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The automatic text summarization task faces great challenges. The main issue in the area is to identify the most informative segments in the input text. Establishing an effective evaluation mechanism has also been identified as a major challenge in the area. Currently, the mainstream solution is to use deep learning for training. However, a serious exposure bias in training prevents them from achieving better results. Therefore, this paper introduces an extractive text summarization model based on a graph matrix and advantage actor-critic (GA2C) method. The articles were pre-processed to generate a graph matrix. Based on the states provided by the graph matrix, the decision-making network made decisions and sent the results to the evaluation network for scoring. The evaluation network got the decision results of the decision-making network and then scored them. The decision-making network modified the probability of the action based on the scores of the evaluation network. Specifically, compared with the baseline reinforcement learning-based extractive summarization (Refresh) model, experimental results on the CNN/Daily Mail dataset showed that the GA2C model led on Rouge-1, Rouge-2 and Rouge-A by 0.70, 9.01 and 2.73, respectively. Moreover, we conducted multiple ablation experiments to verify the GA2C model from different perspectives. Different activation functions and evaluation networks were used in the GA2C model to obtain the best activation function and evaluation network. Two different reward functions (Set fixed reward value for accumulation (ADD), Rouge) and two different similarity matrices (cosine, Jaccard) were combined for the experiments.

Background: Automated summarization of scientific literature and patient records is essential for enhancing clinical decision-making and facilitating precision medicine. Most existing summarization methods are based on single indicators of relevance, offer limited capabilities for information visualization, and do not account for user specific interests. In this work, we develop an interactive content extraction, recognition, and construction system (CERC) that combines machine learning and visualization techniques with domain knowledge for highlighting and extracting salient information from clinical and biomedical text., Methods: A novel sentence-ranking framework multi indicator text summarization, MINTS, is developed for extractive summarization. MINTS uses random forests and multiple indicators of importance for relevance evaluation and ranking of sentences. Indicative summarization is performed using weighted term frequency-inverse document frequency scores of over-represented domain-specific terms. A controlled vocabulary dictionary generated using MeSH, SNOMED-CT, and PubTator is used for determining relevant terms. 35 full-text CRAFT articles were used as the training set. The performance of the MINTS algorithm is evaluated on a test set consisting of the remaining 32 full-text CRAFT articles and 30 clinical case reports using the ROUGE toolkit., Results: The random forests model classified sentences as "good" or "bad" with 87.5% accuracy on the test set. Summarization results from the MINTS algorithm achieved higher ROUGE-1, ROUGE-2, and ROUGE-SU4 scores when compared to methods based on single indicators such as term frequency distribution, position, eigenvector centrality (LexRank), and random selection, p < 0.01. The automatic language translator and the customizable information extraction and pre-processing pipeline for EHR demonstrate that CERC can readily be incorporated within clinical decision support systems to improve quality of care and assist in data-driven and evidence-based informed decision making for direct patient care., Conclusions: We have developed a web-based summarization and visualization tool, CERC ( https://newton.isye.gatech.edu/CERC1/ ), for extracting salient information from clinical and biomedical text. The system ranks sentences by relevance and includes features that can facilitate early detection of medical risks in a clinical setting. The interactive interface allows users to filter content and edit/save summaries. The evaluation results on two test corpuses show that the newly developed MINTS algorithm outperforms methods based on single characteristics of importance.

To inform the development of automated summarization of clinical conversations, this study sought to estimate the proportion of doctor-patient communication in general practice (GP) consultations used for generating a consultation summary. Two researchers with a medical degree read the transcripts of 44 GP consultations and highlighted the phrases to be used for generating a summary of the consultation. For all consultations, less than 20% of all words in the transcripts were needed for inclusion in the summary. On average, 9.1% of all words in the transcripts, 26.6% of all medical terms, and 27.3% of all speaker turns were highlighted. The results indicate that communication content used for generating a consultation summary makes up a small portion of GP consultations, and automated summarization solutions-such as digital scribes-must focus on identifying the 20% relevant information for automatically generating consultation summaries.

Most current automatic summarization methods are for English texts. The distinction between words in Chinese text is large, the types of parts of speech are many and complex, and polysemy or ambiguous words appear frequently. Therefore, compared with English text, Chinese text is more difficult to extract useful feature words. Due to the complex syntax of Chinese, there are currently relatively few automatic summarization methods for Chinese text. In the past, only the important sentences in the original text can be selected and simply arranged to obtain a summary with chaotic sentences and insufficient coherence. Meanwhile, because Chinese short text usually contains more redundant information and the sentence structure is not neat, we propose a topic-based automatic summary method for Chinese short text. Firstly, a key sentence selection method is proposed combining topic words and TF-IDF to obtain the score of each text corresponding to the topic in the original text data. Then the sentence with the highest score as the topic sentence of the topic is selected. Considering that the short text of Weibo may contain a lot of irrelevant information and sometimes even lack some important components of topic, three retouching mechanisms are proposed to improve the conciseness, richness and readability of topic sentence extraction results. We validate our approach on natural disaster and social hot event datasets from Sina Weibo. The experimental results show that the polished topic summary not only reflects the exact relationship between topic sentences and natural disasters or social hot events, but also has rich semantic information. More importantly, we can almost grasp the basic elements of natural disaster or social hot event from the topic sentence, so as to help the government guide disaster relief or meet the needs of users for quickly obtaining information of social hot events.

Background: Doctors must care for many patients simultaneously, and it is time-consuming to find and examine all patients' medical histories. Discharge diagnoses provide hospital staff with sufficient information to enable handling multiple patients; however, the excessive amount of words in the diagnostic sentences poses problems. Deep learning may be an effective solution to overcome this problem, but the use of such a heavy model may also add another obstacle to systems with limited computing resources., Objective: We aimed to build a diagnoses-extractive summarization model for hospital information systems and provide a service that can be operated even with limited computing resources., Methods: We used a Bidirectional Encoder Representations from Transformers (BERT)-based structure with a two-stage training method based on 258,050 discharge diagnoses obtained from the National Taiwan University Hospital Integrated Medical Database, and the highlighted extractive summaries written by experienced doctors were labeled. The model size was reduced using a character-level token, the number of parameters was decreased from 108,523,714 to 963,496, and the model was pretrained using random mask characters in the discharge diagnoses and International Statistical Classification of Diseases and Related Health Problems sets. We then fine-tuned the model using summary labels and cleaned up the prediction results by averaging all probabilities for entire words to prevent character level-induced fragment words. Model performance was evaluated against existing models BERT, BioBERT, and Long Short-Term Memory (LSTM) using the Recall-Oriented Understudy for Gisting Evaluation (ROUGE) L score, and a questionnaire website was built to collect feedback from more doctors for each summary proposal., Results: The area under the receiver operating characteristic curve values of the summary proposals were 0.928, 0.941, 0.899, and 0.947 for BERT, BioBERT, LSTM, and the proposed model (AlphaBERT), respectively. The ROUGE-L scores were 0.697, 0.711, 0.648, and 0.693 for BERT, BioBERT, LSTM, and AlphaBERT, respectively. The mean (SD) critique scores from doctors were 2.232 (0.832), 2.134 (0.877), 2.207 (0.844), 1.927 (0.910), and 2.126 (0.874) for reference-by-doctor labels, BERT, BioBERT, LSTM, and AlphaBERT, respectively. Based on the paired t test, there was a statistically significant difference in LSTM compared to the reference (P<.001), BERT (P=.001), BioBERT (P<.001), and AlphaBERT (P=.002), but not in the other models., Conclusions: Use of character-level tokens in a BERT model can greatly decrease the model size without significantly reducing performance for diagnoses summarization. A well-developed deep-learning model will enhance doctors' abilities to manage patients and promote medical studies by providing the capability to use extensive unstructured free-text notes., (©Yen-Pin Chen, Yi-Ying Chen, Jr-Jiun Lin, Chien-Hua Huang, Feipei Lai. Originally published in JMIR Medical Informatics (http://medinform.jmir.org), 29.04.2020.)

In order to tackle the problem of abstractive summarization of long multi-sentence texts, it is critical to construct an efficient model, which can learn and represent multiple compositionalities better. In this paper, we introduce a temporal hierarchical pointer generator network that can represent multiple compositionalities in order to handle longer sequences of texts with a deep structure. We demonstrate how a multilayer gated recurrent neural network organizes itself with the help of an adaptive timescale in order to represent the compositions. The temporal hierarchical network is implemented with a multiple timescale architecture where the timescale of each layer is also learned during the training process through error backpropagation through time. We evaluate our proposed model using an Introduction-Abstract summarization dataset from scientific articles and the CNN/Daily Mail summarization benchmark dataset. The results illustrate that, we successfully implement a summary generation system for long texts by using the multiple timescale with adaptation concept. We also show that we have improved the summary generation system with our proposed model on the benchmark dataset., (Copyright © 2019 Elsevier Ltd. All rights reserved.)

Objective: It is crucial for clinicians to stay up to date on current literature in order to apply recent evidence to clinical decision making. Automatic summarization systems can help clinicians quickly view an aggregated summary of literature on a topic. Casama, a representation and summarization system based on "contextualized semantic maps," captures the findings of biomedical studies as well as the contexts associated with patient population and study design. This paper presents a user-oriented evaluation of Casama in comparison to a context-free representation, SemRep., Materials and Methods: The effectiveness of the representation was evaluated by presenting users with manually annotated Casama and SemRep summaries of ten articles on driver mutations in cancer. Automatic annotations were evaluated on a collection of articles on EGFR mutation in lung cancer. Seven users completed a questionnaire rating the summarization quality for various topics and applications., Results: Casama had higher median scores than SemRep for the majority of the topics (p≤ 0.00032), all of the applications (p≤ 0.00089), and in overall summarization quality (p≤ 1.5e-05). Casama's manual annotations outperformed Casama's automatic annotations (p = 0.00061)., Discussion: Casama performed particularly well in the representation of strength of evidence, which was highly rated both quantitatively and qualitatively. Users noted that Casama's less granular, more targeted representation improved usability compared to SemRep., Conclusion: This evaluation demonstrated the benefits of a contextualized representation for summarizing biomedical literature on cancer. Iteration on specific areas of Casama's representation, further development of its algorithms, and a clinically-oriented evaluation are warranted., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

This paper describes the information retrieval step in Casama (Contextualized Semantic Maps), a project that summarizes and contextualizes current research papers on driver mutations in non-small cell lung cancer. Casama׳s representation of lung cancer studies aims to capture elements that will assist an end-user in retrieving studies and, importantly, judging their strength. This paper focuses on two types of study metadata: study objective and study design. 430 abstracts on EGFR and ALK mutations in lung cancer were annotated manually. Casama׳s support vector machine (SVM) automatically classified the abstracts by study objective with as much as 129% higher F-scores compared to PubMed׳s built-in filters. A second SVM classified the abstracts by epidemiological study design, suggesting strength of evidence at a more granular level than in previous work. The classification results and the top features determined by the classifiers suggest that this scheme would be generalizable to other mutations in lung cancer, as well as studies on driver mutations in other cancer domains., (Copyright © 2015 Elsevier Ltd. All rights reserved.)

Objective: Automatic summarization of biomedical literature usually relies on domain knowledge from external sources to build rich semantic representations of the documents to be summarized. In this paper, we investigate the impact of the knowledge source used on the quality of the summaries that are generated., Materials and Methods: We present a method for representing a set of documents relevant to a given biological entity or topic as a semantic graph of domain concepts and relations. Different graphs are created by using different combinations of ontologies and vocabularies within the UMLS (including GO, SNOMED-CT, HUGO and all available vocabularies in the UMLS) to retrieve domain concepts, and different types of relationships (co-occurrence and semantic relations from the UMLS Metathesaurus and Semantic Network) are used to link the concepts in the graph. The different graphs are next used as input to a summarization system that produces summaries composed of the most relevant sentences from the original documents., Results and Conclusions: Our experiments demonstrate that the choice of the knowledge source used to model the text has a significant impact on the quality of the automatic summaries. In particular, we find that, when summarizing gene-related literature, using GO, SNOMED-CT and HUGO to extract domain concepts results in significantly better summaries than using all available vocabularies in the UMLS. This finding suggests that successful biomedical summarization requires the selection of the appropriate knowledge source, whose coverage, specificity and relations must be in accordance to the type of the documents to summarize., (Copyright © 2014 Elsevier Inc. All rights reserved.)

Systematic reviews are a widely accepted research method. However, it is increasingly difficult to conduct them to fit with policy and practice timescales, particularly in areas which do not have well indexed, comprehensive bibliographic databases. Text mining technologies offer one possible way forward in reducing the amount of time systematic reviews take to conduct. They can facilitate the identification of relevant literature, its rapid description or categorization, and its summarization. In this paper, we describe the application of four text mining technologies, namely, automatic term recognition, document clustering, classification and summarization, which support the identification of relevant studies in systematic reviews. The contributions of text mining technologies to improve reviewing efficiency are considered and their strengths and weaknesses explored. We conclude that these technologies do have the potential to assist at various stages of the review process. However, they are relatively unknown in the systematic reviewing community, and substantial evaluation and methods development are required before their possible impact can be fully assessed. Copyright © 2011 John Wiley & Sons, Ltd., (Copyright © 2011 John Wiley & Sons, Ltd.)