# A Library Perspective on Supervised Text Processing in Digital Libraries: An Investigation in the Biomedical Domain

arXiv: https://arxiv.org/abs/2411.12752 · HTML: https://mlsanity.com/paper/2411.12752/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 17 of its 48 references that are in the map.
- First posted on arXiv 6 Nov 2024.

## Builds on (most cited first, 17 of 17)

- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Sentence-BERT: Sentence Embeddings using Siamese BERT-Networks](https://mlsanity.com/paper/1908.10084/) (2019)
- [XLNet: Generalized Autoregressive Pretraining for Language Understanding](https://mlsanity.com/paper/1906.08237/) (2019)
- [BioBERT: a pre-trained biomedical language representation model for biomedical text mining](https://mlsanity.com/paper/1901.08746/) (2019)
- [Domain-Specific Language Model Pretraining for Biomedical Natural Language Processing](https://mlsanity.com/paper/2007.15779/) (2020)
- [OLMo: Accelerating the Science of Language Models](https://mlsanity.com/paper/2402.00838/) (2024)
- [Snorkel: Rapid Training Data Creation with Weak Supervision](https://mlsanity.com/paper/1711.10160/) (2017)
- [BioMistral: A Collection of Open-Source Pretrained Large Language Models for Medical Domains](https://mlsanity.com/paper/2402.10373/) (2024)
- [Exploiting Asymmetry for Synthetic Training Data Generation: SynthIE and the Case of Information Extraction](https://mlsanity.com/paper/2303.04132/) (2023)
- [A Survey on Text Classification: From Shallow to Deep Learning](https://mlsanity.com/paper/2008.00364/) (2020)
- [RelationPrompt: Leveraging Prompts to Generate Synthetic Data for Zero-Shot Relation Triplet Extraction](https://mlsanity.com/paper/2203.09101/) (2022)
- [Machine Knowledge: Creation and Curation of Comprehensive Knowledge Bases](https://mlsanity.com/paper/2009.11564/) (2020)
- [PubTator 3.0: an AI-powered Literature Resource for Unlocking Biomedical Knowledge](https://mlsanity.com/paper/2401.11048/) (2024)
- [ORKG-Leaderboards: A Systematic Workflow for Mining Leaderboards as a Knowledge Graph](https://mlsanity.com/paper/2305.11068/) (2023)
- [BioREx: Improving Biomedical Relation Extraction by Leveraging Heterogeneous Datasets](https://mlsanity.com/paper/2306.11189/) (2023)
- [Comparison of biomedical relationship extraction methods and models for knowledge graph creation](https://mlsanity.com/paper/2201.01647/) (2022)
- [A Library Perspective on Nearly-Unsupervised Information Extraction Workflows in Digital Libraries](https://mlsanity.com/paper/2205.00716/) (2022)

## Abstract (arXiv)

Digital libraries that maintain extensive textual collections may want to further enrich their content for certain downstream applications, e.g., building knowledge graphs, semantic enrichment of documents, or implementing novel access paths. All of these applications require some text processing, either to identify relevant entities, extract semantic relationships between them, or to classify documents into some categories. However, implementing reliable, supervised workflows can become quite challenging for a digital library because suitable training data must be crafted, and reliable models must be trained. While many works focus on achieving the highest accuracy on some benchmarks, we tackle the problem from a digital library practitioner. In other words, we also consider trade-offs between accuracy and application costs, dive into training data generation through distant supervision and large language models such as ChatGPT, LLama, and Olmo, and discuss how to design final pipelines. Therefore, we focus on relation extraction and text classification, using the showcase of eight biomedical benchmarks.