The 2008-2011 JSPS Grant-in-Aid for Scientific Research (A)

Inference-based Hypothesis-finding and
its Application to Systems Biology

English | Japanese

Purpose of this Research Project

Systems biology is an emergent field that aims to understand living organisms as biological systems.
In particular, it is important to identify master reactions in metabolic pathways, which are involved in physiological states. If we can obtain these information, it helps the way to macroscopically analyze with previous methods like the one using differential equation.

In order to find such information, we focus on inference methods, induction and abduction, based on
logic-based Artificial Intelligence. Both abduction and induction are used to infer hypotheses in
inductive logic programming (ILP) and are characterized in an ILP system called CF-induction based on SOL-resolution. CF-Induction is the only existing system which is sound and complete for finding inductive hypotheses from full clausal theories, and thus can be used for inducing not only definite clauses but also non-Horn (indefinite) clauses. However, the current inference methods need to improve search space exploration and hypotheses selection.

Therefore we set the following tasks to be achieved in this project:
(A) Improving hypothesis finding methods based on SOL-resolution and CF-Induction.
(B) Developing a hypothesis selection method based on both statistical and non-statistical ways.
(C) Applying those methods to systems biology and evaluating it from a biological viewpoint.

Specifically, we aim at finding hypotheses in systems biology by abduction and induction, then selecting the most likely hypothesis by computing each probability of hypotheses.


Katsumi Inoue National Institute of Informatics, Japan
Taisuke Sato Tokyo Institute of Technology, Japan
Yoshitaka Kameya Tokyo Institute of Technology, Japan
Koji Iwanuma University of Yamanashi, Japan
Hidetomo Nabeshima University of Yamanashi, Japan
Chiaki Sakama Wakayama University, Japan
Asao Fujiyama National Institute of Informatics, Japan


This project is supported by the 2008-2011 JSPS Grant-in-Aid for Scientific Research (A) (No.20240016).

Self Evaluation Report (FY2010)


2008.10.30 - 11.3 The 1st meeting (Co-located with FJ'08)
2009.3.23 - 24 The 2nd meeting
2009.9.21 - 9.25 The 3rd meeting (Co-located with FJ'09)
2010.3.9 The 4th meeting
2010.9.6 The 5th meeting
2011.3.14-15 The 6th meeting
2011.9.12-13 The 7th meeting


Takehide Soh: soh at

Webmaster: Takehide Soh (E-mail soh at