# Benchmarking Literature Retrieval for a Model Organism: A Dictyostelium Case Study

arXiv: https://arxiv.org/abs/2610.03130 · HTML: https://mlsanity.com/paper/2610.03130/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 9 of its 25 references that are in the map.
- First posted on arXiv 2 Oct 2026.

## Builds on (most cited first, 9 of 9)

- [The Llama 3 Herd of Models](https://mlsanity.com/paper/2407.21783/) (2024)
- [MS MARCO: A Human Generated MAchine Reading COmprehension Dataset](https://mlsanity.com/paper/1611.09268/) (2016)
- [MiniLM: Deep Self-Attention Distillation for Task-Agnostic Compression of Pre-Trained Transformers](https://mlsanity.com/paper/2002.10957/) (2020)
- [M3-Embedding: Multi-Linguality, Multi-Functionality, Multi-Granularity Text Embeddings Through Self-Knowledge Distillation](https://mlsanity.com/paper/2402.03216/) (2024)
- [MedCPT: Contrastive Pre-trained Transformers with Large-scale PubMed Search Logs for Zero-shot Biomedical Information Retrieval](https://mlsanity.com/paper/2307.00589/) (2023)
- [RankZephyr: Effective and Robust Zero-Shot Listwise Reranking is a Breeze!](https://mlsanity.com/paper/2312.02724/) (2023)
- [Ragnar"ok: A Reusable RAG Framework and Baselines for TREC 2024 Retrieval-Augmented Generation Track](https://mlsanity.com/paper/2406.16828/) (2024)
- [Declarative Experimentation in Information Retrieval using PyTerrier](https://mlsanity.com/paper/2007.14271/) (2020)
- [Overview of TREC 2025 Biomedical Generative Retrieval (BioGen) Track](https://mlsanity.com/paper/2603.21582/) (2026)

## Abstract (arXiv)

Biological literature retrieval systems are often developed and evaluated using broad biomedical corpora and general-purpose search tasks. However, many curated knowledge bases operate in narrower model-organism domains, where the literature is sparse and terminology is organism-specific. We introduce a retrieval benchmark from dictyBase for Dictyostelium, a model organism in cell and developmental biology. The benchmark consists of curator-generated biological queries linked to PubMed-indexed articles, together with structured gene annotations. Using this benchmark, we study three factors in niche biological retrieval: cross-encoder reranking, gene-aware query expansion, and abstract-only versus full-text retrieval. We report that reranking and gene-aware query expansion improve retrieval selectively: reranking is most useful when the model is well suited to biological evidence matching, whereas curated annotations help clarify compact biological queries by reducing vocabulary mismatch. Full-text chunks substantially improve retrieval when abstracts omit supporting evidence, increasing both candidate recall and top-rank performance, although these cases are harder than queries supported by abstracts. Data and code are publicly available at https://github.com/fulaibaowang/dictycite, and the benchmark dataset is additionally archived on Zenodo.