LADER: Log-Augmented DEnse Retrieval for Biomedical Literature Search

Queries with similar information needs tend to have similar document clicks, especially in biomedical literature search engines where queries are generally short and top documents account for most of the total clicks. Motivated by this, we present a novel architecture for biomedical literature search, namely Log-Augmented DEnse Retrieval (LADER), which is a simple plug-in module that augments a dense retriever with the click logs retrieved from similar training queries. Specifically, LADER finds both similar documents and queries to the given query by a dense retriever. Then, LADER scores relevant (clicked) documents of similar queries weighted by their similarity to the input query. The final document scores by LADER are the average of (1) the document similarity scores from the dense retriever and (2) the aggregated document scores from the click logs of similar queries. Despite its simplicity, LADER achieves new state-of-the-art (SOTA) performance on TripClick, a recently released benchmark for biomedical literature retrieval. On the frequent (HEAD) queries, LADER largely outperforms the best retrieval model by 39% relative NDCG@10 (0.338 v.s. 0.243). LADER also achieves better performance on the less frequent (TORSO) queries with 11% relative NDCG@10 improvement over the previous SOTA (0.303 v.s. 0.272). On the rare (TAIL) queries where similar queries are scarce, LADER still compares favorably to the previous SOTA method (NDCG@10: 0.310 v.s. 0.295). On all queries, LADER can improve the performance of a dense retriever by 24%-37% relative NDCG@10 while not requiring additional training, and further performance improvement is expected from more logs. Our regression analysis has shown that queries that are more frequent, have higher entropy of query similarity and lower entropy of document similarity, tend to benefit more from log augmentation.

[1]  Fei Huang,et al.  RAMM: Retrieval-augmented Biomedical Visual Question Answering with Multi-modal Pre-training , 2023, ACM Multimedia.

[2]  Songfang Huang,et al.  State-of-the-Art Evidence Retriever for Precision Medicine: Algorithm Development and Validation , 2022, JMIR medical informatics.

[3]  Hang Li,et al.  Implicit Feedback for Dense Passage Retrieval: A Counterfactual Approach , 2022, SIGIR.

[4]  Allan Hanbury,et al.  Establishing Strong Baselines for TripClick Health Retrieval , 2022, ECIR.

[5]  Jianfeng Gao,et al.  Domain-Specific Language Model Pretraining for Biomedical Natural Language Processing , 2020, ACM Trans. Comput. Heal..

[6]  M. Mizutani,et al.  BioReader: a Retrieval-Enhanced Text-to-Text Transformer for Biomedical Literature , 2022, EMNLP.

[7]  Jimmy J. Lin,et al.  Pyserini: A Python Toolkit for Reproducible Information Retrieval Research with Sparse and Dense Representations , 2021, SIGIR.

[8]  Carsten Eickhoff,et al.  TripClick: The Log Files of a Large Health Web Search Engine , 2021, SIGIR.

[9]  Paul N. Bennett,et al.  Approximate Nearest Neighbor Negative Contrastive Learning for Dense Text Retrieval , 2020, ICLR.

[10]  Jeff Johnson,et al.  Billion-Scale Similarity Search with GPUs , 2017, IEEE Transactions on Big Data.

[11]  Allan Hanbury,et al.  Local Self-Attention over Long Text for Efficient Document Retrieval , 2020, SIGIR.

[12]  M. Zaharia,et al.  ColBERT: Efficient and Effective Passage Search via Contextualized Late Interaction over BERT , 2020, SIGIR.

[13]  Danqi Chen,et al.  Dense Passage Retrieval for Open-Domain Question Answering , 2020, EMNLP.

[14]  Omer Levy,et al.  Generalization through Memorization: Nearest Neighbor Language Models , 2019, ICLR.

[15]  Lysandre Debut,et al.  HuggingFace's Transformers: State-of-the-art Natural Language Processing , 2019, ArXiv.

[16]  Natalia Gimelshein,et al.  PyTorch: An Imperative Style, High-Performance Deep Learning Library , 2019, NeurIPS.

[17]  Thomas Wolf,et al.  DistilBERT, a distilled version of BERT: smaller, faster, cheaper and lighter , 2019, ArXiv.

[18]  Aidong Zhang,et al.  A survey on literature based discovery approaches in biomedical domain , 2019, J. Biomed. Informatics.

[19]  Iz Beltagy,et al.  SciBERT: A Pretrained Language Model for Scientific Text , 2019, EMNLP.

[20]  Frank Hutter,et al.  Decoupled Weight Decay Regularization , 2017, ICLR.

[21]  Ming-Wei Chang,et al.  BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding , 2019, NAACL.

[22]  Zhiyong Lu,et al.  How user intelligence is improving PubMed , 2018, Nature Biotechnology.

[23]  Zhiyong Lu,et al.  Best Match: New relevance search for PubMed , 2018, PLoS biology.

[24]  Zhiyuan Liu,et al.  Convolutional Neural Networks for Soft-Matching N-Grams in Ad-hoc Search , 2018, WSDM.

[25]  Zhiyuan Liu,et al.  End-to-End Neural Ad-hoc Ranking with Kernel Pooling , 2017, SIGIR.

[26]  Lukasz Kaiser,et al.  Attention is All you Need , 2017, NIPS.

[27]  Gerard de Melo,et al.  PACRR: A Position-Aware Neural IR Model for Relevance Matching , 2017, EMNLP.

[28]  Xueqi Cheng,et al.  Text Matching as Image Recognition , 2016, AAAI.

[29]  M. de Rijke,et al.  Click Models for Web Search , 2015, Click Models for Web Search.

[30]  James Philbin,et al.  FaceNet: A unified embedding for face recognition and clustering , 2015, 2015 IEEE Conference on Computer Vision and Pattern Recognition (CVPR).

[31]  Jimmy Ba,et al.  Adam: A Method for Stochastic Optimization , 2014, ICLR.

[32]  Zhiyong Lu,et al.  Understanding PubMed® user search behavior through log analysis , 2009, Database J. Biol. Databases Curation.

[33]  ChengXiang Zhai,et al.  A comparative study of methods for estimating query language models with pseudo feedback , 2009, CIKM.

[34]  Milad Shokouhi,et al.  Query Expansion Using External Evidence , 2009, ECIR.

[35]  Hugo Zaragoza,et al.  The Probabilistic Relevance Framework: BM25 and Beyond , 2009, Found. Trends Inf. Retr..

[36]  Taghi M. Khoshgoftaar,et al.  A Survey of Collaborative Filtering Techniques , 2009, Adv. Artif. Intell..

[37]  Nick Craswell,et al.  An experimental comparison of click position-bias models , 2008, WSDM '08.

[38]  Ricardo A. Baeza-Yates,et al.  Improving search engines by query clustering , 2007, J. Assoc. Inf. Sci. Technol..

[39]  Jerome A Osheroff,et al.  Research Paper: Answering Physicians' Clinical Questions: Obstacles and Potential Solutions , 2005, J. Am. Medical Informatics Assoc..

[40]  W. Bruce Croft,et al.  Relevance-Based Language Models , 2001, SIGIR '01.