20,826 research outputs found
Representing, reasoning and answering questions about biological pathways - various applications
Biological organisms are composed of numerous interconnected biochemical
processes. Diseases occur when normal functionality of these processes is
disrupted. Thus, understanding these biochemical processes and their
interrelationships is a primary task in biomedical research and a prerequisite
for diagnosing diseases, and drug development. Scientists studying these
processes have identified various pathways responsible for drug metabolism, and
signal transduction, etc.
Newer techniques and speed improvements have resulted in deeper knowledge
about these pathways, resulting in refined models that tend to be large and
complex, making it difficult for a person to remember all aspects of it. Thus,
computer models are needed to analyze them. We want to build such a system that
allows modeling of biological systems and pathways in such a way that we can
answer questions about them.
Many existing models focus on structural and/or factoid questions, using
surface-level knowledge that does not require understanding the underlying
model. We believe these are not the kind of questions that a biologist may ask
someone to test their understanding of the biological processes. We want our
system to answer the kind of questions a biologist may ask. Such questions
appear in early college level text books.
Thus the main goal of our thesis is to develop a system that allows us to
encode knowledge about biological pathways and answer such questions about them
demonstrating understanding of the pathway. To that end, we develop a language
that will allow posing such questions and illustrate the utility of our
framework with various applications in the biological domain. We use some
existing tools with modifications to accomplish our goal.
Finally, we apply our system to real world applications by extracting pathway
knowledge from text and answering questions related to drug development.Comment: thesi
ERDS: Emerging Risks Detection Support : 2007 project report
Rapport over het detecteren van risico's met de veiligheid van voeding. Aan de hand van het melamineschandaal wordt gekeken hoe in een vroegtijdig stadium risico's onderkend kunnen worde
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
Neurocognitive Informatics Manifesto.
Informatics studies all aspects of the structure of natural and artificial information systems. Theoretical and abstract approaches to information have made great advances, but human information processing is still unmatched in many areas, including information management, representation and understanding. Neurocognitive informatics is a new, emerging field that should help to improve the matching of artificial and natural systems, and inspire better computational algorithms to solve problems that are still beyond the reach of machines. In this position paper examples of neurocognitive inspirations and promising directions in this area are given
Evaluating the Potential of Leading Large Language Models in Reasoning Biology Questions
Recent advances in Large Language Models (LLMs) have presented new
opportunities for integrating Artificial General Intelligence (AGI) into
biological research and education. This study evaluated the capabilities of
leading LLMs, including GPT-4, GPT-3.5, PaLM2, Claude2, and SenseNova, in
answering conceptual biology questions. The models were tested on a
108-question multiple-choice exam covering biology topics in molecular biology,
biological techniques, metabolic engineering, and synthetic biology. Among the
models, GPT-4 achieved the highest average score of 90 and demonstrated the
greatest consistency across trials with different prompts. The results
indicated GPT-4's proficiency in logical reasoning and its potential to aid
biology research through capabilities like data analysis, hypothesis
generation, and knowledge integration. However, further development and
validation are still required before the promise of LLMs in accelerating
biological discovery can be realized
Anatomical information science
The Foundational Model of Anatomy (FMA) is a map of the human body. Like maps of other sorts – including the map-like representations we find in familiar anatomical atlases – it is a representation of a certain portion of spatial reality as it exists at a certain (idealized) instant of time. But unlike other maps, the FMA comes in the form of a sophisticated ontology of its objectdomain, comprising some 1.5 million statements of anatomical relations among some 70,000 anatomical kinds. It is further distinguished from other maps in that it represents not some specific portion of spatial reality (say: Leeds in 1996), but rather the generalized or idealized spatial reality associated with a generalized or idealized human being at some generalized or idealized instant of time. It will be our concern in what follows to outline the approach to ontology that is represented by the FMA and to argue that it can serve as the basis for a new type of anatomical information science. We also draw some implications for our understanding of spatial reasoning and spatial ontologies in general
Machine learning and its applications in reliability analysis systems
In this thesis, we are interested in exploring some aspects of Machine Learning (ML) and its application in the Reliability Analysis systems (RAs). We begin by investigating some ML paradigms and their- techniques, go on to discuss the possible applications of ML in improving RAs performance, and lastly give guidelines of the architecture of learning RAs. Our survey of ML covers both levels of Neural Network learning and Symbolic learning. In symbolic process learning, five types of learning and their applications are discussed: rote learning, learning from instruction, learning from analogy, learning from examples, and learning from observation and discovery. The Reliability Analysis systems (RAs) presented in this thesis are mainly designed for maintaining plant safety supported by two functions: risk analysis function, i.e., failure mode effect analysis (FMEA) ; and diagnosis function, i.e., real-time fault location (RTFL). Three approaches have been discussed in creating the RAs. According to the result of our survey, we suggest currently the best design of RAs is to embed model-based RAs, i.e., MORA (as software) in a neural network based computer system (as hardware). However, there are still some improvement which can be made through the applications of Machine Learning. By implanting the 'learning element', the MORA will become learning MORA (La MORA) system, a learning Reliability Analysis system with the power of automatic knowledge acquisition and inconsistency checking, and more. To conclude our thesis, we propose an architecture of La MORA
Knowledge-based Biomedical Data Science 2019
Knowledge-based biomedical data science (KBDS) involves the design and
implementation of computer systems that act as if they knew about biomedicine.
Such systems depend on formally represented knowledge in computer systems,
often in the form of knowledge graphs. Here we survey the progress in the last
year in systems that use formally represented knowledge to address data science
problems in both clinical and biological domains, as well as on approaches for
creating knowledge graphs. Major themes include the relationships between
knowledge graphs and machine learning, the use of natural language processing,
and the expansion of knowledge-based approaches to novel domains, such as
Chinese Traditional Medicine and biodiversity.Comment: Manuscript 43 pages with 3 tables; Supplemental material 43 pages
with 3 table
Knowledge Rich Natural Language Queries over Structured Biological Databases
Increasingly, keyword, natural language and NoSQL queries are being used for
information retrieval from traditional as well as non-traditional databases
such as web, document, image, GIS, legal, and health databases. While their
popularity are undeniable for obvious reasons, their engineering is far from
simple. In most part, semantics and intent preserving mapping of a well
understood natural language query expressed over a structured database schema
to a structured query language is still a difficult task, and research to tame
the complexity is intense. In this paper, we propose a multi-level
knowledge-based middleware to facilitate such mappings that separate the
conceptual level from the physical level. We augment these multi-level
abstractions with a concept reasoner and a query strategy engine to dynamically
link arbitrary natural language querying to well defined structured queries. We
demonstrate the feasibility of our approach by presenting a Datalog based
prototype system, called BioSmart, that can compute responses to arbitrary
natural language queries over arbitrary databases once a syntactic
classification of the natural language query is made
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