Search · four archives
Search · four archives
24 papers · ranked by Valyu relevance
Ciyuan Peng, Feng Xia, Mehdi Naseriparsa, Francesco Osborne
With the explosive growth of artificial intelligence (AI) and big data, it has become vitally important to organize and represent the enormous volume of knowledge appropriately. As graph data, knowledge graphs accumulate and convey knowledge of the real world. It has been well-recognized that knowledge graphs…
Zhenchang Xing, Jiamou Sun, Xin Peng, Xiwei Xu + 1 more
Programming tutorials are often created to demonstrate programming tasks with code examples. However, our study of Stack Overflow questions reveals the low utilization of high-quality programming tutorials, which is caused task description mismatch and code information overload. Document search can find relevant…
Qing Huang, Zhiqiang Yuan, Zhenchang Xing, Zhengkang Zuo + 2 more
'Changjing Wang' 'Xin Xia'] Abstract—Software programming requires both API reference (know-what) knowledge and programming task (know-how) knowledge. Lots of programming know-what and know-how knowledge is documented in text, for example, API reference documentation and programming tutorials. To improve knowledge…
Aidan Hogan, Eva Blomqvist, Michael Cochez, Claudia d’Amato + 14 more
'Gerard de Melo' 'Claudio Gutiérrez' 'Sabrina Kirrane' 'José Emilio Labra Gayo' 'Roberto Navigli' 'Sebastian Neumaier' 'Axel-Cyrille Ngonga Ngomo' 'Axel Polleres' 'Sabbir M. Rashid' 'Anisa Rula' 'Lukas Schmelzeisen' 'Juan Sequeda' 'Steffen Staab' 'Antoine Zimmermann'] AIDAN HOGAN, IMFD, DCC, Universidad de Chile, Chile…
Théo Matricon, Nathanaël Fijalkow, Gaëtan Margueritte
We tackle the problem of automatic generation of computer programs from a few pairs of input-output examples. The starting point of this work is the observation that in many applications a solution program must use external knowledge not present in the examples: we call such programs knowledge-powered since they can…
Amy K Glen, Eric W Deutsch, Stephen A Ramsey, Christina Kendziorski
Knowledge graphs (KGs) have emerged as useful abstractions for integrating heterogeneous biomedical data, making them convenient substrates for data mining and other computational reasoning techniques. The way in which such knowledge graphs are exposed for use varies; some graphs are only available for flat-file…
Gergely Zahoránszky-Kőhalmi, Brandon Walker, Nathan Miller, Brett Yang + 11 more
The recent SmartGraph platform facilitates the execution of complex drug-discovery workflows with ease in the network-pharmacology paradigm. However, at the time of its publication, we identified the need for the development of an Application Programming Interface (API) that could promote biomedical data integration…
Mark Matties
We present an overview of the design and first proof-ofconcept implementation for AIDA, an autonomous intelligent developer agent that develops software from scratch. AIDA takes a software requirements specification and uses reasoning over a semantic knowledge graph to interpret the requirements, then designs and…
Parisa Kordjamshidi, Dan Roth, Kristian Kersting
Data-driven approaches are becoming increasingly common as problem-solving tools in many areas of science and technology. In most cases, machine learning models are the key component of these solutions. Often, a solution involves multiple learning models, along with significant levels of reasoning with the models'…
Amy K. Glen, Chunyu Ma, Luis Mendoza, Finn Womack + 11 more
With the rapidly growing volume of knowledge and data in biomedical databases, improved methods for knowledge-graph-based computational reasoning are needed in order to answer translational questions. Previous efforts to solve such challenging computational reasoning problems have contributed tools and approaches, but…
Zhisheng Huang, Qing Hu, Mingqun Liao, Cong Miao + 2 more
Kawasaki Disease is a vasculitis syndrome that is extremely harmful to children. Kawasaki Disease can cause severe symptoms of ischemic heart disease or develop into ischemic heart disease, leading to death in children. Researchers and clinicians need to analyze various knowledge and data resources to explore aspects…
Tiffany J. Callahan, Ignacio J. Tripodi, Lawrence E. Hunter, William A. Baumgartner
Although knowledge graphs (KGs) are used extensively in biomedical research to model complex phenomena, many KG construction methods remain largely unable to account for the use of different standardized terminologies or vocabularies, are often difficult to use, and perform poorly as the size of the KG increases in…
Lars Vogt, Marcel Konrad, Manuel Prinz
Knowledge graphs and ontologies provide promising technical solutions for implementing the FAIR Principles for Findable, Accessible, Interoperable, and Reusable data and metadata. However, they also come with their own challenges. Nine such challenges are discussed and associated with the criterion of cognitive…
Amy K. Glen, Eric W. Deutsch, Stephen A. Ramsey
1## Introduction Knowledge graphs (KGs) have emerged as useful abstractions for integrating heterogeneous biomedical data, making them convenient substrates for data mining and other computational reasoning techniques. The way in which such knowledge graphs are exposed for use varies; some graphs are only available for…
Amy K. Glen, Eric W. Deutsch, Stephen A. Ramsey
Knowledge graphs are increasingly being used to integrate heterogeneous biomedical knowledge and data. General-purpose graph database management systems such as Neo4j are often used to host and search knowledge graphs, but such tools come with overhead and leave biomedical-specific standards compliance and reasoning to…
Lars Vogt, Kheir Eddine Farfar, Pallavi Karanth, Marcel Konrad + 3 more
Knowledge graphs and ontologies are promising technologies for achieving FAIR (findable, accessible, interoperable, and reusable) data. We identify four challenges as high barriers for the effective use of knowledge graphs. Since the construction of knowledge graphs is a modelling task and every model serves a purpose…
Guangrong Qin, Kamileh Narsinh, Qi Wei, Jared C. Roach + 15 more
As large clinical and multiomics datasets and knowledge resources accumulate, they need to be transformed into computable and actionable information to support automated reasoning. These datasets range from laboratory experiment results to electronic health records (EHRs). Barriers to accessibility and sharing of such…
Frédéric Burdet, Pierre-Marie Allard, Louis-Felix Nothias, Olivier Kirchhoffer + 16 more
Plants have a complex chemo-diversity and represent a reservoir of potential new therapeutic agents. Within a Swiss research project, six scientific research groups from different disciplines are collaborating to investigate a collection of more than 17’000 unique dried plant extracts. It aims to find new bioactive…
Authors not listed
Step-by-step thinking is essential in all domains of chemical sciences and engineering. While machine learning tools are broadly used, algorithms that automate reasoning are far less common. We elaborate on seven categories of human reasoning activities and connect each to applications in chemical science and…
Shilpa Verma, Rajesh Bhatia, Sandeep Harit, Sanjay Batish
The necessity for scholarly knowledge mining and management has grown significantly as academic literature and its linkages to authors produce enormously. Information extraction, ontology matching, and accessing academic components with relations have become more critical than ever. Therefore, with the advancement of…
David N. Nicholson, Daniel S. Himmelstein, Casey S. Greene
Knowledge graphs support multiple research efforts by providing contextual information for biomedical entities, constructing networks, and supporting the interpretation of high-throughput analyses. These databases are populated via some form of manual curation, which is difficult to scale in the context of an…
Michael Statt, Brian Rohr, Dan Guevarra, Ja'Nya Breeden + 2 more
Materials knowledge is inherently hierarchical. While high-level descriptors such as composition and structure are valuable for contextualizing materials data, the data must ultimately be considered in the context of its low-level acquisition details. Graph databases offer an opportunity to represent hierarchical…
Authors not listed
In recent years, the development of large language models (LLMs) has revolutionized various fields of natural science, yet their application in molecular data processing remains constrained due to the reliance on single-modality inputs and outputs. To bridge the gap between experimenters and computational tools, we…
Kan Hatakeyama-Sato, Naoki Yamane, Yasuhiko Igarashi, Yuta Nabae + 1 more
This paper evaluates the capabilities and limitations of the Generative Pre-trained Transformer 4 (GPT-4) in chemical research. Although GPT-4 exhibits remarkable proficiencies, it is evident that the quality of input data significantly affects its performance. We explore GPT-4's potential in chemical tasks, such as…