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Register a new userFine-tuning Pretrained Language Models with Label Attention for Explainable Biomedical Text Classification
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Added by
Bruce Nguyen
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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The massive growth of digital biomedical data is making biomedical text indexing and classification increasingly important. Accordingly, previous research has devised numerous deep learning techniques focused on using feedforward, convolutional or recurrent neural architectures. More recently, fine-tuned transformers-based pretrained models (PTMs) have demonstrated superior performance compared to such models in many natural language processing tasks. However, the direct use of PTMs in the biomedical domain is only limited to the target documents, ignoring the rich semantic information in the label descriptions. In this paper, we develop an improved label attention-based architecture to inject semantic label description into the fine-tuning process of PTMs. Results on two public medical datasets show that the proposed fine-tuning scheme outperforms the conventionally fine-tuned PTMs and prior state-of-the-art models. Furthermore, we show that fine-tuning with the label attention mechanism is interpretable in the interpretability study.
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Inductive transfer learning has greatly impacted computer vision, but existing approaches in NLP still require task-specific modifications and training from scratch. We propose Universal Language Model Fine-tuning (ULMFiT), an effective transfer learning method that can be applied to any task in NLP, and introduce techniques that are key for fine-tuning a language model. Our method significantly outperforms the state-of-the-art on six text classification tasks, reducing the error by 18-24% on the majority of datasets. Furthermore, with only 100 labeled examples, it matches the performance of training from scratch on 100x more data. We open-source our pretrained models and code.
Pretrained language models have shown success in many natural language processing tasks. Many works explore incorporating knowledge into language models. In the biomedical domain, experts have taken decades of effort on building large-scale knowledge bases. For example, the Unified Medical Language System (UMLS) contains millions of entities with their synonyms and defines hundreds of relations among entities. Leveraging this knowledge can benefit a variety of downstream tasks such as named entity recognition and relation extraction. To this end, we propose KeBioLM, a biomedical pretrained language model that explicitly leverages knowledge from the UMLS knowledge bases. Specifically, we extract entities from PubMed abstracts and link them to UMLS. We then train a knowledge-aware language model that firstly applies a text-only encoding layer to learn entity representation and applies a text-entity fusion encoding to aggregate entity representation. Besides, we add two training objectives as entity detection and entity linking. Experiments on the named entity recognition and relation extraction from the BLURB benchmark demonstrate the effectiveness of our approach. Further analysis on a collected probing dataset shows that our model has better ability to model medical knowledge.
Large-scale language models (LMs) pretrained on massive corpora of text, such as GPT-2, are powerful open-domain text generators. However, as our systematic examination reveals, it is still challenging for such models to generate coherent long passages of text (e.g., 1000 tokens), especially when the models are fine-tuned to the target domain on a small corpus. Previous planning-then-generation methods also fall short of producing such long text in various domains. To overcome the limitations, we propose a simple but effective method of generating text in a progressive manner, inspired by generating images from low to high resolution. Our method first produces domain-specific content keywords and then progressively refines them into complete passages in multiple stages. The simple design allows our approach to take advantage of pretrained LMs at each stage and effectively adapt to any target domain given only a small set of examples. We conduct a comprehensive empirical study with a broad set of evaluation metrics, and show that our approach significantly improves upon the fine-tuned large LMs and various planning-then-generation methods in terms of quality and sample efficiency. Human evaluation also validates that our model generations are more coherent.
Deep pretrained language models have achieved great success in the way of pretraining first and then fine-tuning. But such a sequential transfer learning paradigm often confronts the catastrophic forgetting problem and leads to sub-optimal performance. To fine-tune with less forgetting, we propose a recall and learn mechanism, which adopts the idea of multi-task learning and jointly learns pretraining tasks and downstream tasks. Specifically, we propose a Pretraining Simulation mechanism to recall the knowledge from pretraining tasks without data, and an Objective Shifting mechanism to focus the learning on downstream tasks gradually. Experiments show that our method achieves state-of-the-art performance on the GLUE benchmark. Our method also enables BERT-base to achieve better performance than directly fine-tuning of BERT-large. Further, we provide the open-source RecAdam optimizer, which integrates the proposed mechanisms into Adam optimizer, to facility the NLP community.
Exploiting label hierarchies has become a promising approach to tackling the zero-shot multi-label text classification (ZS-MTC) problem. Conventional methods aim to learn a matching model between text and labels, using a graph encoder to incorporate label hierarchies to obtain effective label representations cite{rios2018few}. More recently, pretrained models like BERT cite{devlin2018bert} have been used to convert classification tasks into a textual entailment task cite{yin-etal-2019-benchmarking}. This approach is naturally suitable for the ZS-MTC task. However, pretrained models are underexplored in the existing work because they do not generate individual vector representations for text or labels, making it unintuitive to combine them with conventional graph encoding methods. In this paper, we explore to improve pretrained models with label hierarchies on the ZS-MTC task. We propose a Reinforced Label Hierarchy Reasoning (RLHR) approach to encourage interdependence among labels in the hierarchies during training. Meanwhile, to overcome the weakness of flat predictions, we design a rollback algorithm that can remove logical errors from predictions during inference. Experimental results on three real-life datasets show that our approach achieves better performance and outperforms previous non-pretrained methods on the ZS-MTC task.
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