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Register a new userClinical Text Classification with Rule-based Features and Knowledge-guided Convolutional Neural Networks
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Added by
Liang Yao Dr.
Publication date
2018
fields
Informatics Engineering
and research's language is
English
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No Arabic abstract
Clinical text classification is an important problem in medical natural language processing. Existing studies have conventionally focused on rules or knowledge sources-based feature engineering, but only a few have exploited effective feature learning capability of deep learning methods. In this study, we propose a novel approach which combines rule-based features and knowledge-guided deep learning techniques for effective disease classification. Critical Steps of our method include identifying trigger phrases, predicting classes with very few examples using trigger phrases and training a convolutional neural network with word embeddings and Unified Medical Language System (UMLS) entity embeddings. We evaluated our method on the 2008 Integrating Informatics with Biology and the Bedside (i2b2) obesity challenge. The results show that our method outperforms the state of the art methods.
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Text classification is an important and classical problem in natural language processing. There have been a number of studies that applied convolutional neural networks (convolution on regular grid, e.g., sequence) to classification. However, only a limited number of studies have explored the more flexible graph convolutional neural networks (convolution on non-grid, e.g., arbitrary graph) for the task. In this work, we propose to use graph convolutional networks for text classification. We build a single text graph for a corpus based on word co-occurrence and document word relations, then learn a Text Graph Convolutional Network (Text GCN) for the corpus. Our Text GCN is initialized with one-hot representation for word and document, it then jointly learns the embeddings for both words and documents, as supervised by the known class labels for documents. Our experimental results on multiple benchmark datasets demonstrate that a vanilla Text GCN without any external word embeddings or knowledge outperforms state-of-the-art methods for text classification. On the other hand, Text GCN also learns predictive word and document embeddings. In addition, experimental results show that the improvement of Text GCN over state-of-the-art comparison methods become more prominent as we lower the percentage of training data, suggesting the robustness of Text GCN to less training data in text classification.
The complicated syntax structure of natural language is hard to be explicitly modeled by sequence-based models. Graph is a natural structure to describe the complicated relation between tokens. The recent advance in Graph Neural Networks (GNN) provides a powerful tool to model graph structure data, but simple graph models such as Graph Convolutional Networks (GCN) suffer from over-smoothing problem, that is, when stacking multiple layers, all nodes will converge to the same value. In this paper, we propose a novel Recursive Graphical Neural Networks model (ReGNN) to represent text organized in the form of graph. In our proposed model, LSTM is used to dynamically decide which part of the aggregated neighbor information should be transmitted to upper layers thus alleviating the over-smoothing problem. Furthermore, to encourage the exchange between the local and global information, a global graph-level node is designed. We conduct experiments on both single and multiple label text classification tasks. Experiment results show that our ReGNN model surpasses the strong baselines significantly in most of the datasets and greatly alleviates the over-smoothing problem.
Multiple Sclerosis (MS) is a chronic, inflammatory and degenerative neurological disease, which is monitored by a specialist using the Expanded Disability Status Scale (EDSS) and recorded in unstructured text in the form of a neurology consult note. An EDSS measurement contains an overall EDSS score and several functional subscores. Typically, expert knowledge is required to interpret consult notes and generate these scores. Previous approaches used limited context length Word2Vec embeddings and keyword searches to predict scores given a consult note, but often failed when scores were not explicitly stated. In this work, we present MS-BERT, the first publicly available transformer model trained on real clinical data other than MIMIC. Next, we present MSBC, a classifier that applies MS-BERT to generate embeddings and predict EDSS and functional subscores. Lastly, we explore combining MSBC with other models through the use of Snorkel to generate scores for unlabelled consult notes. MSBC achieves state-of-the-art performance on all metrics and prediction tasks and outperforms the models generated from the Snorkel ensemble. We improve Macro-F1 by 0.12 (to 0.88) for predicting EDSS and on average by 0.29 (to 0.63) for predicting functional subscores over previous Word2Vec CNN and rule-based approaches.
Sequence-to-Sequence (S2S) neural text generation models, especially the pre-trained ones (e.g., BART and T5), have exhibited compelling performance on various natural language generation tasks. However, the black-box nature of these models limits their application in tasks where specific rules (e.g., controllable constraints, prior knowledge) need to be executed. Previous works either design specific model structure (e.g., Copy Mechanism corresponding to the rule the generated output should include certain words in the source input) or implement specialized inference algorithm (e.g., Constrained Beam Search) to execute particular rules through the text generation. These methods require careful design case-by-case and are difficult to support multiple rules concurrently. In this paper, we propose a novel module named Neural Rule-Execution Tracking Machine that can be equipped into various transformer-based generators to leverage multiple rules simultaneously to guide the neural generation model for superior generation performance in a unified and scalable way. Extensive experimental results on several benchmarks verify the effectiveness of our proposed model in both controllable and general text generation.
There is a warning light for the loss of plant habitats worldwide that entails concerted efforts to conserve plant biodiversity. Thus, plant species classification is of crucial importance to address this environmental challenge. In recent years, there is a considerable increase in the number of studies related to plant taxonomy. While some researchers try to improve their recognition performance using novel approaches, others concentrate on computational optimization for their framework. In addition, a few studies are diving into feature extraction to gain significantly in terms of accuracy. In this paper, we propose an effective method for the leaf recognition problem. In our proposed approach, a leaf goes through some pre-processing to extract its refined color image, vein image, xy-projection histogram, handcrafted shape, texture features, and Fourier descriptors. These attributes are then transformed into a better representation by neural network-based encoders before a support vector machine (SVM) model is utilized to classify different leaves. Overall, our approach performs a state-of-the-art result on the Flavia leaf dataset, achieving the accuracy of 99.58% on test sets under random 10-fold cross-validation and bypassing the previous methods. We also release our codes (Scripts are available at https://github.com/dinhvietcuong1996/LeafRecognition) for contributing to the research community in the leaf classification problem.
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