Pierre Larmande

GRU-SCANET: Unleashing the Power of GRU-based Sinusoidal CApture Network for Precision-driven Named Entity Recognition

GRU-SCANET improves biomedical Named Entity Recognition by combining GRUs, attention, and CRF, outperforming existing models across multiple corpora.

PyRice: a Python package for querying Oryza Sativa databases

PyRice provides a Python API to access and query Oryza sativa databases efficiently and uniformly.

Enabling Fast Annotation Process With Table2Annotation Tool

The paper introduces a tool for semantic annotation of scientific text in spreadsheets, leveraging the NCBO Annotator API to improve speed and accuracy.

Candidate gene prioritization using graph embedding

This paper uses graph embedding methods to prioritize candidate genes in rice by integrating gene data from multiple databases and evaluating link prediction performance.

Rice Galaxy: an open resource for plant science

Rice Galaxy provides an open resource for plant science, enabling researchers to perform advanced genomic analyses using shared datasets and tools.

Benchmarking Database Systems for Genomic Selection Implementation

The paper benchmarks six open-source database systems for genomic selection, finding that HDF5 outperforms others in data extraction speed due to efficient allele matrix handling.

Agronomic Linked Data (AgroLD): a Knowledge-based System to Enable Integrative Biology in Agronomy

The paper introduces AgroLD, a knowledge-based system integrating omics data from plant species to enable integrative biology research in agronomy.

Evaluating Named-Entity Recognition approaches in plant molecular biology

The paper evaluates Named-Entity Recognition approaches for plant molecular biology, develops a new benchmark dataset, and finds LSTM-CRF achieves 86% F1 score for gene and protein extraction.