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Nov 10

MKD2World: A Typed Spatial MarkDown World Model For Web Agents

Graphical user interface (GUI) agents can improve decision-making with world-model foresight, provided that predicted states accurately reflect post-action interfaces. Existing state representations fail to jointly capture interface layout, UI semantics, and explicit locations. We introduce Typed Spatial Markdown (TSM), a Markdown-style textual state representation for desktop web interfaces. TSM serializes block-level and atomic-level UI elements according to their spatial relationships, jointly encoding their types, visual semantics, explicit locations, optional control states, and hierarchical membership. To train a screenshot-to-TSM renderer, we construct AtomBlock-WebUI, a dataset with precise annotations at both granularities. By injecting element-type labels into HTML and directly extracting bounding boxes after rendering, we avoid annotation errors caused by post-hoc inference from webpage structures. Building on TSM, we propose MKD2World, a desktop web world model trained in two stages for current-state description and action-conditioned next-state prediction. During inference, the web agent queries MKD2World as needed and performs a ``digest'' step, in which it interprets each predicted state and extracts task-relevant evidence for selecting the best action. Experiments show that MKD2World-9B achieves an EleF1 score of 26.50 on the out-of-domain test set, outperforming GPT-5.6-Sol(14.98) by 11.52 points. Across Online-Mind2Web tasks, MKD2World-9B improves the success rate of the Qwen3.5-35B web agent from 22.94% to 37.61%, achieving competitive performance among leading open-source GUI world models. Code is available at https://github.com/OmniAI-Lab-CUHKSZ/MKD2World.

  • 8 authors
·
Nov 3

Can OpenAI o1 outperform humans in higher-order cognitive thinking?

This study evaluates the performance of OpenAI's o1-preview model in higher-order cognitive domains, including critical thinking, systematic thinking, computational thinking, data literacy, creative thinking, logical reasoning, and scientific reasoning. Using established benchmarks, we compared the o1-preview models's performance to human participants from diverse educational levels. o1-preview achieved a mean score of 24.33 on the Ennis-Weir Critical Thinking Essay Test (EWCTET), surpassing undergraduate (13.8) and postgraduate (18.39) participants (z = 1.60 and 0.90, respectively). In systematic thinking, it scored 46.1, SD = 4.12 on the Lake Urmia Vignette, significantly outperforming the human mean (20.08, SD = 8.13, z = 3.20). For data literacy, o1-preview scored 8.60, SD = 0.70 on Merk et al.'s "Use Data" dimension, compared to the human post-test mean of 4.17, SD = 2.02 (z = 2.19). On creative thinking tasks, the model achieved originality scores of 2.98, SD = 0.73, higher than the human mean of 1.74 (z = 0.71). In logical reasoning (LogiQA), it outperformed humans with average 90%, SD = 10% accuracy versus 86%, SD = 6.5% (z = 0.62). For scientific reasoning, it achieved near-perfect performance (mean = 0.99, SD = 0.12) on the TOSLS,, exceeding the highest human scores of 0.85, SD = 0.13 (z = 1.78). While o1-preview excelled in structured tasks, it showed limitations in problem-solving and adaptive reasoning. These results demonstrate the potential of AI to complement education in structured assessments but highlight the need for ethical oversight and refinement for broader applications.

  • 9 authors
·
Dec 7, 2024

Deep Learning on a Data Diet: Finding Important Examples Early in Training

Recent success in deep learning has partially been driven by training increasingly overparametrized networks on ever larger datasets. It is therefore natural to ask: how much of the data is superfluous, which examples are important for generalization, and how do we find them? In this work, we make the striking observation that, in standard vision datasets, simple scores averaged over several weight initializations can be used to identify important examples very early in training. We propose two such scores -- the Gradient Normed (GraNd) and the Error L2-Norm (EL2N) scores -- and demonstrate their efficacy on a range of architectures and datasets by pruning significant fractions of training data without sacrificing test accuracy. In fact, using EL2N scores calculated a few epochs into training, we can prune half of the CIFAR10 training set while slightly improving test accuracy. Furthermore, for a given dataset, EL2N scores from one architecture or hyperparameter configuration generalize to other configurations. Compared to recent work that prunes data by discarding examples that are rarely forgotten over the course of training, our scores use only local information early in training. We also use our scores to detect noisy examples and study training dynamics through the lens of important examples -- we investigate how the data distribution shapes the loss surface and identify subspaces of the model's data representation that are relatively stable over training.

  • 3 authors
·
Jul 14, 2021

Evaluation of OpenAI o1: Opportunities and Challenges of AGI

This comprehensive study evaluates the performance of OpenAI's o1-preview large language model across a diverse array of complex reasoning tasks, spanning multiple domains, including computer science, mathematics, natural sciences, medicine, linguistics, and social sciences. Through rigorous testing, o1-preview demonstrated remarkable capabilities, often achieving human-level or superior performance in areas ranging from coding challenges to scientific reasoning and from language processing to creative problem-solving. Key findings include: -83.3% success rate in solving complex competitive programming problems, surpassing many human experts. -Superior ability in generating coherent and accurate radiology reports, outperforming other evaluated models. -100% accuracy in high school-level mathematical reasoning tasks, providing detailed step-by-step solutions. -Advanced natural language inference capabilities across general and specialized domains like medicine. -Impressive performance in chip design tasks, outperforming specialized models in areas such as EDA script generation and bug analysis. -Remarkable proficiency in anthropology and geology, demonstrating deep understanding and reasoning in these specialized fields. -Strong capabilities in quantitative investing. O1 has comprehensive financial knowledge and statistical modeling skills. -Effective performance in social media analysis, including sentiment analysis and emotion recognition. The model excelled particularly in tasks requiring intricate reasoning and knowledge integration across various fields. While some limitations were observed, including occasional errors on simpler problems and challenges with certain highly specialized concepts, the overall results indicate significant progress towards artificial general intelligence.

  • 78 authors
·
Sep 27, 2024

FinFIRST: Benchmarking Search Agents for Financial Information Retrieval, Sourcing and Traceability

Financial search is a highly demanding task for LLM agents, requiring not only a correct final answer but also temporally valid information retrieval, authoritative source selection, entity and period alignment, unit and definition consistency, and verifiable evidence for all conclusions. Existing benchmarks predominantly evaluate only the final answer, making it difficult to localize errors or assess whether an answer is well-founded. To address this gap, we introduce FinFIRST (Financial Information Retrieval, Sourcing and Traceability), the first financial benchmark to jointly evaluate answers and supporting evidence through atomic rubrics. FinFIRST comprises 123 expert-authored tasks spanning a graduated difficulty spectrum, constructed from aggregate patterns of real-world financial scenarios through an 18-field taxonomy, a six-axis coverage blueprint, a registry of 138 financial sources, contributions from over 50 finance experts, and a six-stage quality-control pipeline. Each task is accompanied by an evidence-grounded reference package decomposed into atomic criteria across three dimensions: raw-information acquisition, source verification, and computation and answer formation. We evaluate 15 model configurations under a unified tool setting. Claude-Opus-5 achieves the highest atomic score of 87.59%, while GPT-5.6-Sol attains the highest strict pass rate of 71.54%. Computation and answer formation consistently lag behind raw-information acquisition across systems. FinFIRST retains final-answer correctness as the primary objective while making the supporting research process measurable, verifiable, and diagnosable.

  • 11 authors
·
Sep 20

CXR-LLaVA: Multimodal Large Language Model for Interpreting Chest X-ray Images

Purpose: Recent advancements in large language models (LLMs) have expanded their capabilities in a multimodal fashion, potentially replicating the image interpretation of human radiologists. This study aimed to develop open-source multimodal large language model for interpreting chest X-ray images (CXR-LLaVA). We also examined the effect of prompt engineering and model parameters such as temperature and nucleus sampling. Materials and Methods: For training, we collected 659,287 publicly available CXRs: 417,336 CXRs had labels for certain radiographic abnormalities (dataset 1); 241,951 CXRs provided free-text radiology reports (dataset 2). After pre-training the Resnet50 as an image encoder, the contrastive language-image pre-training was used to align CXRs and corresponding radiographic abnormalities. Then, the Large Language Model Meta AI-2 was fine-tuned using dataset 2, which were refined using GPT-4, with generating various question answering scenarios. The code can be found at https://github.com/ECOFRI/CXR_LLaVA. Results: In the test set, we observed that the model's performance fluctuated based on its parameters. On average, it achieved F1 score of 0.34 for five pathologic findings (atelectasis, cardiomegaly, consolidation, edema, and pleural effusion), which was improved to 0.46 through prompt engineering. In the independent set, the model achieved an average F1 score of 0.30 for the same pathologic findings. Notably, for the pediatric chest radiograph dataset, which was unseen during training, the model differentiated abnormal radiographs with an F1 score ranging from 0.84 to 0.85. Conclusion: CXR-LLaVA demonstrates promising potential in CXR interpretation. Both prompt engineering and model parameter adjustments can play pivotal roles in interpreting CXRs.

  • 4 authors
·
Oct 22, 2023

EvalYaks: Instruction Tuning Datasets and LoRA Fine-tuned Models for Automated Scoring of CEFR B2 Speaking Assessment Transcripts

Relying on human experts to evaluate CEFR speaking assessments in an e-learning environment creates scalability challenges, as it limits how quickly and widely assessments can be conducted. We aim to automate the evaluation of CEFR B2 English speaking assessments in e-learning environments from conversation transcripts. First, we evaluate the capability of leading open source and commercial Large Language Models (LLMs) to score a candidate's performance across various criteria in the CEFR B2 speaking exam in both global and India-specific contexts. Next, we create a new expert-validated, CEFR-aligned synthetic conversational dataset with transcripts that are rated at different assessment scores. In addition, new instruction-tuned datasets are developed from the English Vocabulary Profile (up to CEFR B2 level) and the CEFR-SP WikiAuto datasets. Finally, using these new datasets, we perform parameter efficient instruction tuning of Mistral Instruct 7B v0.2 to develop a family of models called EvalYaks. Four models in this family are for assessing the four sections of the CEFR B2 speaking exam, one for identifying the CEFR level of vocabulary and generating level-specific vocabulary, and another for detecting the CEFR level of text and generating level-specific text. EvalYaks achieved an average acceptable accuracy of 96%, a degree of variation of 0.35 levels, and performed 3 times better than the next best model. This demonstrates that a 7B parameter LLM instruction tuned with high-quality CEFR-aligned assessment data can effectively evaluate and score CEFR B2 English speaking assessments, offering a promising solution for scalable, automated language proficiency evaluation.

  • 4 authors
·
Aug 22, 2024 1

CodeElo: Benchmarking Competition-level Code Generation of LLMs with Human-comparable Elo Ratings

With the increasing code reasoning capabilities of existing large language models (LLMs) and breakthroughs in reasoning models like OpenAI o1 and o3, there is a growing need to develop more challenging and comprehensive benchmarks that effectively test their sophisticated competition-level coding abilities. Existing benchmarks, like LiveCodeBench and USACO, fall short due to the unavailability of private test cases, lack of support for special judges, and misaligned execution environments. To bridge this gap, we introduce CodeElo, a standardized competition-level code generation benchmark that effectively addresses all these challenges for the first time. CodeElo benchmark is mainly based on the official CodeForces platform and tries to align with the platform as much as possible. We compile the recent six months of contest problems on CodeForces with detailed information such as contest divisions, problem difficulty ratings, and problem algorithm tags. We introduce a unique judging method in which problems are submitted directly to the platform and develop a reliable Elo rating calculation system that aligns with the platform and is comparable with human participants but has lower variance. By testing on our CodeElo, we provide the Elo ratings of 30 existing popular open-source and 3 proprietary LLMs for the first time. The results show that o1-mini and QwQ-32B-Preview stand out significantly, achieving Elo ratings of 1578 and 1261, respectively, while other models struggle even with the easiest problems, placing in the lowest 20 percent among all human participants. Detailed analysis experiments are also conducted to provide insights into performance across algorithms and comparisons between using C++ and Python, which can suggest directions for future studies.

  • 17 authors
·
Jan 2, 2025 6

ADIEE: Automatic Dataset Creation and Scorer for Instruction-Guided Image Editing Evaluation

Recent advances in instruction-guided image editing underscore the need for effective automated evaluation. While Vision-Language Models (VLMs) have been explored as judges, open-source models struggle with alignment, and proprietary models lack transparency and cost efficiency. Additionally, no public training datasets exist to fine-tune open-source VLMs, only small benchmarks with diverse evaluation schemes. To address this, we introduce ADIEE, an automated dataset creation approach which is then used to train a scoring model for instruction-guided image editing evaluation. We generate a large-scale dataset with over 100K samples and use it to fine-tune a LLaVA-NeXT-8B model modified to decode a numeric score from a custom token. The resulting scorer outperforms all open-source VLMs and Gemini-Pro 1.5 across all benchmarks, achieving a 0.0696 (+17.24%) gain in score correlation with human ratings on AURORA-Bench, and improving pair-wise comparison accuracy by 4.03% (+7.21%) on GenAI-Bench and 4.75% (+9.35%) on AURORA-Bench, respectively, compared to the state-of-the-art. The scorer can act as a reward model, enabling automated best edit selection and model fine-tuning. Notably, the proposed scorer can boost MagicBrush model's average evaluation score on ImagenHub from 5.90 to 6.43 (+8.98%). Our code and models are available at https://github.com/SherryXTChen/ADIEE.git.

  • 4 authors
·
Jul 9, 2025

SVGFaith: A Two-Layer Meta-Evaluation of Faithfulness Metrics for Text-to-SVG Generation

Text-to-SVG systems are commonly evaluated by applying raster-image metrics to rasterised outputs, yet whether these scores capture fine-grained prompt faithfulness remains unclear. We introduce SVGFaith, a two-layer meta-evaluation framework in which the more faithful candidate of each pair is determined by construction or by human judgment. SVGFaith-Diagnostic contains 1,842 controlled contrastive pairs across eight capability axes, split evenly between two directions: two renderings compared against one prompt, and two descriptions compared against one rendering. SVGFaith-Arena contains 1,327 human-annotated comparisons of real generator outputs. On SVGFaith-Diagnostic, CLIP and three other image--text embedding metrics reach at least 0.789 pairwise accuracy on object identity but at most 0.672 on spatial relations and attribute binding, where chance is 0.5. We further introduce SVGFaith-Score, an interpretable pointwise metric. A domain-tuned decomposer turns each prompt into a dependency graph of atomic visual requirements, a visual question answering model scores whether each requirement is satisfied, and a requirement's score is discounted when its prerequisites score low. In addition to the overall score, the per-requirement scores show which requirements are judged unsatisfied and which inherit discounts from their prerequisites. SVGFaith-Score significantly outperforms all nine baselines, including a Qwen3.5-122B-A10B judge, on Arena and in both Diagnostic directions. Code and data: https://github.com/Yukinonooo/SVGFaith.

  • 9 authors
·
Nov 3

Generalist Foundation Models Are Not Clinical Enough for Hospital Operations

Hospitals and healthcare systems rely on operational decisions that determine patient flow, cost, and quality of care. Despite strong performance on medical knowledge and conversational benchmarks, foundation models trained on general text may lack the specialized knowledge required for these operational decisions. We introduce Lang1, a family of models (100M-7B parameters) pretrained on a specialized corpus blending 80B clinical tokens from NYU Langone Health's EHRs and 627B tokens from the internet. To rigorously evaluate Lang1 in real-world settings, we developed the REalistic Medical Evaluation (ReMedE), a benchmark derived from 668,331 EHR notes that evaluates five critical tasks: 30-day readmission prediction, 30-day mortality prediction, length of stay, comorbidity coding, and predicting insurance claims denial. In zero-shot settings, both general-purpose and specialized models underperform on four of five tasks (36.6%-71.7% AUROC), with mortality prediction being an exception. After finetuning, Lang1-1B outperforms finetuned generalist models up to 70x larger and zero-shot models up to 671x larger, improving AUROC by 3.64%-6.75% and 1.66%-23.66% respectively. We also observed cross-task scaling with joint finetuning on multiple tasks leading to improvement on other tasks. Lang1-1B effectively transfers to out-of-distribution settings, including other clinical tasks and an external health system. Our findings suggest that predictive capabilities for hospital operations require explicit supervised finetuning, and that this finetuning process is made more efficient by in-domain pretraining on EHR. Our findings support the emerging view that specialized LLMs can compete with generalist models in specialized tasks, and show that effective healthcare systems AI requires the combination of in-domain pretraining, supervised finetuning, and real-world evaluation beyond proxy benchmarks.

newyorkuniversity New York University
·
Nov 17, 2025 3

GottBERT: a pure German Language Model

Lately, pre-trained language models advanced the field of natural language processing (NLP). The introduction of Bidirectional Encoders for Transformers (BERT) and its optimized version RoBERTa have had significant impact and increased the relevance of pre-trained models. First, research in this field mainly started on English data followed by models trained with multilingual text corpora. However, current research shows that multilingual models are inferior to monolingual models. Currently, no German single language RoBERTa model is yet published, which we introduce in this work (GottBERT). The German portion of the OSCAR data set was used as text corpus. In an evaluation we compare its performance on the two Named Entity Recognition (NER) tasks Conll 2003 and GermEval 2014 as well as on the text classification tasks GermEval 2018 (fine and coarse) and GNAD with existing German single language BERT models and two multilingual ones. GottBERT was pre-trained related to the original RoBERTa model using fairseq. All downstream tasks were trained using hyperparameter presets taken from the benchmark of German BERT. The experiments were setup utilizing FARM. Performance was measured by the F_{1} score. GottBERT was successfully pre-trained on a 256 core TPU pod using the RoBERTa BASE architecture. Even without extensive hyper-parameter optimization, in all NER and one text classification task, GottBERT already outperformed all other tested German and multilingual models. In order to support the German NLP field, we publish GottBERT under the AGPLv3 license.

  • 5 authors
·
Dec 3, 2020

PageRecall: Measuring Page Selection in Literature-Grounded Question Answering

We describe our system for LitTraceQA (GroundLM @ EMNLP 2026): given a research question, retrieve the relevant papers from a pool of 27,487, cite the page and the table or figure where the answer lives, and answer in a requested format. Our main finding is that evidence grounding is limited by retrieval, not by reading. The page selector put the annotator's page, which we call the gold page, in front of the model that locates evidence only about half the time (52.6% gold-page recall), while that model, given the page, cited the right one in 45 of the 48 locators it emitted (94%). When the page was missing it rarely said so: of 45 such cases it returned nothing 14 times, a wrong page 24 times, and a correct page 7 times, so the pipeline failed quietly almost twice as often as it failed visibly. Since the failure was that the right page was never shown, the fix is to stop choosing: each retrieved paper fits in the model's context, so we show it whole. Page ranking survives only as a fallback inside papers too long to fit, which no test-split paper was, and gold-page recall reaches 100% on the papers we can parse. Separately, questions that identify their target by position rather than content, such as "the first author of the 24th reference", are served by parsing rather than retrieval: we resolve the bibliography into an addressable list, which also supplies identifiers the evidence metric scores. The final system scores 0.762 paper F_1, 0.441 evidence F_1 and 0.920 multiple-choice accuracy on the held-out test split. Because the pipeline depends on a closed model without seed control, we release a harness that verifies the paper's central claims against committed artifacts.

  • 1 authors
·
Sep 15

PRISM: Pathology Reliability In Scarce-label Medicine. A Tile-level Benchmark of Pathology Foundation Models

Pathology foundation models are typically benchmarked on classification performance at full label availability and on in-distribution test sets, while calibration, behavior at low label budgets, and robustness under cross-institutional shift are seldom evaluated jointly. We introduce PRISM, a tile-level benchmark that measures the reliability of pathology foundation models along four axes: model choice, label fraction, calibration, and out-of-distribution transfer. PRISM evaluates eight foundation models (CLIP, PLIP, CONCH, UNI, Virchow2, GigaPath, H-Optimus-0, Midnight) on six tile-level datasets at six label fractions (1% to 100%) with three seeds (864 linear probe runs), extended with a five-hospital Camelyon17 study of 20 directed transfer pairs. Four phenomena emerge. (i) Under full supervision, AUROC rank predicts post-temperature calibration rank consistently across datasets (Spearman rho = 0.52, I^2 = 0%), whereas at 1% labels the relationship becomes dataset-specific (rho = -0.24, I^2 = 67%). (ii) On harder datasets the linear probe collapses to a single predicted class below a dataset-specific label fraction. (iii) Whether additional source-domain labels help or harm target calibration tracks how well the probe transfers: below a transfer AUROC of roughly 0.85, more labels worsen target ECE in 86-88% of combinations. (iv) Temperature scaling fails to reduce ECE in 49 of 288 cells, miscalibration is predominantly under-confidence, and a source-fitted temperature is harmful under failing transfer. PRISM is released as a pip-installable package with reference results for all 288 cells. Code and data: https://github.com/alicemkyn/prism-benchmark

  • 1 authors
·
Oct 26

A Natural Language Processing Pipeline of Chinese Free-text Radiology Reports for Liver Cancer Diagnosis

Despite the rapid development of natural language processing (NLP) implementation in electronic medical records (EMRs), Chinese EMRs processing remains challenging due to the limited corpus and specific grammatical characteristics, especially for radiology reports. In this study, we designed an NLP pipeline for the direct extraction of clinically relevant features from Chinese radiology reports, which is the first key step in computer-aided radiologic diagnosis. The pipeline was comprised of named entity recognition, synonyms normalization, and relationship extraction to finally derive the radiological features composed of one or more terms. In named entity recognition, we incorporated lexicon into deep learning model bidirectional long short-term memory-conditional random field (BiLSTM-CRF), and the model finally achieved an F1 score of 93.00%. With the extracted radiological features, least absolute shrinkage and selection operator and machine learning methods (support vector machine, random forest, decision tree, and logistic regression) were used to build the classifiers for liver cancer prediction. For liver cancer diagnosis, random forest had the highest predictive performance in liver cancer diagnosis (F1 score 86.97%, precision 87.71%, and recall 86.25%). This work was a comprehensive NLP study focusing on Chinese radiology reports and the application of NLP in cancer risk prediction. The proposed NLP pipeline for the radiological feature extraction could be easily implemented in other kinds of Chinese clinical texts and other disease predictive tasks.

  • 9 authors
·
Apr 10, 2020

UniME-V2: MLLM-as-a-Judge for Universal Multimodal Embedding Learning

Universal multimodal embedding models are foundational to various tasks. Existing approaches typically employ in-batch negative mining by measuring the similarity of query-candidate pairs. However, these methods often struggle to capture subtle semantic differences among candidates and lack diversity in negative samples. Moreover, the embeddings exhibit limited discriminative ability in distinguishing false and hard negatives. In this paper, we leverage the advanced understanding capabilities of MLLMs to enhance representation learning and present a novel Universal Multimodal Embedding (UniME-V2) model. Our approach first constructs a potential hard negative set through global retrieval. We then introduce the MLLM-as-a-Judge mechanism, which utilizes MLLMs to assess the semantic alignment of query-candidate pairs and generate soft semantic matching scores. These scores serve as a foundation for hard negative mining, mitigating the impact of false negatives and enabling the identification of diverse, high-quality hard negatives. Furthermore, the semantic matching scores are used as soft labels to mitigate the rigid one-to-one mapping constraint. By aligning the similarity matrix with the soft semantic matching score matrix, the model learns semantic distinctions among candidates, significantly enhancing its discriminative capacity. To further improve performance, we propose UniME-V2-Reranker, a reranking model trained on our mined hard negatives through a joint pairwise and listwise optimization approach. We conduct comprehensive experiments on the MMEB benchmark and multiple retrieval tasks, demonstrating that our method achieves state-of-the-art performance on average across all tasks.

  • 9 authors
·
Oct 15, 2025 2

FRAKE: Fusional Real-time Automatic Keyword Extraction

Keyword extraction is the process of identifying the words or phrases that express the main concepts of text to the best of one's ability. Electronic infrastructure creates a considerable amount of text every day and at all times. This massive volume of documents makes it practically impossible for human resources to study and manage them. Nevertheless, the need for these documents to be accessed efficiently and effectively is evident in numerous purposes. A blog, news article, or technical note is considered a relatively long text since the reader aims to learn the subject based on keywords or topics. Our approach consists of a combination of two models: graph centrality features and textural features. The proposed method has been used to extract the best keyword among the candidate keywords with an optimal combination of graph centralities, such as degree, betweenness, eigenvector, closeness centrality and etc, and textural, such as Casing, Term position, Term frequency normalization, Term different sentence, Part Of Speech tagging. There have also been attempts to distinguish keywords from candidate phrases and consider them on separate keywords. For evaluating the proposed method, seven datasets were used: Semeval2010, SemEval2017, Inspec, fao30, Thesis100, pak2018, and Wikinews, with results reported as Precision, Recall, and F- measure. Our proposed method performed much better in terms of evaluation metrics in all reviewed datasets compared with available methods in literature. An approximate 16.9% increase was witnessed in F-score metric and this was much more for the Inspec in English datasets and WikiNews in forgone languages.

  • 3 authors
·
Apr 10, 2021

Improving the Performance of Radiology Report De-identification with Large-Scale Training and Benchmarking Against Cloud Vendor Methods

Objective: To enhance automated de-identification of radiology reports by scaling transformer-based models through extensive training datasets and benchmarking performance against commercial cloud vendor systems for protected health information (PHI) detection. Materials and Methods: In this retrospective study, we built upon a state-of-the-art, transformer-based, PHI de-identification pipeline by fine-tuning on two large annotated radiology corpora from Stanford University, encompassing chest X-ray, chest CT, abdomen/pelvis CT, and brain MR reports and introducing an additional PHI category (AGE) into the architecture. Model performance was evaluated on test sets from Stanford and the University of Pennsylvania (Penn) for token-level PHI detection. We further assessed (1) the stability of synthetic PHI generation using a "hide-in-plain-sight" method and (2) performance against commercial systems. Precision, recall, and F1 scores were computed across all PHI categories. Results: Our model achieved overall F1 scores of 0.973 on the Penn dataset and 0.996 on the Stanford dataset, outperforming or maintaining the previous state-of-the-art model performance. Synthetic PHI evaluation showed consistent detectability (overall F1: 0.959 [0.958-0.960]) across 50 independently de-identified Penn datasets. Our model outperformed all vendor systems on synthetic Penn reports (overall F1: 0.960 vs. 0.632-0.754). Discussion: Large-scale, multimodal training improved cross-institutional generalization and robustness. Synthetic PHI generation preserved data utility while ensuring privacy. Conclusion: A transformer-based de-identification model trained on diverse radiology datasets outperforms prior academic and commercial systems in PHI detection and establishes a new benchmark for secure clinical text processing.

  • 8 authors
·
Nov 6, 2025

EgyBERT: A Large Language Model Pretrained on Egyptian Dialect Corpora

This study presents EgyBERT, an Arabic language model pretrained on 10.4 GB of Egyptian dialectal texts. We evaluated EgyBERT's performance by comparing it with five other multidialect Arabic language models across 10 evaluation datasets. EgyBERT achieved the highest average F1-score of 84.25% and an accuracy of 87.33%, significantly outperforming all other comparative models, with MARBERTv2 as the second best model achieving an F1-score 83.68% and an accuracy 87.19%. Additionally, we introduce two novel Egyptian dialectal corpora: the Egyptian Tweets Corpus (ETC), containing over 34.33 million tweets (24.89 million sentences) amounting to 2.5 GB of text, and the Egyptian Forums Corpus (EFC), comprising over 44.42 million sentences (7.9 GB of text) collected from various Egyptian online forums. Both corpora are used in pretraining the new model, and they are the largest Egyptian dialectal corpora to date reported in the literature. Furthermore, this is the first study to evaluate the performance of various language models on Egyptian dialect datasets, revealing significant differences in performance that highlight the need for more dialect-specific models. The results confirm the effectiveness of EgyBERT model in processing and analyzing Arabic text expressed in Egyptian dialect, surpassing other language models included in the study. EgyBERT model is publicly available on https://huggingface.co/faisalq/EgyBERT.

  • 1 authors
·
Aug 6, 2024

AD-BERT: Using Pre-trained contextualized embeddings to Predict the Progression from Mild Cognitive Impairment to Alzheimer's Disease

Objective: We develop a deep learning framework based on the pre-trained Bidirectional Encoder Representations from Transformers (BERT) model using unstructured clinical notes from electronic health records (EHRs) to predict the risk of disease progression from Mild Cognitive Impairment (MCI) to Alzheimer's Disease (AD). Materials and Methods: We identified 3657 patients diagnosed with MCI together with their progress notes from Northwestern Medicine Enterprise Data Warehouse (NMEDW) between 2000-2020. The progress notes no later than the first MCI diagnosis were used for the prediction. We first preprocessed the notes by deidentification, cleaning and splitting, and then pretrained a BERT model for AD (AD-BERT) based on the publicly available Bio+Clinical BERT on the preprocessed notes. The embeddings of all the sections of a patient's notes processed by AD-BERT were combined by MaxPooling to compute the probability of MCI-to-AD progression. For replication, we conducted a similar set of experiments on 2563 MCI patients identified at Weill Cornell Medicine (WCM) during the same timeframe. Results: Compared with the 7 baseline models, the AD-BERT model achieved the best performance on both datasets, with Area Under receiver operating characteristic Curve (AUC) of 0.8170 and F1 score of 0.4178 on NMEDW dataset and AUC of 0.8830 and F1 score of 0.6836 on WCM dataset. Conclusion: We developed a deep learning framework using BERT models which provide an effective solution for prediction of MCI-to-AD progression using clinical note analysis.

  • 12 authors
·
Nov 6, 2022