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Medical information extraction consists of a group of natural language processing (NLP) tasks, which collaboratively convert clinical text to pre-defined structured formats. Current state-of-the-art (SOTA) NLP models are highly integrated…

Computation and Language · Computer Science 2022-03-09 Enwei Zhu , Qilin Sheng , Huanwan Yang , Jinpeng Li

$\textbf{Objective}$ Develop an automatic diagnostic system which only uses textual admission information from Electronic Health Records (EHRs) and assist clinicians with a timely and statistically proved decision tool. The hope is that the…

Computation and Language · Computer Science 2017-12-08 Christy Li , Dimitris Konomis , Graham Neubig , Pengtao Xie , Carol Cheng , Eric Xing

We introduce SWE-PRBench, a benchmark of 350 pull requests with human-annotated ground truth for evaluating AI code review quality. Evaluated against an LLM-as-judge framework validated at kappa=0.75, 8 frontier models detect only 15-31% of…

Software Engineering · Computer Science 2026-03-30 Deepak Kumar

Recognizing biomedical concepts in the text is vital for ontology refinement, knowledge graph construction, and concept relationship discovery. However, traditional concept recognition methods, relying on explicit mention identification,…

Computation and Language · Computer Science 2025-11-26 Shanshan Liu , Noriki Nishida , Rumana Ferdous Munne , Narumi Tokunaga , Yuki Yamagata , Kouji Kozaki , Yuji Matsumoto

Typically, information extraction (IE) requires a pipeline approach: first, a sequence labeling model is trained on manually annotated documents to extract relevant spans; then, when a new document arrives, a model predicts spans which are…

Computation and Language · Computer Science 2021-10-12 Benjamin Townsend , Eamon Ito-Fisher , Lily Zhang , Madison May

A meaningful understanding of clinical protocols and patient pathways helps improve healthcare outcomes. Electronic health records (EHR) reflect real-world treatment behaviours that are used to enhance healthcare management but present…

Machine Learning · Computer Science 2021-10-05 Adrian Caruana , Madhushi Bandara , Daniel Catchpoole , Paul J Kennedy

Drug development and pharmacovigilance are frequently bottlenecked by legacy clinical reporting pipelines. These monolithic systems encode regulatory-grade logic but resist AI integration by producing opaque output with no machine-readable…

Software Engineering · Computer Science 2026-05-15 Jaime Yan

Composed Image Retrieval (CIR) is a multimodal retrieval task where a query consists of a reference image and a textual modification, and the goal is to retrieve a target image satisfying both. In principle, strong performance on CIR…

The extraction of relevant data from Electronic Health Records (EHRs) is crucial to identifying symptoms and automating epidemiological surveillance processes. By harnessing the vast amount of unstructured text in EHRs, we can detect…

Computation and Language · Computer Science 2025-02-10 Juliano Genari , Guilherme Tegoni Goedert

Evaluating large language models (LLMs) for medical applications remains challenging due to benchmark saturation, limited data accessibility, and insufficient coverage of relevant tasks. Existing suites have either saturated, heavily depend…

Doctors and patients alike increasingly use Large Language Models (LLMs) to diagnose clinical cases. However, unlike domains such as math or coding, where correctness can be objectively defined by the final answer, medical diagnosis…

Computation and Language · Computer Science 2025-05-21 Kevin Wu , Eric Wu , Rahul Thapa , Kevin Wei , Angela Zhang , Arvind Suresh , Jacqueline J. Tao , Min Woo Sun , Alejandro Lozano , James Zou

Supervised and semi-supervised semantic segmentation algorithms require significant amount of annotated data to achieve a good performance. In many situations, the data is either not available or the annotation is expensive. The objective…

Computer Vision and Pattern Recognition · Computer Science 2023-05-31 Ram Krishna Pandey , Akshit Achara

In this paper, we describe novel components for extracting clinically relevant information from medical conversations which will be available as Google APIs. We describe a transformer-based Recurrent Neural Network Transducer (RNN-T) model…

Machine Learning · Computer Science 2021-04-07 Hagen Soltau , Mingqiu Wang , Izhak Shafran , Laurent El Shafey

Optical Character Recognition (OCR) plays a crucial role in digitizing historical and multilingual documents, yet OCR errors - imperfect extraction of text, including character insertion, deletion, and substitution can significantly impact…

Computation and Language · Computer Science 2025-09-22 Bhawna Piryani , Jamshid Mozafari , Abdelrahman Abdallah , Antoine Doucet , Adam Jatowt

Clinical EEG interpretation requires reasoning over full EEG sessions and integrating signal patterns with clinical context. Existing EEG foundation models are largely designed for short-window decoding and do not incorporate clinical…

Artificial Intelligence · Computer Science 2026-05-12 Peng Cao , Ali Mirzazadeh , Jong Woo Lee , Aleksandar Videnovic , Dina Katabi

Medical concept extraction from electronic health records underpins many downstream applications, yet remains challenging because medically meaningful concepts are frequently implied rather than explicitly stated in medical narratives.…

Computation and Language · Computer Science 2026-05-21 Zhichao Yang , Gregory D. Lyng , Sanjit Singh Batra , Robert E. Tillman

To safely deploy deep learning models in the clinic, a quality assurance framework is needed for routine or continuous monitoring of input-domain shift and the models' performance without ground truth contours. In this work, cardiac…

Image and Video Processing · Electrical Eng. & Systems 2023-05-22 Xiyao Jin , Yao Hao , Jessica Hilliard , Zhehao Zhang , Maria A. Thomas , Hua Li , Abhinav K. Jha , Geoffrey D. Hugo

State-of-the-art neural models typically encode document-query pairs using cross-attention for re-ranking. To this end, models generally utilize an encoder-only (like BERT) paradigm or an encoder-decoder (like T5) approach. These paradigms,…

Computation and Language · Computer Science 2022-04-26 Kai Hui , Honglei Zhuang , Tao Chen , Zhen Qin , Jing Lu , Dara Bahri , Ji Ma , Jai Prakash Gupta , Cicero Nogueira dos Santos , Yi Tay , Don Metzler

Recently introduced transformer-based article encoders (TAEs) designed to produce similar vector representations for mutually related scientific articles have demonstrated strong performance on benchmark datasets for scientific article…

Information Retrieval · Computer Science 2022-09-13 Zoran Medić , Jan Šnajder

Laboratory workflows in pharmaceutical and biomedical research encode substantial tacit knowledge -- expert judgment about failure conditions, decision branching logic, and contextual dependencies -- that remains inaccessible to protocol…