Related papers: HINO: a BFO-aligned ontology representing human mo…
Benefiting from diverse instruction datasets, contemporary Large Language Models (LLMs) perform effectively as AI assistants in collaborating with humans. However, LLMs still struggle to generate natural and colloquial responses in…
The interactions between DNA, RNA, and proteins are fundamental to biological processes, as illustrated by the central dogma of molecular biology. Although modern biological pre-trained models have achieved great success in analyzing these…
We argue that ontology-structured knowledge graphs can play a crucial role in generating predictions about future events. By leveraging the semantic framework provided by Basic Formal Ontology (BFO) and Common Core Ontologies (CCO), we…
Many optimization algorithm benchmarking platforms allow users to share their experimental data to promote reproducible and reusable research. However, different platforms use different data models and formats, which drastically complicates…
Heterogeneous information network (HIN) has been widely used to characterize entities of various types and their complex relations. Recent attempts either rely on explicit path reachability to leverage path-based semantic relatedness or…
The complexity of many biological, social and technological systems stems from the richness of the interactions among their units. Over the past decades, a great variety of complex systems has been successfully described as networks whose…
The Belief-Desire-Intention (BDI) model is a cornerstone for representing rational agency in artificial intelligence and cognitive sciences. Yet, its integration into structured, semantically interoperable knowledge representations remains…
Recent advances in AI for science have highlighted the power of contrastive learning in bridging heterogeneous biological data modalities. Building on this paradigm, we propose HIPPO (HIerarchical Protein-Protein interaction prediction…
A new suggestion for pattern formation in biological systems is proposed. The interaction of two signaling pathways provides complex patterning. The interaction of two pathways involves few of the biochemical complexities of the pathways.…
Objective: Human-curated disease ontologies are widely used for diagnostic evaluation, treatment and data comparisons over time, and clinical decision support. The classification principles underlying these ontologies are guided by the…
We present a novel framework for understanding node target search in systems organized as hierarchical networks-within-networks. Our work generalizes traditional search models on complex networks, where the mean-first passage time is…
Big Data architectures allow to flexibly store and process heterogeneous data, from multiple sources, in their original format. The structure of those data, commonly supplied by means of REST APIs, is continuously evolving. Thus data…
This paper discusses the representation of ontologies in the first-order logical environment {\ttfamily FOLE}. An ontology defines the primitives with which to model the knowledge resources for a community of discourse. These primitives…
Legacy scientific workflows, and the services within them, often present scarce and unstructured (i.e. textual) descriptions. This makes it difficult to find, share and reuse them, thus dramatically reducing their value to the community.…
Considering the evolution of the semantic wiki engine based platforms, two main approaches could be distinguished: Ontologies for Wikis (OfW) and Wikis for Ontologies (WfO). OfW vision requires existing ontologies to be imported. Most of…
Data integration and mediation have become central concerns of information technology over the past few decades. With the advent of the Web and the rapid increases in the amount of data and the number of Web documents and users, researchers…
Natural language is understandable by human and not machine. None technical persons can only use natural language to specify their business requirements. However, the current version of Business process management and notation (BPMN) tools…
Ontologies play a critical role in Semantic Web technologies by providing a structured and standardized way to represent knowledge and enabling machines to understand the meaning of data. Several taxonomies and ontologies have been…
Academic networks in the real world can usually be portrayed as heterogeneous information networks (HINs) with multi-type, universally connected nodes and multi-relationships. Some existing studies for the representation learning of…
Various hypotheses exist about the paths used for communication between the nodes of complex networks. Most studies simply suppose that communication goes via shortest paths, while others have more explicit assumptions about how routing…