Serena Lotreck's repositories
knowledge-graph
Code exploring the creation of knowledge graphs from plant science papers
msu-datathon-4-justice
MSU team's code for the QSIDE Datathon4Justice
multi-omics
Code for multi-omic deep learning integration project
INCA-isotopomer-simulation-generator
Code to run simulations of 13-C labelling data using INCA (MATLAB)
bratiaa
Inter-annotator agreement for Brat annotation projects
desiccation-network
Code for the project Drying to Connect: A bibliometric analysis of desiccation tolerance research across the kingdoms of life.
dygiepp
Span-based system for named entity, relation, and event extraction.
forum-lesson-plan
Lesson 6 for Foundations in Computational Plant Science (NRT-IMPACTS)
git-tutorial
Toy repo for teaching how to use git/GitHub
literature-genes
Code to identify gene candidates involved in desiccation tolerance from the literature
obie-wan
Improved entity and relation extraction in the plant sciences through ontology-based information extraction
pickle-corpus-code
Code for the manuscript "In a PICKLE: Entity and relation annotation guidelines for the molecular plant sciences"
yeast-interpretability
Using machine learning interpretability methods to study yeast genetic interaction
goatools
Python library to handle Gene Ontology (GO) terms
handson-ml2
A series of Jupyter notebooks that walk you through the fundamentals of Machine Learning and Deep Learning in Python using Scikit-Learn, Keras and TensorFlow 2.
lm-evaluation-harness
A framework for few-shot evaluation of autoregressive language models.
ML-Pipeline
Shiu Lab code base for Machine Learning implemented in SciKit-Learn
ontogpt
LLM-based ontological extraction tools, including SPIRES
plant-history
Using NLP techniques to explore the prevalance of topics of study in the plant sciences over the last 100 years
PURE
NAACL'2021: A Frustratingly Easy Approach for Entity and Relation Extraction
serenalotreck
Github profile README
taxonerd
TaxoNERD : recognizing taxonomic entities using deep models