Issues

• add logistic regerssion to find out stressor

  ProjecticumDataScience/AOP-Evidence-Scorer#19 · Filter by author alena-sava opened on Dec 7, 2025

• add relationship extraction

  ProjecticumDataScience/AOP-Evidence-Scorer#18 · Filter by author alena-sava opened on Nov 17, 2025

• remove Daan from repositrory

  ProjecticumDataScience/AOP-Evidence-Scorer#17 · Filter by author alena-sava opened on Nov 10, 2025

• add triple extraction

  ProjecticumDataScience/AOP-Evidence-Scorer#16 · Filter by author alena-sava opened on Nov 4, 2025

• gene module, detecting genes in articles

  ProjecticumDataScience/AOP-Evidence-Scorer#15 · Filter by author alena-sava opened on Oct 26, 2025

• genome module

  ProjecticumDataScience/AOP-Evidence-Scorer#14 · Filter by author alena-sava opened on Oct 26, 2025

• model tuning

  ProjecticumDataScience/AOP-Evidence-Scorer#13 · Filter by author alena-sava opened on Oct 3, 2025

• Integration with the AOP pipeline After extracting entities → pass them to the next stage (for example, linking chemical–endpoint–effect).

  ProjecticumDataScience/AOP-Evidence-Scorer#12 · Filter by author alena-sava opened on Sep 28, 2025

• Improvement through additional features Rule-based matching (spaCy Matcher) for rare chemicals or biological terms. Post-processing: normalization of names (map NEFA → non-esterified fatty acids).

  ProjecticumDataScience/AOP-Evidence-Scorer#11 · Filter by author alena-sava opened on Sep 28, 2025

• Building a baseline test system

  ProjecticumDataScience/AOP-Evidence-Scorer#10 · Filter by author alena-sava opened on Sep 28, 2025

• Fine-tuning spaCy NER

  ProjecticumDataScience/AOP-Evidence-Scorer#9 · Filter by author alena-sava opened on Sep 28, 2025

• Create annotations for validation and testing to evaluate the model's quality. If you only have CHEMICAL and SPECIES, consider whether you need to add other entities (like endpoints, genes, processes).

  ProjecticumDataScience/AOP-Evidence-Scorer#8 · Filter by author alena-sava opened on Sep 28, 2025

• Preparing data for training / fine-tuning the model Convert entities_ner.csv into a format that spaCy uses for training (DocBin or .spacy).

  ProjecticumDataScience/AOP-Evidence-Scorer#7 · Filter by author alena-sava opened on Sep 28, 2025