Emanuele Cavalleri

An Open-Source Knowledge Graph Ecosystem for the Life Sciences

Translational research requires data at multiple scales of biological organization. Advancements in sequencing and multi-omics technologies have increased the availability of these data, but...

RNA-KG: An ontology-based knowledge graph for representing interactions involving RNA molecules

The "RNA world" represents a novel frontier for the study of fundamental biological processes and human diseases and is paving the way for the development of new drugs tailored to the patient's...

Fine-Tuning of Conditional Transformers Improves the Generation of Functionally Characterized Proteins

On the Extraction of Meaningful RNA Interactions from Scientific Publications through LLMs and SPIRES

SPIREX: Improving LLM-based relation extraction from RNA-focused scientific literature using graph machine learning

A Meta-Graph for the Construction of an RNA-Centered Knowledge Graph

Construction and Enhancement of an RNA-Based Knowledge Graph for Discovering New RNA Drugs

Better Negatives, Better Predictions: Negative Sample Selection Strategies for Enhancing Biomedical KG Edge Classification

Towards the Construction of an RNA-centered Knowledge Graph

Initial achievements in relation extraction from RNA-focused scientific papers

A Semantic Schema-Based Catalog for Identifying Joinable Columns via LLMs

Prompt engineering approaches for working with biomedical knowledge graphs through LLMs

SchemaLink: An Intelligent Web Editor for LinkML Schema Curation

Motivation: LinkML is a suitable language for the representation of the structural and content constraints of different kinds of biomedical data. Even if it is a quite recent proposal, it has been...

Plausibility-Driven Prioritization of Candidate Biomedical Annotations

The rapid growth of biomedical knowledge has made the validation of automatically generated biological annotations a major bottleneck in biomedical curation. While computational methods can...

RNA-KG v2.0: An RNA-centered Knowledge Graph with Properties

RNA-KG is a recently developed knowledge graph that integrates the interactions involving coding and non-coding RNA molecules extracted from public data sources. It can be used to support the...

Het-node2vec: second order random walk sampling for heterogeneous multigraphs embedding

Many real-world problems are naturally modeled as heterogeneous graphs, where nodes and edges represent multiple types of entities and relations. Existing learning models for heterogeneous graph...