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Dec 29

Diagnosis extraction from unstructured Dutch echocardiogram reports using span- and document-level characteristic classification

Clinical machine learning research and AI driven clinical decision support models rely on clinically accurate labels. Manually extracting these labels with the help of clinical specialists is often time-consuming and expensive. This study tests the feasibility of automatic span- and document-level diagnosis extraction from unstructured Dutch echocardiogram reports. We included 115,692 unstructured echocardiogram reports from the UMCU a large university hospital in the Netherlands. A randomly selected subset was manually annotated for the occurrence and severity of eleven commonly described cardiac characteristics. We developed and tested several automatic labelling techniques at both span and document levels, using weighted and macro F1-score, precision, and recall for performance evaluation. We compared the performance of span labelling against document labelling methods, which included both direct document classifiers and indirect document classifiers that rely on span classification results. The SpanCategorizer and MedRoBERTa.nl models outperformed all other span and document classifiers, respectively. The weighted F1-score varied between characteristics, ranging from 0.60 to 0.93 in SpanCategorizer and 0.96 to 0.98 in MedRoBERTa.nl. Direct document classification was superior to indirect document classification using span classifiers. SetFit achieved competitive document classification performance using only 10\% of the training data. Utilizing a reduced label set yielded near-perfect document classification results. We recommend using our published SpanCategorizer and MedRoBERTa.nl models for span- and document-level diagnosis extraction from Dutch echocardiography reports. For settings with limited training data, SetFit may be a promising alternative for document classification.

  • 7 authors
·
Aug 13, 2024

Extending TrOCR for Text Localization-Free OCR of Full-Page Scanned Receipt Images

Digitization of scanned receipts aims to extract text from receipt images and save it into structured documents. This is usually split into two sub-tasks: text localization and optical character recognition (OCR). Most existing OCR models only focus on the cropped text instance images, which require the bounding box information provided by a text region detection model. Introducing an additional detector to identify the text instance images in advance adds complexity, however instance-level OCR models have very low accuracy when processing the whole image for the document-level OCR, such as receipt images containing multiple text lines arranged in various layouts. To this end, we propose a localization-free document-level OCR model for transcribing all the characters in a receipt image into an ordered sequence end-to-end. Specifically, we finetune the pretrained instance-level model TrOCR with randomly cropped image chunks, and gradually increase the image chunk size to generalize the recognition ability from instance images to full-page images. In our experiments on the SROIE receipt OCR dataset, the model finetuned with our strategy achieved 64.4 F1-score and a 22.8% character error rate (CER), respectively, which outperforms the baseline results with 48.5 F1-score and 50.6% CER. The best model, which splits the full image into 15 equally sized chunks, gives 87.8 F1-score and 4.98% CER with minimal additional pre or post-processing of the output. Moreover, the characters in the generated document-level sequences are arranged in the reading order, which is practical for real-world applications.

  • 3 authors
·
Dec 11, 2022

Spatially-Grounded Document Retrieval via Patch-to-Region Relevance Propagation

Late-interaction multimodal retrieval models like ColPali achieve state-of-the-art document retrieval by embedding pages as images and computing fine-grained similarity between query tokens and visual patches. However, they return entire pages rather than specific regions, limiting utility for retrieval-augmented generation (RAG) where precise context is paramount. Conversely, OCR-based systems extract structured text with bounding box coordinates but lack semantic grounding for relevance assessment. We propose a hybrid architecture that unifies these paradigms: using ColPali's patch-level similarity scores as spatial relevance filters over OCR-extracted regions. We formalize the coordinate mapping between vision transformer patch grids and OCR bounding boxes, introduce intersection metrics for relevance propagation, and establish theoretical bounds on area efficiency. We evaluate on BBox-DocVQA with ground-truth bounding boxes. For within-page localization (given correct page retrieval), ColQwen3-4B with percentile-50 thresholding achieves 59.7% hit rate at [email protected] (84.4% at [email protected], 35.8% at [email protected]), with mean IoU of 0.569, compared to ~6.7% for random region selection. Our approach reduces context tokens by 28.8% compared to returning all OCR regions and by 52.3% compared to full-page image tokens. Our approach operates at inference time without additional training. We release Snappy, an open-source implementation at https://github.com/athrael-soju/Snappy.

  • 1 authors
·
Dec 2

SCORE: A Semantic Evaluation Framework for Generative Document Parsing

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 TEDS-misclassify such diversity as error, penalizing valid interpretations and obscuring system behavior. We introduce SCORE (Structural and COntent Robust Evaluation), an interpretation-agnostic framework that integrates (i) adjusted edit distance for robust content fidelity, (ii) token-level diagnostics to distinguish hallucinations from omissions, (iii) table evaluation with spatial tolerance and semantic alignment, and (iv) hierarchy-aware consistency checks. Together, these dimensions enable evaluation that embraces representational diversity while enforcing semantic rigor. Across 1,114 pages spanning a holistic benchmark and a field dataset, SCORE consistently revealed cross-dataset performance patterns missed by standard metrics. In 2-5% of pages with ambiguous table structures, traditional metrics penalized systems by 12-25% on average, leading to distorted rankings. SCORE corrected these cases, recovering equivalence between alternative but valid interpretations. Moreover, by normalizing generative outputs into a format-agnostic representation, SCORE reproduces traditional scores (e.g., table F1 up to 0.93) without requiring object-detection pipelines, demonstrating that generative parsing alone suffices for comprehensive evaluation. By exposing how interpretive diversity impacts evaluation outcomes and providing multi-dimensional, interpretable diagnostics, SCORE establishes foundational principles for semantically grounded, fair, and practical benchmarking of modern document parsing systems.

  • 6 authors
·
Sep 16

PromptRE: Weakly-Supervised Document-Level Relation Extraction via Prompting-Based Data Programming

Relation extraction aims to classify the relationships between two entities into pre-defined categories. While previous research has mainly focused on sentence-level relation extraction, recent studies have expanded the scope to document-level relation extraction. Traditional relation extraction methods heavily rely on human-annotated training data, which is time-consuming and labor-intensive. To mitigate the need for manual annotation, recent weakly-supervised approaches have been developed for sentence-level relation extraction while limited work has been done on document-level relation extraction. Weakly-supervised document-level relation extraction faces significant challenges due to an imbalanced number "no relation" instances and the failure of directly probing pretrained large language models for document relation extraction. To address these challenges, we propose PromptRE, a novel weakly-supervised document-level relation extraction method that combines prompting-based techniques with data programming. Furthermore, PromptRE incorporates the label distribution and entity types as prior knowledge to improve the performance. By leveraging the strengths of both prompting and data programming, PromptRE achieves improved performance in relation classification and effectively handles the "no relation" problem. Experimental results on ReDocRED, a benchmark dataset for document-level relation extraction, demonstrate the superiority of PromptRE over baseline approaches.

  • 4 authors
·
Oct 13, 2023

DeAR: Dual-Stage Document Reranking with Reasoning Agents via LLM Distillation

Large Language Models (LLMs) have transformed listwise document reranking by enabling global reasoning over candidate sets, yet single models often struggle to balance fine-grained relevance scoring with holistic cross-document analysis. We propose DeepAgentRank (\DeAR), an open-source framework that decouples these tasks through a dual-stage approach, achieving superior accuracy and interpretability. In Stage 1, we distill token-level relevance signals from a frozen 13B LLaMA teacher into a compact \{3, 8\}B student model using a hybrid of cross-entropy, RankNet, and KL divergence losses, ensuring robust pointwise scoring. In Stage 2, we attach a second LoRA adapter and fine-tune on 20K GPT-4o-generated chain-of-thought permutations, enabling listwise reasoning with natural-language justifications. Evaluated on TREC-DL19/20, eight BEIR datasets, and NovelEval-2306, \DeAR surpasses open-source baselines by +5.1 nDCG@5 on DL20 and achieves 90.97 nDCG@10 on NovelEval, outperforming GPT-4 by +3.09. Without fine-tuning on Wikipedia, DeAR also excels in open-domain QA, achieving 54.29 Top-1 accuracy on Natural Questions, surpassing baselines like MonoT5, UPR, and RankGPT. Ablations confirm that dual-loss distillation ensures stable calibration, making \DeAR a highly effective and interpretable solution for modern reranking systems.Dataset and code available at https://github.com/DataScienceUIBK/DeAR-Reranking..

  • 4 authors
·
Aug 23

Autoregressive Search Engines: Generating Substrings as Document Identifiers

Knowledge-intensive language tasks require NLP systems to both provide the correct answer and retrieve supporting evidence for it in a given corpus. Autoregressive language models are emerging as the de-facto standard for generating answers, with newer and more powerful systems emerging at an astonishing pace. In this paper we argue that all this (and future) progress can be directly applied to the retrieval problem with minimal intervention to the models' architecture. Previous work has explored ways to partition the search space into hierarchical structures and retrieve documents by autoregressively generating their unique identifier. In this work we propose an alternative that doesn't force any structure in the search space: using all ngrams in a passage as its possible identifiers. This setup allows us to use an autoregressive model to generate and score distinctive ngrams, that are then mapped to full passages through an efficient data structure. Empirically, we show this not only outperforms prior autoregressive approaches but also leads to an average improvement of at least 10 points over more established retrieval solutions for passage-level retrieval on the KILT benchmark, establishing new state-of-the-art downstream performance on some datasets, while using a considerably lighter memory footprint than competing systems. Code and pre-trained models at https://github.com/facebookresearch/SEAL.

  • 6 authors
·
Apr 22, 2022

Three-stage binarization of color document images based on discrete wavelet transform and generative adversarial networks

The efficient extraction of text information from the background in degraded color document images is an important challenge in the preservation of ancient manuscripts. The imperfect preservation of ancient manuscripts has led to different types of degradation over time, such as page yellowing, staining, and ink bleeding, seriously affecting the results of document image binarization. This work proposes an effective three-stage network method to image enhancement and binarization of degraded documents using generative adversarial networks (GANs). Specifically, in Stage-1, we first split the input images into multiple patches, and then split these patches into four single-channel patch images (gray, red, green, and blue). Then, three single-channel patch images (red, green, and blue) are processed by the discrete wavelet transform (DWT) with normalization. In Stage-2, we use four independent generators to separately train GAN models based on the four channels on the processed patch images to extract color foreground information. Finally, in Stage-3, we train two independent GAN models on the outputs of Stage-2 and the resized original input images (512x512) as the local and global predictions to obtain the final outputs. The experimental results show that the Avg-Score metrics of the proposed method are 77.64, 77.95, 79.05, 76.38, 75.34, and 77.00 on the (H)-DIBCO 2011, 2013, 2014, 2016, 2017, and 2018 datasets, which are at the state-of-the-art level. The implementation code for this work is available at https://github.com/abcpp12383/ThreeStageBinarization.

  • 6 authors
·
Nov 29, 2022