60,727 research outputs found
Encoding Higher Level Extensions of Petri Nets in Answer Set Programming
Answering realistic questions about biological systems and pathways similar
to the ones used by text books to test understanding of students about
biological systems is one of our long term research goals. Often these
questions require simulation based reasoning. To answer such questions, we need
formalisms to build pathway models, add extensions, simulate, and reason with
them. We chose Petri Nets and Answer Set Programming (ASP) as suitable
formalisms, since Petri Net models are similar to biological pathway diagrams;
and ASP provides easy extension and strong reasoning abilities. We found that
certain aspects of biological pathways, such as locations and substance types,
cannot be represented succinctly using regular Petri Nets. As a result, we need
higher level constructs like colored tokens. In this paper, we show how Petri
Nets with colored tokens can be encoded in ASP in an intuitive manner, how
additional Petri Net extensions can be added by making small code changes, and
how this work furthers our long term research goals. Our approach can be
adapted to other domains with similar modeling needs
The PITA System: Tabling and Answer Subsumption for Reasoning under Uncertainty
Many real world domains require the representation of a measure of
uncertainty. The most common such representation is probability, and the
combination of probability with logic programs has given rise to the field of
Probabilistic Logic Programming (PLP), leading to languages such as the
Independent Choice Logic, Logic Programs with Annotated Disjunctions (LPADs),
Problog, PRISM and others. These languages share a similar distribution
semantics, and methods have been devised to translate programs between these
languages. The complexity of computing the probability of queries to these
general PLP programs is very high due to the need to combine the probabilities
of explanations that may not be exclusive. As one alternative, the PRISM system
reduces the complexity of query answering by restricting the form of programs
it can evaluate. As an entirely different alternative, Possibilistic Logic
Programs adopt a simpler metric of uncertainty than probability. Each of these
approaches -- general PLP, restricted PLP, and Possibilistic Logic Programming
-- can be useful in different domains depending on the form of uncertainty to
be represented, on the form of programs needed to model problems, and on the
scale of the problems to be solved. In this paper, we show how the PITA system,
which originally supported the general PLP language of LPADs, can also
efficiently support restricted PLP and Possibilistic Logic Programs. PITA
relies on tabling with answer subsumption and consists of a transformation
along with an API for library functions that interface with answer subsumption
Logic Integer Programming Models for Signaling Networks
We propose a static and a dynamic approach to model biological signaling
networks, and show how each can be used to answer relevant biological
questions. For this we use the two different mathematical tools of
Propositional Logic and Integer Programming. The power of discrete mathematics
for handling qualitative as well as quantitative data has so far not been
exploited in Molecular Biology, which is mostly driven by experimental
research, relying on first-order or statistical models. The arising logic
statements and integer programs are analyzed and can be solved with standard
software. For a restricted class of problems the logic models reduce to a
polynomial-time solvable satisfiability algorithm. Additionally, a more dynamic
model enables enumeration of possible time resolutions in poly-logarithmic
time. Computational experiments are included
Comparative analysis of knowledge representation and reasoning requirements across a range of life sciences textbooks.
BackgroundUsing knowledge representation for biomedical projects is now commonplace. In previous work, we represented the knowledge found in a college-level biology textbook in a fashion useful for answering questions. We showed that embedding the knowledge representation and question-answering abilities in an electronic textbook helped to engage student interest and improve learning. A natural question that arises from this success, and this paper's primary focus, is whether a similar approach is applicable across a range of life science textbooks. To answer that question, we considered four different textbooks, ranging from a below-introductory college biology text to an advanced, graduate-level neuroscience textbook. For these textbooks, we investigated the following questions: (1) To what extent is knowledge shared between the different textbooks? (2) To what extent can the same upper ontology be used to represent the knowledge found in different textbooks? (3) To what extent can the questions of interest for a range of textbooks be answered by using the same reasoning mechanisms?ResultsOur existing modeling and reasoning methods apply especially well both to a textbook that is comparable in level to the text studied in our previous work (i.e., an introductory-level text) and to a textbook at a lower level, suggesting potential for a high degree of portability. Even for the overlapping knowledge found across the textbooks, the level of detail covered in each textbook was different, which requires that the representations must be customized for each textbook. We also found that for advanced textbooks, representing models and scientific reasoning processes was particularly important.ConclusionsWith some additional work, our representation methodology would be applicable to a range of textbooks. The requirements for knowledge representation are common across textbooks, suggesting that a shared semantic infrastructure for the life sciences is feasible. Because our representation overlaps heavily with those already being used for biomedical ontologies, this work suggests a natural pathway to include such representations as part of the life sciences curriculum at different grade levels
- …