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Register a new userSciFive: a text-to-text transformer model for biomedical literature
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Long Phan
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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In this report, we introduce SciFive, a domain-specific T5 model that has been pre-trained on large biomedical corpora. Our model outperforms the current SOTA methods (i.e. BERT, BioBERT, Base T5) on tasks in named entity relation, relation extraction, natural language inference, and question-answering. We show that text-generation methods have significant potential in a broad array of biomedical NLP tasks, particularly those requiring longer, more complex outputs. Our results support the exploration of more difficult text generation tasks and the development of new methods in this area
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Biomedical text mining is becoming increasingly important as the number of biomedical documents rapidly grows. With the progress in natural language processing (NLP), extracting valuable information from biomedical literature has gained popularity among researchers, and deep learning has boosted the development of effective biomedical text mining models. However, directly applying the advancements in NLP to biomedical text mining often yields unsatisfactory results due to a word distribution shift from general domain corpora to biomedical corpora. In this article, we investigate how the recently introduced pre-trained language model BERT can be adapted for biomedical corpora. We introduce BioBERT (Bidirectional Encoder Representations from Transformers for Biomedical Text Mining), which is a domain-specific language representation model pre-trained on large-scale biomedical corpora. With almost the same architecture across tasks, BioBERT largely outperforms BERT and previous state-of-the-art models in a variety of biomedical text mining tasks when pre-trained on biomedical corpora. While BERT obtains performance comparable to that of previous state-of-the-art models, BioBERT significantly outperforms them on the following three representative biomedical text mining tasks: biomedical named entity recognition (0.62% F1 score improvement), biomedical relation extraction (2.80% F1 score improvement) and biomedical question answering (12.24% MRR improvement). Our analysis results show that pre-training BERT on biomedical corpora helps it to understand complex biomedical texts. We make the pre-trained weights of BioBERT freely available at https://github.com/naver/biobert-pretrained, and the source code for fine-tuning BioBERT available at https://github.com/dmis-lab/biobert.
The recent Text-to-Text Transfer Transformer (T5) leveraged a unified text-to-text format and scale to attain state-of-the-art results on a wide variety of English-language NLP tasks. In this paper, we introduce mT5, a multilingual variant of T5 that was pre-trained on a new Common Crawl-based dataset covering 101 languages. We detail the design and modified training of mT5 and demonstrate its state-of-the-art performance on many multilingual benchmarks. We also describe a simple technique to prevent accidental translation in the zero-shot setting, where a generative model chooses to (partially) translate its prediction into the wrong language. All of the code and model checkpoints used in this work are publicly available.
Two important tasks at the intersection of knowledge graphs and natural language processing are graph-to-text (G2T) and text-to-graph (T2G) conversion. Due to the difficulty and high cost of data collection, the supervised data available in the two fields are usually on the magnitude of tens of thousands, for example, 18K in the WebNLG~2017 dataset after preprocessing, which is far fewer than the millions of data for other tasks such as machine translation. Consequently, deep learning models for G2T and T2G suffer largely from scarce training data. We present CycleGT, an unsupervised training method that can bootstrap from fully non-parallel graph and text data, and iteratively back translate between the two forms. Experiments on WebNLG datasets show that our unsupervised model trained on the same number of data achieves performance on par with several fully supervised models. Further experiments on the non-parallel GenWiki dataset verify that our method performs the best among unsupervised baselines. This validates our framework as an effective approach to overcome the data scarcity problem in the fields of G2T and T2G. Our code is available at https://github.com/QipengGuo/CycleGT.
We motivate and propose a suite of simple but effective improvements for concept-to-text generation called SAPPHIRE: Set Augmentation and Post-hoc PHrase Infilling and REcombination. We demonstrate their effectiveness on generative commonsense reasoning, a.k.a. the CommonGen task, through experiments using both BART and T5 models. Through extensive automatic and human evaluation, we show that SAPPHIRE noticeably improves model performance. An in-depth qualitative analysis illustrates that SAPPHIRE effectively addresses many issues of the baseline model generations, including lack of commonsense, insufficient specificity, and poor fluency.
We study the pre-train + fine-tune strategy for data-to-text tasks. Our experiments indicate that text-to-text pre-training in the form of T5, enables simple, end-to-end transformer based models to outperform pipelined neural architectures tailored for data-to-text generation, as well as alternative language model based pre-training techniques such as BERT and GPT-2. Importantly, T5 pre-training leads to better generalization, as evidenced by large improvements on out-of-domain test sets. We hope our work serves as a useful baseline for future research, as transfer learning becomes ever more prevalent for data-to-text tasks.
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