@inproceedings{arazkhani-etal-2026-kalimba,
    title = "{KALIMBA}: Knowledge-Assisted Literature Mining for Biological Interaction Analysis",
    author = "Arazkhani, Niloofar  and
      Kotecki, Maciej  and
      Cochran, Brent  and
      Miskov-Zivanov, Natasa",
    editor = "Demner-Fushman, Dina  and
      Ananiadou, Sophia  and
      Roberts, Kirk  and
      Tsujii, Junichi",
    booktitle = "{B}io{NLP} 2026",
    month = jul,
    year = "2026",
    address = "San Diego, California",
    publisher = "Association for Computational Linguistics",
    url = "https://preview.aclanthology.org/ingest-acl-workshops/2026.bionlp-1.71/",
    pages = "880--889",
    ISBN = "979-8-89176-434-7",
    abstract = "The exponential growth of biomedical literature has made manual curation of biological interaction networks increasingly difficult. Existing automated biological interaction extraction systems address the scaling challenge but treat extraction as a final step, delivering structured output with limited or no integrated support for biologists to interactively verify, correct and contextually interrogate extracted interactions against their source evidence within the same environment. We present Knowledge-Assisted Literature Mining for Biological Interaction Analysis (KALIMBA), an end-to-end, human-in-the-loop platform that integrates three complementary extraction methods (NLP-only, LLM-only, and hybrid) alongside expert annotation and evidence-grounded conversational querying through retrieval-augmented generation (RAG) chat module driven by a dual-context prompt, within a single unified workflow. Evaluation on a corpus of 40 signaling-focused papers demonstrates that the LLM-only back-end recovers substantially more interactions than the NLP-only approach. RAG chat evaluation by a domain expert confirms that the conversational module provides scientifically grounded responses that support curation decisions beyond what the structured interaction table alone conveys."
}