Enhancing Document Retrieval for Curating N-ary Relations in Knowledge Bases

Curation of biomedical knowledge bases (KBs) relies on extracting accurate multi-entity relational facts from the literature - a process that remains largely manual and expert-driven. An essential step in this workflow is retrieving documents that can support or complete partially observed n-ary relations. We present a neural retrieval model designed to assist KB curation by identifying documents that help fill in missing relation arguments and provide relevant contextual evidence. To reduce dependence on scarce gold-standard training data, we exploit existing KB records to construct weakly supervised training sets. Our approach introduces two key technical contributions: (i) a layered contrastive loss that enables learning from noisy and incomplete relational structures, and (ii) a balanced sampling strategy that generates high-quality negatives from diverse KB records. On two biomedical retrieval benchmarks, our approach achieves state-of-the-art performance, outperforming strong baselines in NDCG@10 by 5.7 and 3.7 percentage points, respectively.

Using LLMs to label medical papers according to the CIViC evidence model

We introduce the sequence classification problem CIViC Evidence to the field of medical NLP. CIViC Evidence denotes the multi-label classification problem of assigning labels of clinical evidence to abstracts of scientific papers which have examined various combinations of genomic variants, cancer types, and treatment approaches. We approach CIViC Evidence using different language models: We fine-tune pretrained checkpoints of BERT and RoBERTa on the CIViC Evidence dataset and challenge their performance with models of the same architecture which have been pretrained on domain-specific text. In this context, we find that BiomedBERT and BioLinkBERT can outperform BERT on CIViC Evidence (+0.8% and +0.9% absolute improvement in class-support weighted F1 score). All transformer-based models show a clear performance edge when compared to a logistic regression trained on bigram tf-idf scores (+1.5 - 2.7% improved F1 score). We compare the aforementioned BERT-like models to OpenAI's GPT-4 in a few-shot setting (on a small subset of our original test dataset), demonstrating that, without additional prompt-engineering or fine-tuning, GPT-4 performs worse on CIViC Evidence than our six fine-tuned models (66.1% weighted F1 score compared to 71.8% for the best fine-tuned model). However, performance gets reasonably close to the benchmark of a logistic regression model trained on bigram tf-idf scores (67.7% weighted F1 score).

HunFlair2 in a cross-corpus evaluation of biomedical named entity recognition and normalization tools

With the exponential growth of the life science literature, biomedical text mining (BTM) has become an essential technology for accelerating the extraction of insights from publications. Identifying named entities (e.g., diseases, drugs, or genes) in texts and their linkage to reference knowledge bases are crucial steps in BTM pipelines to enable information aggregation from different documents. However, tools for these two steps are rarely applied in the same context in which they were developed. Instead, they are applied in the wild, i.e., on application-dependent text collections different from those used for the tools' training, varying, e.g., in focus, genre, style, and text type. This raises the question of whether the reported performance of BTM tools can be trusted for downstream applications. Here, we report on the results of a carefully designed cross-corpus benchmark for named entity extraction, where tools were applied systematically to corpora not used during their training. Based on a survey of 28 published systems, we selected five for an in-depth analysis on three publicly available corpora encompassing four different entity types. Comparison between tools results in a mixed picture and shows that, in a cross-corpus setting, the performance is significantly lower than the one reported in an in-corpus setting. HunFlair2 showed the best performance on average, being closely followed by PubTator. Our results indicate that users of BTM tools should expect diminishing performances when applying them in the wild compared to original publications and show that further research is necessary to make BTM tools more robust.