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Over the past decade, there has been a steep rise in the data-driven analysis in major areas of medicine, such as clinical decision support system, survival analysis, patient similarity analysis, image analytics etc. Most of the data in the…

Information Retrieval · Computer Science 2020-10-06 Sheikh Shams Azam , Manoj Raju , Venkatesh Pagidimarri , Vamsi Kasivajjala

Multi-organ segmentation holds paramount significance in many clinical tasks. In practice, compared to large fully annotated datasets, multiple small datasets are often more accessible and organs are not labelled consistently. Normally, an…

Computer Vision and Pattern Recognition · Computer Science 2025-03-31 Zhendi Gong , Susan Francis , Eleanor Cox , Stamatios N. Sotiropoulos , Dorothee P. Auer , Guoping Qiu , Andrew P. French , Xin Chen

Human in-the-loop quality assurance (QA) is typically performed after medical image segmentation to ensure that the systems are performing as intended, as well as identifying and excluding outliers. By performing QA on large-scale,…

Image and Video Processing · Electrical Eng. & Systems 2019-11-14 Ho Hin Lee , Yucheng Tang , Olivia Tang , Yuchen Xu , Yunqiang Chen , Dashan Gao , Shizhong Han , Riqiang Gao , Michael R. Savona , Richard G. Abramson , Yuankai Huo , Bennett A. Landman

Optical Character Recognition (OCR) is an established task with the objective of identifying the text present in an image. While many off-the-shelf OCR models exist, they are often trained for either scientific (e.g., formulae) or generic…

Computation and Language · Computer Science 2024-03-26 Nan Zhang , Connor Heaton , Sean Timothy Okonsky , Prasenjit Mitra , Hilal Ezgi Toraman

We introduce RealKIE, a benchmark of five challenging datasets aimed at advancing key information extraction methods, with an emphasis on enterprise applications. The datasets include a diverse range of documents including SEC S1 Filings,…

Computation and Language · Computer Science 2025-10-07 Benjamin Townsend , Madison May , Katherine Mackowiak , Christopher Wells

Electronic health record (EHR) systems present clinicians with vast repositories of clinical information, creating a significant cognitive burden where critical details are easily overlooked. While Large Language Models (LLMs) offer…

Computation and Language · Computer Science 2026-03-17 Samuel Thio , Matthew Lewis , Spiros Denaxas , Richard JB Dobson

Scientific Literature charts often contain complex visual elements, including multi-plot figures, flowcharts, structural diagrams and etc. Evaluating multimodal models using these authentic and intricate charts provides a more accurate…

Computation and Language · Computer Science 2024-12-18 Lingdong Shen , Qigqi , Kun Ding , Gaofeng Meng , Shiming Xiang

Embedding models have become essential for retrieval-augmented generation (RAG) tasks, semantic clustering, and text re-ranking. But despite their growing use, many of these come with notable limitations. For example, Jina fails to capture…

Information Retrieval · Computer Science 2025-05-21 Anand Selvadurai , Jasheen Shaik , Girish Chandrasekar , ShriRadhaKrishnan Balamurugan , Eswara Reddy

Multi-modal generative document parsing systems challenge traditional evaluation: unlike deterministic OCR or layout models, they often produce semantically correct yet structurally divergent outputs. Conventional metrics-CER, WER, IoU, or…

Computation and Language · Computer Science 2025-09-25 Renyu Li , Antonio Jimeno Yepes , Yao You , Kamil Pluciński , Maximilian Operlejn , Crag Wolfe

This paper proposes a structure-aware decoding method based on large language models to address the difficulty of traditional approaches in maintaining both semantic integrity and structural consistency in nested and overlapping entity…

Computation and Language · Computer Science 2026-01-29 Zhimin Qiu , Di Wu , Feng Liu , Yuxiao Wang

Despite diverse efforts to mine various modalities of medical data, the conversations between physicians and patients at the time of care remain an untapped source of insights. In this paper, we leverage this data to extract structured…

Machine Learning · Computer Science 2020-07-15 Kundan Krishna , Amy Pavel , Benjamin Schloss , Jeffrey P. Bigham , Zachary C. Lipton

EEG foundation models achieve state-of-the-art clinical performance, yet the internal computations driving their predictions remain opaque: a barrier to clinical trust. We apply TopK Sparse Autoencoders (SAEs) across three architecturally…

Information extraction from conversational data is particularly challenging because the task-centric nature of conversation allows for effective communication of implicit information by humans, but is challenging for machines. The…

Computation and Language · Computer Science 2022-06-23 Sopan Khosla , Shikhar Vashishth , Jill Fain Lehman , Carolyn Rose

Extracting key information from scientific papers has the potential to help researchers work more efficiently and accelerate the pace of scientific progress. Over the last few years, research on Scientific Information Extraction (SciIE)…

Computation and Language · Computer Science 2023-12-19 Yuhan Li , Jian Wu , Zhiwei Yu , Börje F. Karlsson , Wei Shen , Manabu Okumura , Chin-Yew Lin

Semi-structured content in HTML tables, lists, and infoboxes accounts for a substantial share of factual data on the web, yet the formatting complicates usage, and reliably extracting structured information from them remains challenging.…

Computation and Language · Computer Science 2025-10-03 Shicheng Liu , Kai Sun , Lisheng Fu , Xilun Chen , Xinyuan Zhang , Zhaojiang Lin , Rulin Shao , Yue Liu , Anuj Kumar , Wen-tau Yih , Xin Luna Dong

Extracting structured information from scientific literature is critical for accelerating discovery, yet Large Language Models (LLMs) often struggle in specialized domains that require expert knowledge and generalize poorly across tasks. We…

Computation and Language · Computer Science 2026-05-22 Tek Raj Chhetri , Yibei Chen , Puja Trivedi , Dorota Jarecka , Saif Haobsh , Patrick Ray , Lydia Ng , Satrajit S. Ghosh

Extracting fine-grained experimental findings from literature can provide dramatic utility for scientific applications. Prior work has developed annotation schemas and datasets for limited aspects of this problem, failing to capture the…

Computation and Language · Computer Science 2024-04-26 Aakanksha Naik , Bailey Kuehl , Erin Bransom , Doug Downey , Tom Hope

Medical order extraction is essential for structuring actionable clinical information, supporting decision-making, and enabling downstream applications such as documentation and workflow automation. Orders may be embedded in diverse…

Computation and Language · Computer Science 2025-10-14 A H M Rezaul Karim , Ozlem Uzuner

Noisy labels, inevitably existing in pseudo segmentation labels generated from weak object-level annotations, severely hampers model optimization for semantic segmentation. Previous works often rely on massive hand-crafted losses and…

Computer Vision and Pattern Recognition · Computer Science 2024-01-23 Shenwang Jiang , Jianan Li , Ying Wang , Wenxuan Wu , Jizhou Zhang , Bo Huang , Tingfa Xu

Radiology report generation (RRG) for diagnostic images, such as chest X-rays, plays a pivotal role in both clinical practice and AI. Traditional free-text reports suffer from redundancy and inconsistent language, complicating the…

Computer Vision and Pattern Recognition · Computer Science 2025-08-05 Yingshu Li , Yunyi Liu , Zhanyu Wang , Xinyu Liang , Lingqiao Liu , Lei Wang , Luping Zhou