Related papers: Constructing Information-Lossless Biological Knowl…
Evidence plays a crucial role in any biomedical research narrative, providing justification for some claims and refutation for others. We seek to build models of scientific argument using information extraction methods from full-text…
Knowledge base construction is crucial for summarising, understanding and inferring relationships between biomedical entities. However, for many practical applications such as drug discovery, the scarcity of relevant facts (e.g. gene X is…
Biomedical research papers use significantly different language and jargon when compared to typical English text, which reduces the utility of pre-trained NLP models in this domain. Meanwhile Medline, a database of biomedical abstracts,…
All scientific interpretations of statistical outputs depend on background (auxiliary) assumptions that are rarely delineated or explicitly interrogated. These include not only the usual modeling assumptions, but also deeper assumptions…
Data collection and research methodology represents a critical part of the research pipeline. On the one hand, it is important that we collect data in a way that maximises the validity of what we are measuring, which may involve the use of…
Learning disentangled representations of natural language is essential for many NLP tasks, e.g., conditional text generation, style transfer, personalized dialogue systems, etc. Similar problems have been studied extensively for other forms…
Knowledge-based question answering relies on the availability of facts, the majority of which cannot be found in structured sources (e.g. Wikipedia info-boxes, Wikidata). One of the major components of extracting facts from unstructured…
What is information, physically, and why does it so reliably emerge in living, cultural, and technological systems? Existing theories quantify uncertainty, cost, or compressibility, but do not identify which physical structures count as…
Knowledge graph construction typically relies either on predefined ontologies or on schema-free extraction. Ontology-driven pipelines enforce consistent typing but require costly schema design and maintenance, whereas schema-free methods…
Learning structural information from observational data is central to producing new knowledge outside the training corpus. This holds for mechanistic understanding in scientific discovery as well as flexible test-time compositional…
We consider biological individuality in terms of information theoretic and graphical principles. Our purpose is to extract through an algorithmic decomposition system-environment boundaries supporting individuality. We infer or detect…
Information extraction (IE) in scientific literature has facilitated many down-stream tasks. OpenIE, which does not require any relation schema but identifies a relational phrase to describe the relationship between a subject and an object,…
We present an analysis of the problem of identifying biological context and associating it with biochemical events in biomedical texts. This constitutes a non-trivial, inter-sentential relation extraction task. We focus on biological…
Many real world systems need to operate on heterogeneous information networks that consist of numerous interacting components of different types. Examples include systems that perform data analysis on biological information networks; social…
It is not obvious what fraction of all the potential information residing in the molecules and structures of living systems is significant or meaningful to the system. Sets of random sequences or identically repeated sequences, for example,…
Relational facts are an important component of human knowledge, which are hidden in vast amounts of text. In order to extract these facts from text, people have been working on relation extraction (RE) for years. From early pattern matching…
The idea of preserving conditional beliefs emerged recently as a new paradigm apt to guide the revision of epistemic states. Conditionals are substantially different from propositional beliefs and need specific treatment. In this paper, we…
Advances in science are being sought in newly available opportunities to collect massive quantities of data about complex systems. While key advances are being made in detailed mapping of systems, how to relate this data to solving many of…
Rather than using text for scientific research reports, we have proposed developing highly-structured reports with rich semantic models. In this paper, we consider detailed structures for the components of research reports using a modeling…
Nature has inspired various ground-breaking technological developments in applications ranging from robotics to aerospace engineering and the manufacturing of medical devices. However, accessing the information captured in scientific…