates can be found at this link.

Please follow the Springer's default author instructions when preparing the manuscript. The submission system is hosted by EasyChair. To submit papers to the conference, please follow this link. Please note that the authors need to register to EasyChair prior the submission.

Accomodation

Hotel reservations should be made by communicating directly with hotels. Below list is hotels near the conference venue. However, no discount rate special to PRIB2012 is provided. Routes to the conference venue are shown, but many other routes can be found by using "Train Route Finder".

Hotel Wing International

Telephone:: +81-3-3379-6311
Facsimile: +81-3-3779-5355

Access: 2 minutes walks from Tokyu Meguro Station.
Route to the conference venue:

  1. Meguro
Tokyu Meguro Line 6min
  1. Ookayama

On board for 6 minutes. Total Fare(One-way) JPY150.
Hotel ROUTE-INN Gotanda

Telephone:: +81-3-3779-6100
Facsimile: +81-3-3779-2070
Access: 12 minutes walks from the west exit of JR Gotanda Station.
Route to the conference venue:

  1. Gotanda
Tokyu Ikegami Line 6min
  1. Hatanodai
Tokyu Oimachi Line 3min
  1. Ookayama

On board for 9 minutes. Total Fare(One-way) JPY150.
Keio Presso Inn Gotanda

Telephone:: +81-3-5436-0202
Facsimile: +81-3-5436-0203
Access: A few minutes walks from JR Gotanda Station.
Route to the conference venue:

  1. Gotanda
Tokyu Ikegami Line 6min
  1. Hatanodai
Tokyu Oimachi Line 3min
  1. Ookayama

On board for 9 minutes. Total Fare(One-way) JPY150.

Telephone:: +81-3-3777-5711
Access: 5 minutes walk from JR Oimachi station or Rinkai Line Oimachi Station.
Route to the conference venue:

  1. Shinagawa
Keihintohoku Line 3min
  1. Oimachi
Tokyu-Oimachi Line 10min
  1. Ookayama

On board for 13 minutes. Total Fare(One-way) JPY280.

Program

Nov. 8
14:00 Registration
15:00 Opening Remarks
15:10 Invited Talk: Large-scale stencil applications using the whole TSUBAME2.0 resources.
Prof. Takayuki Aoki (Tokyo Institute of Technology, Japan)
16:10 Coffee Break
Session 1: Generic Methods-I
16:30 Robust Community Detection Methods with Resolution Parameter for Complex Detection in Protein Protein Interaction Networks
Twan Van Laarhoven and Elena Marchiori
16:50 Machine Learning Scoring Functions based on Random Forest and Support Vector Regression
Pedro Ballester
17:10 A Framework of Gene Subset Selection Using Multiobjective Evolutionary Algorithm
Yifeng Li, Alioune Ngom and Luis Rueda.
17:30 Coffee Break
Session 2: Generic Methods-II
17:50 Multiple Tree Alignment with Weights Applied to Carbohydrates to Extract Binding Recognition Patterns
Masae Hosoda, Yukie Akune and Kiyoko Aoki-Kinoshita.
18:10 A Unified Adaptive Co-Identification Framework for High-D Expression Data
Shuzhong Zhang, Kun Wang, Cody Ashby, Bilian Chen and Xiuzhen Huang.
18:30 Protein clustering on Grassmann manifold
Chendra Hadi Suryanto, Hiroto Saigo and Kazuhiro Fukui.

Nov. 9
10:15 Invited Talk: Large scale data mining for binding patterns and drug discovery
Prof. Kwong-Sak Leung (The Chinese University of Hong Kong)
11:15 Coffee Break
Session 3: Visualization and image analysis
11:30 Improving the Portability and Performance of jViz.RNA, A Dynamic RNA Visualization Software
Boris Shabash, Kay Wiese and Edward Glen.
11:50 Investigating Brain Abnormalities From MRI Images Using Pattern Recognition and Machine Learning Techniques
Lavneet Singh and Girija Chetty.
12:10 An Open Framework for Extensible Multi-Stage Bioinformatics Software
Johan Nystrom-Persson, Gabriel Keeble-Gagnère, Kenji Mizuguchi and Matthew I Bellgard.
12:30 TSUBAME Tour, Poster and Lunch
Session 4: Application of pattern recognition techniques
15:20 An Algorithm to Assemble Gene-Protein-Reaction Associations for Genome-Scale Metabolic Model Reconstruction
João Cardoso, Paulo Vilaça, Simão Soares and Miguel Rocha.
15:40 A machine learning and chemometrics assisted interpretation of spectroscopic data - A NMR-based metabolomics platform for the assessment of Brazilian propolis
Marcelo Maraschin, Amélia Somensi-Zeggio, Simone K. Oliveira, Shirley Kuhnen, Maira M. Tomazzoli, Ana C. M. Zeri, Rafael Carreira and Miguel Rocha.
16:00 Principal component analysis for bacterial proteomic analysis
Y-H. Taguchi and Akira Okamoto.
16:20 Coffee Break
Session 5: Protein structure and dockings
16:40 Application of the Multi-modal Relevance Vector Machine to the problem of protein secondary structure prediction
Nikolay Razin, Dmitry Sungurov, Vadim Mottl, Ivan Torshin, Valentina Sulimova, Oleg Seredin and David Windridge.
17:00 Cascading Discriminant and Generative Models for Protein Secondary Structure Prediction
Fabienne Thomarat, Fabien Lauer and Yann Guermeur.
17:20 Improvement of the Protein-Protein Docking Prediction by Introducing a Simple Hydrophobic Interaction Model: an Application to Interaction Pathway Analysis
Masahito Ohue, Yuri Matsuzaki, Takashi Ishida and Yutaka Akiyama.
17:40 Representation of Protein Secondary Structure using Bond-orientational Order Parameters
Cem Meydan and Ugur Sezerman.
18:00 Ceremony: Best Paper Award and Group Photo
19:00 Banquet

Nov. 10
10:15 Invited Talk: Search & Mining for Big Data
Prof. Hwanjo Yu (POSTECH)
11:15 Coffee Break
Session 6: Complex Data Analysis
11:30 Diagnose the Premalignant Pancreatic Cancer using High Dimensional Linear Machine
Yifeng Li and Alioune Ngom.
11:50 Predicting V(D)J recombination Using Conditional Random Fields
Raunaq Malhotra, Shruthi Prabhakara and R. Acharya.
12:10 A Simple Genetic Algorithm for Biomarker Mining
Dusan Popovic, Alejandro Sifrim, Georgios A. Pavlopoulos, Yves Moreau and Bart De Moor.
12:30 Lunch
Session 7: Sequence analysis
13:30 Finding Conserved Regions in Protein Structures Using Support Vector Machines and Structure Alignment
Tatsuya Akutsu, Morihiro Hayashida and Takeyuki Tamura.
13:50 Aligning Discovered Patterns from Protein Family Sequences
En-Shiun Annie Lee, Enhui Zhuang and Andrew K.C. Wong.
14:10 Application of the Burrows-Wheeler Transform for Searching for Approximate Tandem Repeats
Agnieszka Danek, Rafał Pokrzywa, Izabela Makałowska and Andrzej Polański.
14:30 Pattern recognition for subfamily level classification of GPCRs using motif distillation and distinguishing power evaluation
Ahmet Sinan Yavuz, Bugra Ozer and Ugur Sezerman.
14:50 Concluding remarks

Invited Speakers

Prof. Hwanjo Yu from Postech, Korea.

Search & Mining for Big Data

This talk will discuss search and mining research in Big data
generation. First, examples of recently developed search and mining
applications will be introduced such as relevance feedback PubMed
search engine, georeferenced search system, novel recommendation
methods, and location privacy protection methods. Then, we will
discuss Big data platform trends and discuss research issues in
developing search and mining applications for Big data.

Prof. Kwong-Sak Leung from The Chinese University of Hong Kong.

Large scale data mining for binding patterns and drug discovery

Today, we have huge amount of bioinformatics data and databases on Web mostly free. They are treasures to be mined. Two large scale data mining research projects are to be presented: (1) Discovering approximate protein-DNA binding core sequence patterns, and (2) Computer-aided drug discovery, concentrating on protein-ligand docking and de novo drug design based on optimizing the conformations of 3D protein-ligand interactions. Encouraging results have been achieved to better understand gene regulation, and to more effectively and efficiently synthesize and discover drug candidates with computers, respectively. Novel techniques to handle millions of data items using novel algorithms, data indexing and GPU will be given.

Research team: Professor Kwong Sak Leung, Dr Tak Ming Chan and Hongjian Li

Prof. Takayuki Aoki from Tokyo Institute of Technology

Large-scale stencil applications using the whole TSUBAME2.0 resources.

Real-world simulations based on fluid dynamics require huge amount of computer resources. Only by large-scale computation on world top-class supercomputers the computational demands can be satisfied. Most stencil applications such as CFD are memory-bound problems and GPU has both high computational performance and memory bandwidth suitable for them. We demonstrate three stencil applications carried out on the whole TSUBAME 2.0 system, which has 2.4 PFLOPS of the peak performance at the Tokyo Institute of Technology. First, we introduce high resolution meso-scale atmosphere model ASUCA that is being developed by the Japan Meteorological Agency (JMA) for the purpose of the next-generation weather forecasting service. We have succeeded in a weather prediction with 500-m resolution (cf. Current JMA weather forecast uses 5km mesh). We also show an air flow simulation for 10 km x 10 km area of a central part of Tokyo with 1-m resolution by Lattice Boltzmann method, in which a new Large-Eddy Simulation model has been employed. Finally we talk about a phase-field simulation to develop new materials by studying the dendritic solidification of Al-Si alloy. We achieved 2.0 PFLOPS in single precision, which is 44.5% of the peak performance.

Takayuki Aoki received a BSc in Applied Physics (1983), an MSc in Energy Science and Dr.Sci (1989) from Tokyo Institute of Technology, has been a professor in Tokyo Institute of Technology since 2001 and the deputy director of the Global Scientific Information and Computing Center since 2009. He received the Computational Mechanics Achievement Award from Japan Society of Mechanical Engineers and many awards and honors in GPU computing, scientific visualization, and others. His team got the Gordon Bell Prize, Special Achievement in Scalability and Time-to-Solution in 2011. He was also recognized as a CUDA fellow by NVIDIA in 2012.

Conference Venue

Ferrite Memorial Room (3F),
The Centennial Hall,
Ookayama Area,
Tokyo Institute of Technology,
Japan.
The access map to Ookayama area is provided in here. The location of the Centennial Hall is near the Main gate, as shown below. The map of the campus is also available here.