28-29 September 2009: Workshop at Roskilde University
The workshop takes place in room 42.2-02 (bldg. 42, level 2, room 02: ISL/PLIS-lab); participation only.Preliminary schedule
The following time table is flexible, which means that if we start an interesting discussion during one presentation, we may postpone the next sessions, even until the following day. And we can decide to swop presentation.Only lunch breaks and the workshop dinner are fixed.
Monday, September 28 9:00 Welcome, Presentation 9:10-9:40 Overview of the LoSt project - what have been achieved so far, goals and activities for the remaining project period Henning Christiansen 9:40-10:20 Searching for hard-to-find genes, or: What we may (hope) to do better than the others Ole Skovgaard 10:20-10:30 Short break 10:30-11:30 Bayesian and non-Bayesian parameter estimation for PRISM programs James Cussens 11:30-11:50 Break 11:50-12:30 Layered model of analysis Ole Torp Lassen 12:30 Lunch 13:30-14:10 Bayesian coordinating HMMs for sequence analysis Henning Christiansen 14:10-14:50 Probabilistic Logic Models of mRNA sequence and secondary structure Søren Mørk 14:50-15:00 Short break 15:00-15:40 HMM approximation of CFGs Christian Theil Have (joint work with Ole Torp Lassen) 15:40-16:10 Break 16:10-16:50 Constrained HMM for Easygene Matthieu Petit 16:50-17:30 (Perhaps re-schedule one of the two talks scheduled for Tuesday; below) 17:30-18:30 (at latest) Discussion: open problems, where to put our attention Conclude: Topics for detailed work in the rest of the workshop, what, who, when. 18:30 Departure for the Workshop Dinner Tuesday, September 19 9:00-9:50 Manfred Jaeger Relational information gain - with applications to bio-databases 9:50-10:00 Short break 10:00 Starting detailed work in (perhaps) smaller groups 11:15-11:30 break 11:30-12:30 More detailed work 10:30 Short break and detailed work, until 12:30-13:30 Lunch 13:30-14:20 EM clustering with GO scoring Nicos Angelopoulos 14:20-14:40 Break 14:40-16:00 Detailed work 16:00-17:00 Reports from the working groups, suggestions for future collaborations
Host
prof. Henning Christiansen, henning@ruc.dk, PLIS research group, CBIT Institute, at Roskilde University and the LoSt project, For directions on how to get to Roskilde University, go here and also here4 March 2009: Mini Workshop at Roskilde University
Announcement
Dear LoSt participants, external partners and other interested parties,First of all, welcome to
Christian Theil Have as new PhD student in the project, starting officially March 1.
On Wednesday, March 4, next week we will organize a mini workshop starting 15:30 in the afternoon with different contributions in probabilistic-logic modelling. Workshop program; (timing include discussions, changing computers, etc.)
Program
15:30 | Welcome and overview of the LoSt project Henning Christiansen |
15:35 | A focus on Overlapping Genes: The problem and current investigations
Ana Capatana |
Recent progress in the LoSt project | |
15:55 | Optimization by decomposition: Chopping and evaluation Ole Torp Lassen |
16:15 | PRISM programs with annotation: Optimzation
by program analysis and transformation Henning Christiansen |
16:35 | Coffee, tea, fruit, ... |
17:00 | Coordinating HMMs and other sorts of Constrained HMMs Matthieu Petit |
In depth with constraints and failure | |
17:20 | The implementation of an EM algorithm for Stochastic Logic Programs
MCMC over distributional logic programs
clustering via EM with mclust package of R
Nicos Angelopoulos |
17:50 | Stochastic Definite Clause Grammars
Christian Theil Have |
18:10 | Final discussion: Most pressing problems and possible new directions |
18:40 | The end |
Host
prof. Henning Christiansen, henning@ruc.dk, PLIS research group, CBIT Institute, at Roskilde University and the LoSt project, For directions on how to get to Roskilde University, go here and also here5 May 2008: Research seminar at Roskilde University
Announcement
A methodology for Bayesian machine learning and
its application to ligand discovery
by Nicos Angelopoulos, Edinburgh University
Roskilde University, room 42-2.37,
Monday May 5, 2008, 12.15-13.00
Abstract
The talk describes a probabilistic logic programming language in the context of Bayesian knowledge representation. An MCMC algorithm operating on model structures defined in the language and its implementation are also described. The system has recently been used to provide a Bayesian analysis of high-dimensional descriptor data for the pyruvate kinase protein.
Classification trees have been learnt from experimentally determined binding affinity data. The algorithm has performed better than two Neural Network approaches. In addition, it can be more easily run on a distributed environment and lends itself naturally to classifying sets with missing data. The approach has been used to select and rank potential biologically active compounds and could provide a powerful tool in compound testing.
Host
prof. Henning Christiansen, henning@ruc.dk, PLIS research group, CBIT Institute, at Roskilde University and the LoSt project, For directions on how to get to Roskilde University, go here and also here5-6 February 2008: Workshop at Roskilde University
Announcement
This is first internal workshop in LoSt project; LoSt is the acronym for the project "Logic-statistic analysis of biological sequence data".
Place: Roskilde University, CBIT Institute, Rooms 42-2.37 and 42-1.37
Participation: By invitation only.
Workshop program (preliminary)
Tuesday 5 Feb 2008 (Room 42-2.37) | |
10:00-10:30 |
Henning Christiansen, Roskilde University:
Presentation of project and workshop participants Overall project goals with an emphasis on computational issues |
10:30-11:10 |
Ole Torp Lassen, Roskilde University:
Combining HMM and SCFG in PRISM, and approaching complexity problems by preprocessing with an additional HMM. |
11:20-12:00 |
Bjarne Knudsen, Peter Johannes Steffensen, CLC bio:
How a producer of competitive bioinformatics software may contribute to and benefit from the LoSt project. Integration of PRISM-like methods and CLC bio's software. |
12:00-13:00 | Lunch (the foyer of bldg. 0) |
13:00-14:00 |
Taisuke Sato, Japan Institute of Technology:
Background and intentions of PRISM, history and development, applications; perspectives for future developments and applications. |
14:15-15:00 |
Yoshitaka Kameya, Japan Institute of Technology:
Algorithms and data structures in PRISM with emphasis on complexity and bottlenecks for complex problems. |
15:00-18:00 |
Coffee, General discussion Working groups and PRISM hands-on |
18:00 approx. | Departure by taxi to ... |
18:30- |
Workshop dinner Restaurant Mumm, Roskilde |
Wednesday 6 Feb 2008 (Room 42-1.37) | |
9:00-9:45 |
Ole Skovgaard, Roskilde University:
On Chr. Hansen's role in the project Introduction to gene finding |
9:50-10:25 |
Søren Mørk, Roskilde University:
Overview of PhD project |
10:30-11:15 |
John Gallagher, Roskilde University:
Applications of program analysis and transformation for optimization of logic-statistic programs. |
11:30-12:15 |
Manfred Jaeger, Aalborg University:
An overview of Logic-Statistic methods and systems |
12:15-13:15 | Lunch (the foyer of bldg. 0) |
13:15-13:30 |
Bjarne Knudsen, CLC bio:
A smart little box containing the Smith-Waterman algorithm |
13:30-15:00 | Working groups (?) |
15:10-15:25 |
Taisuke Sato, Japan Institute of Technology:
Summary of the workshop and recommendation for the project |
15:25-16:00 | Panel discussion |
Concluding remarks |