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1. Accounting for sentence position and legal domain sentence embedding in learning to classify case sentences

   Xu, Huihui (December 2021, Legal knowledge and information systems)

   In this paper, we treat sentence annotation as a classification task. We employ sequence-to-sequence models to take sentence position information into account in identifying case law sentences as issues, conclusions, or reasons. We also compare the legal domain specific sentence embedding with other general purpose sentence embeddings to gauge the effect of legal domain knowledge, captured during pre-training, on text classification. We deployed the models on both summaries and full-text decisions. We found that the sentence position information is especially useful for full-text sentence classification. We also verified that legal domain specific sentence embeddings perform better, and that meta-sentence embedding can further enhance performance when sentence position information is included. 

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2. Identify diabetic retinopathy-related clinical concepts and their attributes using transformer-based natural language processing methods

   https://doi.org/10.1186/s12911-022-01996-2  

   Yu, Zehao; Yang, Xi; Sweeting, Gianna L.; Ma, Yinghan; Stolte, Skylar E.; Fang, Ruogu; Wu, Yonghui (September 2022, BMC Medical Informatics and Decision Making)

   Abstract Background Diabetic retinopathy (DR) is a leading cause of blindness in American adults. If detected, DR can be treated to prevent further damage causing blindness. There is an increasing interest in developing artificial intelligence (AI) technologies to help detect DR using electronic health records. The lesion-related information documented in fundus image reports is a valuable resource that could help diagnoses of DR in clinical decision support systems. However, most studies for AI-based DR diagnoses are mainly based on medical images; there is limited studies to explore the lesion-related information captured in the free text image reports. Methods In this study, we examined two state-of-the-art transformer-based natural language processing (NLP) models, including BERT and RoBERTa, compared them with a recurrent neural network implemented using Long short-term memory (LSTM) to extract DR-related concepts from clinical narratives. We identified four different categories of DR-related clinical concepts including lesions, eye parts, laterality, and severity, developed annotation guidelines, annotated a DR-corpus of 536 image reports, and developed transformer-based NLP models for clinical concept extraction and relation extraction. We also examined the relation extraction under two settings including ‘gold-standard’ setting—where gold-standard concepts were used–and end-to-end setting. Results For concept extraction, the BERT model pretrained with the MIMIC III dataset achieve the best performance (0.9503 and 0.9645 for strict/lenient evaluation). For relation extraction, BERT model pretrained using general English text achieved the best strict/lenient F1-score of 0.9316. The end-to-end system, BERT_general_e2e, achieved the best strict/lenient F1-score of 0.8578 and 0.8881, respectively. Another end-to-end system based on the RoBERTa architecture, RoBERTa_general_e2e, also achieved the same performance as BERT_general_e2e in strict scores. Conclusions This study demonstrated the efficiency of transformer-based NLP models for clinical concept extraction and relation extraction. Our results show that it’s necessary to pretrain transformer models using clinical text to optimize the performance for clinical concept extraction. Whereas, for relation extraction, transformers pretrained using general English text perform better. 

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3. Concept Detection and Caption Prediction in ImageCLEFmedical Caption 2023 with Convolutional Neural Networks; Vision and Text-to-Text Transfer Transformers

   Hasan M; Layode O; Rahman M. (October 2023, Working Notes of the Conference and Labs of the Evaluation Forum (CLEF 2023))

   Aliannejadi, M; Faggioli, G; Ferro, N; Vlachos, M. (Ed.)

   This work discusses the participation of CS_Morgan in the Concept Detection and Caption Prediction tasks of the ImageCLEFmedical 2023 Caption benchmark evaluation campaign. The goal of this task is to automatically identify relevant concepts and their locations in images, as well as generate coherent captions for the images. The dataset used for this task is a subset of the extended Radiology Objects in Context (ROCO) dataset. The implementation approach employed by us involved the use of pre-trained Convolutional Neural Networks (CNNs), Vision Transformer (ViT), and Text-to-Text Transfer Transformer (T5) architectures. These models were leveraged to handle the different aspects of the tasks, such as concept detection and caption generation. In the Concept Detection task, the objective was to classify multiple concepts associated with each image. We utilized several deep learning architectures with ‘sigmoid’ activation to enable multilabel classification using the Keras framework. We submitted a total of five (5) runs for this task, and the best run achieved an F1 score of 0.4834, indicating its effectiveness in detecting relevant concepts in the images. For the Caption Prediction task, we successfully submitted eight (8) runs. Our approach involved combining the ViT and T5 models to generate captions for the images. For the caption prediction task, the ranking is based on the BERTScore, and our best run achieved a score of 0.5819 based on generating captions using the fine-tuned T5 model from keywords generated using the pretrained ViT as the encoder. 

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4. AutoName: A Corpus-Based Set Naming Framework

   https://doi.org/10.1145/3404835.3463100  

   Huang, Zhiqi; Rahimi, Razieh; Yu, Puxuan; Shang, Jingbo; Allan, James (July 2021, Proceedings of The 44th International ACM SIGIR Conference on Research and Development in Information Retrieval (SIGIR 21))

   null (Ed.)

   Inferring the set name of semantically grouped entities is useful in many tasks related to natural language processing and information retrieval. Previous studies mainly draw names from knowledge bases to ensure high quality, but that limits the candidate scope. We propose an unsupervised framework, AutoName, that exploits large-scale text corpora to name a set of query entities. Specifically, it first extracts hypernym phrases as candidate names from query-related documents via probing a pre-trained language model. A hierarchical density-based clustering is then applied to form potential concepts for these candidate names. Finally, AutoName ranks candidates and picks the top one as the set name based on constituents of the phrase and the semantic similarity of their concepts. We also contribute a new benchmark dataset for this task, consisting of 130 entity sets with name labels. Experimental results show that AutoName generates coherent and meaningful set names and significantly outperforms all compared methods. Further analyses show that AutoName is able to offer explanations for extracted names using the sentences most relevant to the corresponding concept. 

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5. Language in a Bottle: Language Model Guided Concept Bottlenecks for Interpretable Image Classification

   Yang, Yue and (June 2023, Proceedings of the IEEE/CVF Conference on Computer Vision and Pattern Recognition (CVPR))

   Concept Bottleneck Models (CBM) are inherently interpretable models that factor model decisions into human-readable concepts. They allow people to easily understand why a model is failing, a critical feature for high-stakes applications. CBMs require manually specified concepts and often under-perform their black box counterparts, preventing their broad adoption. We address these shortcomings and are first to show how to construct high-performance CBMs without manual specification of similar accuracy to black box models. Our approach, Language Guided Bottlenecks (LaBo), leverages a language model, GPT-3, to define a large space of possible bottlenecks. Given a problem domain, LaBo uses GPT-3 to produce factual sentences about categories to form candidate concepts. LaBo efficiently searches possible bottlenecks through a novel submodular utility that promotes the selection of discriminative and diverse information. Ultimately, GPT-3's sentential concepts can be aligned to images using CLIP, to form a bottleneck layer. Experiments demonstrate that LaBo is a highly effective prior for concepts important to visual recognition. In the evaluation with 11 diverse datasets, LaBo bottlenecks excel at few-shot classification: they are 11.7% more accurate than black box linear probes at 1 shot and comparable with more data. Overall, LaBo demonstrates that inherently interpretable models can be widely applied at similar, or better, performance than black box approaches. 

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