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Carsten Eickhoff

Carsten Eickhoff contributes to research discovery and scholarly infrastructure.

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Computation and Language Information Retrieval Artificial Intelligence Machine Learning Applications Computer Vision cs.CY Digital Libraries eess.SP

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preprint2026arXiv

PubMed-Ophtha: An open resource for training ophthalmology vision-language models on scientific literature

Vision-language models hold considerable promise for ophthalmology, but their development depends on large-scale, high-quality image-text datasets that remain scarce. We present PubMed-Ophtha, a hierarchical dataset of 102,023 ophthalmological image-caption pairs extracted from 15,842 open-access articles in PubMed Central. Unlike existing datasets, figures are extracted directly from article PDFs at full resolution and decomposed into their constituent panels, panel identifiers, and individual images. Each image is annotated with its imaging modality -- color fundus photography, optical coherence tomography, retinal imaging, or other -- and a mark status indicating the presence of annotation marks such as arrows. Figure captions are split into panel-level subcaptions using a two-step LLM approach, achieving a mean average sentence BLEU score of 0.913 on human-annotated data. Panel and image detection models reach a mAP@0.50 of 0.909 and 0.892, respectively, and figure extraction achieves a median IoU of 0.997. To support reproducibility, we additionally release the human-annotated ground-truth data, all trained models, and the full dataset generation pipeline.

preprint2026arXiv

The Persona Paradox: Medical Personas as Behavioral Priors in Clinical Language Models

Persona conditioning can be viewed as a behavioral prior for large language models (LLMs) and is often assumed to confer expertise and improve safety in a monotonic manner. However, its effects on high-stakes clinical decision-making remain poorly characterized. We systematically evaluate persona-based control in clinical LLMs, examining how professional roles (e.g., Emergency Department physician, nurse) and interaction styles (bold vs.\ cautious) influence behavior across models and medical tasks. We assess performance on clinical triage and patient-safety tasks using multidimensional evaluations that capture task accuracy, calibration, and safety-relevant risk behavior. We find systematic, context-dependent, and non-monotonic effects: Medical personas improve performance in critical care tasks, yielding gains of up to $\sim+20\%$ in accuracy and calibration, but degrade performance in primary-care settings by comparable margins. Interaction style modulates risk propensity and sensitivity, but it's highly model-dependent. While aggregated LLM-judge rankings favor medical over non-medical personas in safety-critical cases, we found that human clinicians show moderate agreement on safety compliance (average Cohen's $κ= 0.43$) but indicate a low confidence in 95.9\% of their responses on reasoning quality. Our work shows that personas function as behavioral priors that introduce context-dependent trade-offs rather than guarantees of safety or expertise. The code is available at https://github.com/rsinghlab/Persona\_Paradox.

preprint2026arXiv

Understanding Wacky Weights: A Dissection of SPLADE's Learned Term Importance

Learned sparse retrieval models such as SPLADE combine the effectiveness of neural architectures with the efficiency of inverted indices. As these models assign weights to terms from a fixed vocabulary, interpretability is often touted as a major benefit of these models. However, the emergence of wacky weights, i.e., expansion terms that appear semantically unrelated to the input, limits interpretability. While prior research has anecdotally observed this phenomenon, there is a lack of systematic understanding regarding their origins, prevalence, and contribution to retrieval effectiveness. In this paper, we reproduce SPLADE-v2 to systematically investigate wacky weights across the SPLADE family of models. We present a comprehensive dissection of wacky weights, providing a formal definition of wackiness based on the lexical utility of expansion terms. Furthermore, we introduce a novel measure to compare the prevalence of these tokens across models with varying vocabularies and sparsity levels. Beyond reproducing the original SPLADE-v2, we train it with various loss functions, datasets, and backbone transformers to isolate the factors contributing to wackiness. Our results show that larger vocabularies are associated with a higher prevalence of wacky tokens, while stricter sparsity regularizers are associated with lower prevalence. Finally, we find that wacky weights are used primarily for in-domain effectiveness rather than out-of-domain generalization.

preprint2025arXiv

A Survey on LLM-Assisted Clinical Trial Recruitment

Recent advances in LLMs have greatly improved general-domain NLP tasks. Yet, their adoption in critical domains, such as clinical trial recruitment, remains limited. As trials are designed in natural language and patient data is represented as both structured and unstructured text, the task of matching trials and patients benefits from knowledge aggregation and reasoning abilities of LLMs. Classical approaches are trial-specific and LLMs with their ability to consolidate distributed knowledge hold the potential to build a more general solution. Yet recent applications of LLM-assisted methods rely on proprietary models and weak evaluation benchmarks. In this survey, we are the first to analyze the task of trial-patient matching and contextualize emerging LLM-based approaches in clinical trial recruitment. We critically examine existing benchmarks, approaches and evaluation frameworks, the challenges to adopting LLM technologies in clinical research and exciting future directions.

preprint2023arXiv

Unsupervised Multivariate Time-Series Transformers for Seizure Identification on EEG

Epilepsy is one of the most common neurological disorders, typically observed via seizure episodes. Epileptic seizures are commonly monitored through electroencephalogram (EEG) recordings due to their routine and low expense collection. The stochastic nature of EEG makes seizure identification via manual inspections performed by highly-trained experts a tedious endeavor, motivating the use of automated identification. The literature on automated identification focuses mostly on supervised learning methods requiring expert labels of EEG segments that contain seizures, which are difficult to obtain. Motivated by these observations, we pose seizure identification as an unsupervised anomaly detection problem. To this end, we employ the first unsupervised transformer-based model for seizure identification on raw EEG. We train an autoencoder involving a transformer encoder via an unsupervised loss function, incorporating a novel masking strategy uniquely designed for multivariate time-series data such as EEG. Training employs EEG recordings that do not contain any seizures, while seizures are identified with respect to reconstruction errors at inference time. We evaluate our method on three publicly available benchmark EEG datasets for distinguishing seizure vs. non-seizure windows. Our method leads to significantly better seizure identification performance than supervised learning counterparts, by up to 16% recall, 9% accuracy, and 9% Area under the Receiver Operating Characteristics Curve (AUC), establishing particular benefits on highly imbalanced data. Through accurate seizure identification, our method could facilitate widely accessible and early detection of epilepsy development, without needing expensive label collection or manual feature extraction.

preprint2022arXiv

NEWTS: A Corpus for News Topic-Focused Summarization

Text summarization models are approaching human levels of fidelity. Existing benchmarking corpora provide concordant pairs of full and abridged versions of Web, news or, professional content. To date, all summarization datasets operate under a one-size-fits-all paradigm that may not reflect the full range of organic summarization needs. Several recently proposed models (e.g., plug and play language models) have the capacity to condition the generated summaries on a desired range of themes. These capacities remain largely unused and unevaluated as there is no dedicated dataset that would support the task of topic-focused summarization. This paper introduces the first topical summarization corpus NEWTS, based on the well-known CNN/Dailymail dataset, and annotated via online crowd-sourcing. Each source article is paired with two reference summaries, each focusing on a different theme of the source document. We evaluate a representative range of existing techniques and analyze the effectiveness of different prompting methods.

preprint2022arXiv

Pretraining on Interactions for Learning Grounded Affordance Representations

Lexical semantics and cognitive science point to affordances (i.e. the actions that objects support) as critical for understanding and representing nouns and verbs. However, study of these semantic features has not yet been integrated with the "foundation" models that currently dominate language representation research. We hypothesize that predictive modeling of object state over time will result in representations that encode object affordance information "for free". We train a neural network to predict objects' trajectories in a simulated interaction and show that our network's latent representations differentiate between both observed and unobserved affordances. We find that models trained using 3D simulations from our SPATIAL dataset outperform conventional 2D computer vision models trained on a similar task, and, on initial inspection, that differences between concepts correspond to expected features (e.g., roll entails rotation). Our results suggest a way in which modern deep learning approaches to grounded language learning can be integrated with traditional formal semantic notions of lexical representations.

preprint2022arXiv

Wasserstein Adversarial Learning based Temporal Knowledge Graph Embedding

Research on knowledge graph embedding (KGE) has emerged as an active field in which most existing KGE approaches mainly focus on static structural data and ignore the influence of temporal variation involved in time-aware triples. In order to deal with this issue, several temporal knowledge graph embedding (TKGE) approaches have been proposed to integrate temporal and structural information in recent years. However, these methods only employ a uniformly random sampling to construct negative facts. As a consequence, the corrupted samples are often too simplistic for training an effective model. In this paper, we propose a new temporal knowledge graph embedding framework by introducing adversarial learning to further refine the performance of traditional TKGE models. In our framework, a generator is utilized to construct high-quality plausible quadruples and a discriminator learns to obtain the embeddings of entities and relations based on both positive and negative samples. Meanwhile, we also apply a Gumbel-Softmax relaxation and the Wasserstein distance to prevent vanishing gradient problems on discrete data; an inherent flaw in traditional generative adversarial networks. Through comprehensive experimentation on temporal datasets, the results indicate that our proposed framework can attain significant improvements based on benchmark models and also demonstrate the effectiveness and applicability of our framework.

preprint2022arXiv

When BERT Fails -- The Limits of EHR Classification

Transformers are powerful text representation learners, useful for all kinds of clinical decision support tasks. Although they outperform baselines on readmission prediction, they are not infallible. Here, we look into one such failure case, and report patterns that lead to inferior predictive performance.

preprint2020arXiv

Brown University at TREC Deep Learning 2019

This paper describes Brown University's submission to the TREC 2019 Deep Learning track. We followed a 2-phase method for producing a ranking of passages for a given input query: In the the first phase, the user's query is expanded by appending 3 queries generated by a transformer model which was trained to rephrase an input query into semantically similar queries. The expanded query can exhibit greater similarity in surface form and vocabulary overlap with the passages of interest and can therefore serve as enriched input to any downstream information retrieval method. In the second phase, we use a BERT-based model pre-trained for language modeling but fine-tuned for query - document relevance prediction to compute relevance scores for a set of 1000 candidate passages per query and subsequently obtain a ranking of passages by sorting them based on the predicted relevance scores. According to the results published in the official Overview of the TREC Deep Learning Track 2019, our team ranked 3rd in the passage retrieval task (including full ranking and re-ranking), and 2nd when considering only re-ranking submissions.

preprint2020arXiv

Diagnosis Prevalence vs. Efficacy in Machine-learning Based Diagnostic Decision Support

Many recent studies use machine learning to predict a small number of ICD-9-CM codes. In practice, on the other hand, physicians have to consider a broader range of diagnoses. This study aims to put these previously incongruent evaluation settings on a more equal footing by predicting ICD-9-CM codes based on electronic health record properties and demonstrating the relationship between diagnosis prevalence and system performance. We extracted patient features from the MIMIC-III dataset for each admission. We trained and evaluated 43 different machine learning classifiers. Among this pool, the most successful classifier was a Multi-Layer Perceptron. In accordance with general machine learning expectation, we observed all classifiers' F1 scores to drop as disease prevalence decreased. Scores fell from 0.28 for the 50 most prevalent ICD-9-CM codes to 0.03 for the 1000 most prevalent ICD-9-CM codes. Statistical analyses showed a moderate positive correlation between disease prevalence and efficacy (0.5866).

preprint2020arXiv

Mining Misdiagnosis Patterns from Biomedical Literature

Diagnostic errors can pose a serious threat to patient safety, leading to serious harm and even death. Efforts are being made to develop interventions that allow physicians to reassess for errors and improve diagnostic accuracy. Our study presents an exploration of misdiagnosis patterns mined from PubMed abstracts. Article titles containing certain phrases indicating misdiagnosis were selected and frequencies of these misdiagnoses calculated. We present the resulting patterns in the form of a directed graph with frequency-weighted misdiagnosis edges connecting diagnosis vertices. We find that the most commonly misdiagnosed diseases were often misdiagnosed as many different diseases, with each misdiagnosis having a relatively low frequency, rather than as a single disease with greater probability. Additionally, while a misdiagnosis relationship may generally exist, the relationship was often found to be one-sided.

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