Related papers: semanticSBML 2.0 - A Collection of Online Services…
In computational biology, biological entities such as genes or proteins are usually annotated with terms extracted from Gene Ontology (GO). The functional similarity among terms of an ontology is evaluated by using Semantic Similarity…
Automatic Service Composition is a research direction aimed at facilitating the usage of atomic web services. Particularly, the goal is to build workflows of services that solve specific queries, which cannot be resolved by any single…
Training sophisticated machine learning (ML) models requires large datasets that are difficult or expensive to collect for many applications. If prior knowledge about system dynamics is available, mechanistic representations can be used to…
We present BSTModelKit.jl, an open-source Julia package for constructing, solving, and analyzing Biochemical Systems Theory (BST) models of biochemical networks. The package implements S-system representations, a canonical power-law…
We present CQELS 2.0, the second version of Continuous Query Evaluation over Linked Streams. CQELS 2.0 is a platform-agnostic federated execution framework towards semantic stream fusion. In this version, we introduce a novel…
Web services is a collection of technologies that client-server model use also to exchange information. The Web services uses XML as the message wrapper to exchange information but the XML is always verbose and hence incurs latency in the…
The tasks of semantic web service (discovery, selection, composition, and execution) are supposed to enable seamless interoperation between systems, whereby human intervention is kept at a minimum. In the field of Web service description…
We describe a binding schema markup language (BSML) for describing data interchange between scientific codes. Such a facility is an important constituent of scientific problem solving environments (PSEs). BSML is designed to integrate with…
With the development of the Large Language Models (LLMs), a large range of LLM-based Text-to-SQL(Text2SQL) methods have emerged. This survey provides a comprehensive review of LLM-based Text2SQL studies. We first enumerate classic…
Synthesizing a reactive system from specifications given in linear temporal logic (LTL) is a classical problem, finding its applications in safety-critical systems design. These systems are typically represented using either Mealy machines…
The benefit of using ontologies, defined by the respective data standards, is shown. It is presented how ontologies can be used for the semantic enrichment of data and how this can contribute to the vision of the semantic web to become…
Many sciences have made significant breakthroughs by adopting online tools that help organize, structure and mine information that is too detailed to be printed in journals. In this paper, we introduce OpenML, a place for machine learning…
XNMR is a system designed to explore the results of combining the well-founded semantics system XSB with the stable-models evaluator SMODELS. Its main goal is to work as a tool for fast and interactive exploration of knowledge bases.
Scientists construct and analyze computational models to understand the world. That understanding comes from efforts to augment, combine, and compare models of related phenomena. We propose SemanticModels.jl, a system that leverages…
Interpreting biological networks becomes challenging when molecular components, such as genes or proteins, participate in numerous interactions, resulting in densely connected regions and overlapping interactions that obscure functional…
Here we give a detailed description of MOLS 2.0.The source code and binary of MOLS 2.0 are distributed free (under GNU Lesser General Public License) for the scientific community. They are freely available for download at…
We present the second generation of a rule-based language called Biochemical Space Language (BCSL) that combines the advantages of different approaches and thus makes an effort to overcome several problems with existing solutions. The key…
A brief informal overview on the BioPAX and SBML standards for formal presentation of complex biological knowledge.
Sequential sampling models (SSMs) are a widely used framework describing decision-making as a stochastic, dynamic process of evidence accumulation. SSMs popularity across cognitive science has driven the development of various software…
Recent developments in machine learning (ML) techniques enable users to extract, transmit, and reproduce information semantics via ML-based semantic communication (SemCom). This significantly increases network spectral efficiency and…