This paper presents a description of our system in SMM4H-2022, where we participated in task 1a,task 4, and task 6 to task 10. There are three main challenges in SMM4H-2022, namely the domain shift problem, the prediction bias due to category imbalance, and the noise in informal text. In this paper, we propose a unified framework for the classification and named entity recognition tasks to solve the challenges, and it can be applied to both English and Spanish scenarios. The results of our system are higher than the median F1-scores for 7 tasks and significantly exceed the F1-scores for 6 tasks. The experimental results demonstrate the effectiveness of our system.
The ICD coding task aims at assigning codes of the International Classification of Diseases in clinical notes. Since manual coding is very laborious and prone to errors, many methods have been proposed for the automatic ICD coding task. However, existing works either ignore the long-tail of code frequency or the noisy clinical notes. To address the above issues, we propose an Interactive Shared Representation Network with Self-Distillation Mechanism. Specifically, an interactive shared representation network targets building connections among codes while modeling the co-occurrence, consequently alleviating the long-tail problem. Moreover, to cope with the noisy text issue, we encourage the model to focus on the clinical note’s noteworthy part and extract valuable information through a self-distillation learning mechanism. Experimental results on two MIMIC datasets demonstrate the effectiveness of our method.
This is the system description of the CASIA_Unisound team for Task 1, Task 7b, and Task 8 of the sixth Social Media Mining for Health Applications (SMM4H) shared task in 2021. Targeting on deal with two shared challenges, the colloquial text and the imbalance annotation, among those tasks, we apply a customized pre-trained language model and propose various training strategies. Experimental results show the effectiveness of our system. Moreover, we got an F1-score of 0.87 in task 8, which is the highest among all participates.
Biomedical Concept Normalization (BCN) is widely used in biomedical text processing as a fundamental module. Owing to numerous surface variants of biomedical concepts, BCN still remains challenging and unsolved. In this paper, we exploit biomedical concept hypernyms to facilitate BCN. We propose Biomedical Concept Normalizer with Hypernyms (BCNH), a novel framework that adopts list-wise training to make use of both hypernyms and synonyms, and also employs norm constraint on the representation of hypernym-hyponym entity pairs. The experimental results show that BCNH outperforms the previous state-of-the-art model on the NCBI dataset.
In this paper, we introduce CroAno, a web-based crowd annotation platform for the Chinese named entity recognition (NER). Besides some basic features for crowd annotation like fast tagging and data management, CroAno provides a systematic solution for improving label consistency of Chinese NER dataset. 1) Disagreement Adjudicator: CroAno uses a multi-dimensional highlight mode to visualize instance-level inconsistent entities and makes the revision process user-friendly. 2) Inconsistency Detector: CroAno employs a detector to locate corpus-level label inconsistency and provides users an interface to correct inconsistent entities in batches. 3) Prediction Error Analyzer: We deconstruct the entity prediction error of the model to six fine-grained entity error types. Users can employ this error system to detect corpus-level inconsistency from a model perspective. To validate the effectiveness of our platform, we use CroAno to revise two public datasets. In the two revised datasets, we get an improvement of +1.96% and +2.57% F1 respectively in model performance.
The International Classification of Diseases (ICD) provides a standardized way for classifying diseases, which endows each disease with a unique code. ICD coding aims to assign proper ICD codes to a medical record. Since manual coding is very laborious and prone to errors, many methods have been proposed for the automatic ICD coding task. However, most of existing methods independently predict each code, ignoring two important characteristics: Code Hierarchy and Code Co-occurrence. In this paper, we propose a Hyperbolic and Co-graph Representation method (HyperCore) to address the above problem. Specifically, we propose a hyperbolic representation method to leverage the code hierarchy. Moreover, we propose a graph convolutional network to utilize the code co-occurrence. Experimental results on two widely used datasets demonstrate that our proposed model outperforms previous state-of-the-art methods.
Electronic Medical Records (EMRs) have become key components of modern medical care systems. Despite the merits of EMRs, many doctors suffer from writing them, which is time-consuming and tedious. We believe that automatically converting medical dialogues to EMRs can greatly reduce the burdens of doctors, and extracting information from medical dialogues is an essential step. To this end, we annotate online medical consultation dialogues in a window-sliding style, which is much easier than the sequential labeling annotation. We then propose a Medical Information Extractor (MIE) towards medical dialogues. MIE is able to extract mentioned symptoms, surgeries, tests, other information and their corresponding status. To tackle the particular challenges of the task, MIE uses a deep matching architecture, taking dialogue turn-interaction into account. The experimental results demonstrate MIE is a promising solution to extract medical information from doctor-patient dialogues.
In this paper, we introduce Clinical-Coder, an online system aiming to assign ICD codes to Chinese clinical notes. ICD coding has been a research hotspot of clinical medicine, but the interpretability of prediction hinders its practical application. We exploit a Dilated Convolutional Attention network with N-gram Matching mechanism (DCANM) to capture semantic features for non-continuous words and continuous n-gram words, concentrating on explaining the reason why each ICD code to be predicted. The experiments demonstrate that our approach is effective and that our system is able to provide supporting information in clinical decision making.
The multiple relation extraction task tries to extract all relational facts from a sentence. Existing works didn’t consider the extraction order of relational facts in a sentence. In this paper we argue that the extraction order is important in this task. To take the extraction order into consideration, we apply the reinforcement learning into a sequence-to-sequence model. The proposed model could generate relational facts freely. Widely conducted experiments on two public datasets demonstrate the efficacy of the proposed method.
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.
Named entity recognition (NER) is an important task in natural language processing area, which needs to determine entities boundaries and classify them into pre-defined categories. For Chinese NER task, there is only a very small amount of annotated data available. Chinese NER task and Chinese word segmentation (CWS) task have many similar word boundaries. There are also specificities in each task. However, existing methods for Chinese NER either do not exploit word boundary information from CWS or cannot filter the specific information of CWS. In this paper, we propose a novel adversarial transfer learning framework to make full use of task-shared boundaries information and prevent the task-specific features of CWS. Besides, since arbitrary character can provide important cues when predicting entity type, we exploit self-attention to explicitly capture long range dependencies between two tokens. Experimental results on two different widely used datasets show that our proposed model significantly and consistently outperforms other state-of-the-art methods.