Computational and Mathematical Methods in Medicine

Recently, the character-word lattice structure has been proved to be effective for Chinese named entity recognition (NER) by incorporating the word information. However, since the lattice structure is complex and dynamic, the lattice-based models are hard to fully utilize the parallel computation of GPUs and usually have a low inference speed. In this paper, we propose FLAT: Flat-LAttice Transformer for Chinese NER, which converts the lattice structure into a flat structure consisting of spans. Each span corresponds to a character or latent word and its position in the original lattice. With the power of Transformer and well-designed position encoding, FLAT can fully leverage the lattice information and has an excellent parallel ability. Experiments on four datasets show FLAT outperforms other lexicon-based models in performance and efficiency.

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FLAT: Chinese NER Using Flat-Lattice Transformer

Pre-trained language models have attracted increasing attention in the biomedical domain, inspired by their great success in the general natural language domain. Among the two main branches of pre-trained language models in the general language domain, i.e. BERT (and its variants) and GPT (and its variants), the first one has been extensively studied in the biomedical domain, such as BioBERT and PubMedBERT. While they have achieved great success on a variety of discriminative downstream biomedical tasks, the lack of generation ability constrains their application scope. In this paper, we propose BioGPT, a domain-specific generative Transformer language model pre-trained on large-scale biomedical literature. We evaluate BioGPT on six biomedical natural language processing tasks and demonstrate that our model outperforms previous models on most tasks. Especially, we get 44.98%, 38.42% and 40.76% F1 score on BC5CDR, KD-DTI and DDI end-to-end relation extraction tasks, respectively, and 78.2% accuracy on PubMedQA, creating a new record. Our case study on text generation further demonstrates the advantage of BioGPT on biomedical literature to generate fluent descriptions for biomedical terms.

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BioGPT: Generative Pre-trained Transformer for Biomedical Text Generation and Mining

Recently, many works have tried to augment the performance of Chinese named entity recognition (NER) using word lexicons. As a representative, Lattice-LSTM (Zhang and Yang, 2018) has achieved new benchmark results on several public Chinese NER datasets. However, Lattice-LSTM has a complex model architecture. This limits its application in many industrial areas where real-time NER responses are needed. 
In this work, we propose a simple but effective method for incorporating the word lexicon into the character representations. This method avoids designing a complicated sequence modeling architecture, and for any neural NER model, it requires only subtle adjustment of the character representation layer to introduce the lexicon information. Experimental studies on four benchmark Chinese NER datasets show that our method achieves an inference speed up to 6.15 times faster than those of state-ofthe-art methods, along with a better performance. The experimental results also show that the proposed method can be easily incorporated with pre-trained models like BERT.

Simplify the Usage of Lexicon in Chinese NER

Recently, many works have tried to augment the performance of Chinese named entity recognition (NER) using word lexicons. As a representative, Lattice-LSTM has achieved new benchmark results on several public Chinese NER datasets. However, Lattice-LSTM has a complex model architecture. This limits its application in many industrial areas where real-time NER responses are needed. In this work, we propose a simple but effective method for incorporating the word lexicon into the character representations. This method avoids designing a complicated sequence modeling architecture, and for any neural NER model, it requires only subtle adjustment of the character representation layer to introduce the lexicon information. Experimental studies on four benchmark Chinese NER datasets show that our method achieves an inference speed up to 6.15 times faster than those of state-of-the-art methods, along with a better performance. The experimental results also show that the proposed method can be easily incorporated with pre-trained models like BERT.

The lack of word boundaries information has been seen as one of the main obstacles to develop a high performance Chinese named entity recognition (NER) system. Fortunately, the automatically constructed lexicon contains rich word boundaries information and word semantic information. However, integrating lexical knowledge in Chinese NER tasks still faces challenges when it comes to self-matched lexical words as well as the nearest contextual lexical words. We present a Collaborative Graph Network to solve these challenges. Experiments on various datasets show that our model not only outperforms the state-of-the-art (SOTA) results, but also achieves a speed that is six to fifteen times faster than that of the SOTA model.

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Leverage Lexical Knowledge for Chinese Named Entity Recognition via Collaborative Graph Network.

Unlike other domains, medical texts are inevitably accompanied by private information, so sharing or copying these texts is strictly restricted. However, training a medical relation extraction model requires collecting these privacy-sensitive texts and storing them on one machine, which comes in conflict with privacy protection. In this paper, we propose a privacy-preserving medical relation extraction model based on federated learning, which enables training a central model with no single piece of private local data being shared or exchanged. Though federated learning has distinct advantages in privacy protection, it suffers from the communication bottleneck, which is mainly caused by the need to upload cumbersome local parameters. To overcome this bottleneck, we leverage a strategy based on knowledge distillation. Such a strategy uses the uploaded predictions of ensemble local models to train the central model without requiring uploading local parameters. Experiments on three publicly available medical relation extraction datasets demonstrate the effectiveness of our method.

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FedED: Federated Learning via Ensemble Distillation for Medical Relation Extraction

The joint entity and relation extraction task aims to extract all relational triples from a sentence. In essence, the relational triples contained in a sentence are unordered. However, previous seq2seq based models require to convert the set of triples into a sequence in the training phase. To break this bottleneck, we treat joint entity and relation extraction as a direct set prediction problem, so that the extraction model can get rid of the burden of predicting the order of multiple triples. To solve this set prediction problem, we propose networks featured by transformers with non-autoregressive parallel decoding. Unlike autoregressive approaches that generate triples one by one in a certain order, the proposed networks directly output the final set of triples in one shot. Furthermore, we also design a set-based loss that forces unique predictions via bipartite matching. Compared with cross-entropy loss that highly penalizes small shifts in triple order, the proposed bipartite matching loss is invariant to any permutation of predictions; thus, it can provide the proposed networks with a more accurate training signal by ignoring triple order and focusing on relation types and entities. Experiments on two benchmark datasets show that our proposed model significantly outperforms current state-of-the-art methods. Training code and trained models will be available at this http URL.

Joint Entity and Relation Extraction with Set Prediction Networks.

Humans can distinguish new categories very efficiently with few examples, largely due to the fact that human beings can leverage knowledge obtained from relevant tasks. However, deep learning based text classification model tends to struggle to achieve satisfactory performance when labeled data are scarce. Inspired by human intelligence, we propose to introduce external knowledge into few-shot learning to imitate human knowledge. A novel parameter generator network is investigated to this end, which is able to use the external knowledge to generate different metrics for different tasks. Armed with this network, similar tasks can use similar metrics while different tasks use different metrics. Through experiments, we demonstrate that our method outperforms the SoTA few-shot text classification models.

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Knowledge Guided Metric Learning for Few-Shot Text Classification.

Question answering over dialogue, a specialized machine reading comprehension task, aims to comprehend a dialogue and to answer specific questions. Despite many advances, existing approaches for this task did not consider dialogue structure and background knowledge (e.g., relationships between speakers). In this paper, we introduce a new approach for the task, featured by its novelty in structuring dialogue and integrating background knowledge for reasoning. Specifically, different from previous “structure-less” approaches, our method organizes a dialogue as a “relational graph”, using edges to represent relationships between entities. To encode this relational graph, we devise a relational graph convolutional network (R-GCN), which can traverse the graph’s topological structure and effectively encode multi-relational knowledge for reasoning. The extensive experiments have justified the effectiveness of our approach over competitive baselines. Moreover, a deeper analysis shows that our model is better at tackling complex questions requiring relational reasoning and defending adversarial attacks with distracting sentences.

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Dianbo Sui

Papers

Leverage Lexical Knowledge for Chinese Named Entity Recognition via Collaborative Graph Network.

FedED: Federated Learning via Ensemble Distillation for Medical Relation Extraction

Joint Entity and Relation Extraction with Set Prediction Networks.

Knowledge Guided Metric Learning for Few-Shot Text Classification.

Graph-Based Knowledge Integration for Question Answering over Dialogue