Medical image retrieval is a valuable field for supporting clinical decision-making, yet current methods primarily support 2D images and require fully annotated queries, limiting clinical flexibility. To address this, we propose RadiomicsRetrieval, a 3D content-based retrieval framework bridging handcrafted radiomics descriptors with deep learning-based embeddings at the tumor level. Unlike existing 2D approaches, RadiomicsRetrieval fully exploits volumetric data to leverage richer spatial context in medical images. We employ a promptable segmentation model (e.g., SAM) to derive tumor-specific image embeddings, which are aligned with radiomics features extracted from the same tumor via contrastive learning. These representations are further enriched by anatomical positional embedding (APE). As a result, RadiomicsRetrieval enables flexible querying based on shape, location, or partial feature sets. Extensive experiments on both lung CT and brain MRI public datasets demonstrate that radiomics features significantly enhance retrieval specificity, while APE provides global anatomical context essential for location-based searches. Notably, our framework requires only minimal user prompts (e.g., a single point), minimizing segmentation overhead and supporting diverse clinical scenarios. The capability to query using either image embeddings or selected radiomics attributes highlights its adaptability, potentially benefiting diagnosis, treatment planning, and research on large-scale medical imaging repositories. Our code is available at https://github.com/nainye/RadiomicsRetrieval.
Surgical risk identification is critical for patient safety and reducing preventable medical errors. While multimodal large language models (MLLMs) show promise for automated operating room (OR) risk detection, they often exhibit visual-semantic knowledge conflicts (VS-KC), failing to identify visual safety violations despite understanding textual rules. To address this, we introduce a dataset comprising over 34,000 synthetic images generated by diffusion models, depicting operating room scenes containing entities that violate established safety rules. These images were created to alleviate data scarcity and examine MLLMs vulnerabilities. In addition, the dataset includes 214 human-annotated images that serve as a gold-standard reference for validation. This comprehensive dataset, spanning diverse perspectives, stages, and configurations, is designed to expose and study VS-KC. Fine-tuning on OR-VSKC significantly improves MLLMs' detection of trained conflict entities and generalizes well to new viewpoints for these entities, but performance on untrained entity types remains poor, highlighting learning specificity and the need for comprehensive training. The main contributions of this work include: (1) a data generation methodology tailored for rule-violation scenarios; (2) the release of the OR-VSKC dataset and its associated benchmark as open-source resources; and (3) an empirical analysis of violation-sensitive knowledge consistency in representative MLLMs. The dataset and appendix are available at https://github.com/zgg2577/VS-KC.
Understanding and modeling enzyme-substrate interactions is crucial for catalytic mechanism research, enzyme engineering, and metabolic engineering. Although a large number of predictive methods have emerged, they do not incorporate prior knowledge of enzyme catalysis to rationally modulate general protein-molecule features that are misaligned with catalytic patterns. To address this issue, we introduce a two-stage progressive framework, OmniESI, for enzyme-substrate interaction prediction through conditional deep learning. By decomposing the modeling of enzyme-substrate interactions into a two-stage progressive process, OmniESI incorporates two conditional networks that respectively emphasize enzymatic reaction specificity and crucial catalysis-related interactions, facilitating a gradual feature modulation in the latent space from general protein-molecule domain to catalysis-aware domain. On top of this unified architecture, OmniESI can adapt to a variety of downstream tasks, including enzyme kinetic parameter prediction, enzyme-substrate pairing prediction, enzyme mutational effect prediction, and enzymatic active site annotation. Under the multi-perspective performance evaluation of in-distribution and out-of-distribution settings, OmniESI consistently delivered superior performance than state-of-the-art specialized methods across seven benchmarks. More importantly, the proposed conditional networks were shown to internalize the fundamental patterns of catalytic efficiency while significantly improving prediction performance, with only negligible parameter increases (0.16%), as demonstrated by ablation studies on key components. Overall, OmniESI represents a unified predictive approach for enzyme-substrate interactions, providing an effective tool for catalytic mechanism cracking and enzyme engineering with strong generalization and broad applicability.
Elucidating the biomechanical behavior of the myocardium is crucial for understanding cardiac physiology, but cannot be directly inferred from clinical imaging and typically requires finite element (FE) simulations. However, conventional FE methods are computationally expensive and often fail to reproduce observed cardiac motions. We propose IMC-PINN-FE, a physics-informed neural network (PINN) framework that integrates imaged motion consistency (IMC) with FE modeling for patient-specific left ventricular (LV) biomechanics. Cardiac motion is first estimated from MRI or echocardiography using either a pre-trained attention-based network or an unsupervised cyclic-regularized network, followed by extraction of motion modes. IMC-PINN-FE then rapidly estimates myocardial stiffness and active tension by fitting clinical pressure measurements, accelerating computation from hours to seconds compared to traditional inverse FE. Based on these parameters, it performs FE modeling across the cardiac cycle at 75x speedup. Through motion constraints, it matches imaged displacements more accurately, improving average Dice from 0.849 to 0.927, while preserving realistic pressure-volume behavior. IMC-PINN-FE advances previous PINN-FE models by introducing back-computation of material properties and better motion fidelity. Using motion from a single subject to reconstruct shape modes also avoids the need for large datasets and improves patient specificity. IMC-PINN-FE offers a robust and efficient approach for rapid, personalized, and image-consistent cardiac biomechanical modeling.
Detecting harmful content is a crucial task in the landscape of NLP applications for Social Good, with hate speech being one of its most dangerous forms. But what do we mean by hate speech, how can we define it, and how does prompting different definitions of hate speech affect model performance? The contribution of this work is twofold. At the theoretical level, we address the ambiguity surrounding hate speech by collecting and analyzing existing definitions from the literature. We organize these definitions into a taxonomy of 14 Conceptual Elements-building blocks that capture different aspects of hate speech definitions, such as references to the target of hate (individual or groups) or of the potential consequences of it. At the experimental level, we employ the collection of definitions in a systematic zero-shot evaluation of three LLMs, on three hate speech datasets representing different types of data (synthetic, human-in-the-loop, and real-world). We find that choosing different definitions, i.e., definitions with a different degree of specificity in terms of encoded elements, impacts model performance, but this effect is not consistent across all architectures.
We derive a single-cell level understanding of metabolism in an isogenic cyanobacterial population by integrating secondary ion mass spectrometry (SIMS) derived multi-isotope uptake measurements of Synechocystis sp. PCC6803 with a statistical inference protocol based on Liebig's law of the minimum, the maximum entropy principle, and constraint-based modeling. We find the population is structured in two metabolically distinct clusters: cells optimizing carbon yield while excessively turning over nitrogen, and cells which act reciprocally, optimizing nitrogen yield and excessively turning over carbon. This partition enables partial heterotrophy within the population via metabolic exchange, likely in the form of organic acids. Exchange increases the feasible metabolic space, and mixotrophic cells achieve the fastest growth rates. Metabolic flux analysis at the single-cell level reveals heterogeneity in carbon fixation rates, Rubisco specificity, and nitrogen assimilation. Our results provide a necessary foundation for understanding how population level phenotypes arise from the collective contributions of distinct individuals.
Large language models (LLMs) are used globally across many languages, but their English-centric pretraining raises concerns about cross-lingual disparities for cultural awareness, often resulting in biased outputs. However, comprehensive multilingual evaluation remains challenging due to limited benchmarks and questionable translation quality. To better assess these disparities, we introduce MAKIEval, an automatic multilingual framework for evaluating cultural awareness in LLMs across languages, regions, and topics. MAKIEval evaluates open-ended text generation, capturing how models express culturally grounded knowledge in natural language. Leveraging Wikidata's multilingual structure as a cross-lingual anchor, it automatically identifies cultural entities in model outputs and links them to structured knowledge, enabling scalable, language-agnostic evaluation without manual annotation or translation. We then introduce four metrics that capture complementary dimensions of cultural awareness: granularity, diversity, cultural specificity, and consensus across languages. We assess 7 LLMs developed from different parts of the world, encompassing both open-source and proprietary systems, across 13 languages, 19 countries and regions, and 6 culturally salient topics (e.g., food, clothing). Notably, we find that models tend to exhibit stronger cultural awareness in English, suggesting that English prompts more effectively activate culturally grounded knowledge. We publicly release our code and data.
Designing regulatory DNA sequences that achieve precise cell-type-specific gene expression is crucial for advancements in synthetic biology, gene therapy and precision medicine. Although transformer-based language models (LMs) can effectively capture patterns in regulatory DNA, their generative approaches often struggle to produce novel sequences with reliable cell-specific activity. Here, we introduce Ctrl-DNA, a novel constrained reinforcement learning (RL) framework tailored for designing regulatory DNA sequences with controllable cell-type specificity. By formulating regulatory sequence design as a biologically informed constrained optimization problem, we apply RL to autoregressive genomic LMs, enabling the models to iteratively refine sequences that maximize regulatory activity in targeted cell types while constraining off-target effects. Our evaluation on human promoters and enhancers demonstrates that Ctrl-DNA consistently outperforms existing generative and RL-based approaches, generating high-fitness regulatory sequences and achieving state-of-the-art cell-type specificity. Moreover, Ctrl-DNA-generated sequences capture key cell-type-specific transcription factor binding sites (TFBS), short DNA motifs recognized by regulatory proteins that control gene expression, demonstrating the biological plausibility of the generated sequences.
Diffusion models exhibit excellent sample quality, but existing guidance methods often require additional model training or are limited to specific tasks. We revisit guidance in diffusion models from the perspective of variational inference and control, introducing Diffusion Trajectory Matching (DTM) that enables guiding pretrained diffusion trajectories to satisfy a terminal cost. DTM unifies a broad class of guidance methods and enables novel instantiations. We introduce a new method within this framework that achieves state-of-the-art results on several linear, non-linear, and blind inverse problems without requiring additional model training or specificity to pixel or latent space diffusion models. Our code will be available at https://github.com/czi-ai/oc-guidance
Hand washing is a crucial part of personal hygiene. Hand washing detection is a relevant topic for wearable sensing with applications in the medical and professional fields. Hand washing detection can be used to aid workers in complying with hygiene rules. Hand washing detection using body-worn IMU-based sensor systems has been shown to be a feasible approach, although, for some reported results, the specificity of the detection was low, leading to a high rate of false positives. In this work, we present a novel, open-source prototype device that additionally includes a humidity, temperature, and barometric sensor. We contribute a benchmark dataset of 10 participants and 43 hand-washing events and perform an evaluation of the sensors' benefits. Added to that, we outline the usefulness of the additional sensor in both the annotation pipeline and the machine learning models. By visual inspection, we show that especially the humidity sensor registers a strong increase in the relative humidity during a hand-washing activity. A machine learning analysis of our data shows that distinct features benefiting from such relative humidity patterns remain to be identified.
During the finetuning stage of text generation tasks, standard cross-entropy loss treats all tokens equally. This can lead models to overemphasize high-frequency, low-information tokens, neglecting lower-frequency tokens crucial for specificity and informativeness in generated content. This paper introduces a novel loss function, Power-Law Decay Loss (PDL), specifically designed to optimize the finetuning process for text generation. The core motivation for PDL stems from observations in information theory and linguistics: the informativeness of a token is often inversely proportional to its frequency of occurrence. PDL re-weights the contribution of each token in the standard cross-entropy loss based on its frequency in the training corpus, following a power-law decay. Specifically, the weights for high-frequency tokens are reduced, while low-frequency, information-dense tokens are assigned higher weights. This mechanism guides the model during finetuning to focus more on learning and generating tokens that convey specific and unique information, thereby enhancing the quality, diversity, and informativeness of the generated text. We theoretically elaborate on the motivation and construction of PDL and discuss its potential applications and advantages across various text generation finetuning tasks, such as abstractive summarization, dialogue systems, and style transfer.
Recently, post hoc explanation methods have emerged to enhance model transparency by attributing model outputs to input features. However, these methods face challenges due to their specificity to certain neural network architectures and data modalities. Existing explainable artificial intelligence (XAI) frameworks have attempted to address these challenges but suffer from several limitations. These include limited flexibility to diverse model architectures and data modalities due to hard-coded implementations, a restricted number of supported XAI methods because of the requirements for layer-specific operations of attribution methods, and sub-optimal recommendations of explanations due to the lack of evaluation and optimization phases. Consequently, these limitations impede the adoption of XAI technology in real-world applications, making it difficult for practitioners to select the optimal explanation method for their domain. To address these limitations, we introduce \textbf{PnPXAI}, a universal XAI framework that supports diverse data modalities and neural network models in a Plug-and-Play (PnP) manner. PnPXAI automatically detects model architectures, recommends applicable explanation methods, and optimizes hyperparameters for optimal explanations. We validate the framework's effectiveness through user surveys and showcase its versatility across various domains, including medicine and finance.
Background: There are many challenges and opportunities in the clinical deployment of AI tools in radiology. The current study describes a radiology software platform called NeoMedSys that can enable efficient deployment and refinements of AI models. We evaluated the feasibility and effectiveness of running NeoMedSys for three months in real-world clinical settings and focused on improvement performance of an in-house developed AI model (VIOLA-AI) designed for intracranial hemorrhage (ICH) detection. Methods: NeoMedSys integrates tools for deploying, testing, and optimizing AI models with a web-based medical image viewer, annotation system, and hospital-wide radiology information systems. A pragmatic investigation was deployed using clinical cases of patients presenting to the largest Emergency Department in Norway (site-1) with suspected traumatic brain injury (TBI) or patients with suspected stroke (site-2). We assessed ICH classification performance as VIOLA-AI encountered new data and underwent pre-planned model retraining. Performance metrics included sensitivity, specificity, accuracy, and the area under the receiver operating characteristic curve (AUC). Results: NeoMedSys facilitated iterative improvements in the AI model, significantly enhancing its diagnostic accuracy. Automated bleed detection and segmentation were reviewed in near real-time to facilitate re-training VIOLA-AI. The iterative refinement process yielded a marked improvement in classification sensitivity, rising to 90.3% (from 79.2%), and specificity that reached 89.3% (from 80.7%). The bleed detection ROC analysis for the entire sample demonstrated a high area-under-the-curve (AUC) of 0.949 (from 0.873). Model refinement stages were associated with notable gains, highlighting the value of real-time radiologist feedback.
Breast cancer is the most frequently diagnosed human cancer in the United States at present. Early detection is crucial for its successful treatment. X-ray mammography and digital breast tomosynthesis are currently the main methods for breast cancer screening. However, both have known limitations in terms of their sensitivity and specificity to breast cancers, while also frequently causing patient discomfort due to the requirement for breast compression. Breast computed tomography is a promising alternative, however, to obtain high-quality images, the X-ray dose needs to be sufficiently high. As the breast is highly radiosensitive, dose reduction is particularly important. Phase-contrast computed tomography (PCT) has been shown to produce higher-quality images at lower doses and has no need for breast compression. It is demonstrated in the present study that, when imaging full fresh mastectomy samples with PCT, deep learning-based image denoising can further reduce the radiation dose by a factor of 16 or more, without any loss of image quality. The image quality has been assessed both in terms of objective metrics, such as spatial resolution and contrast-to-noise ratio, as well as in an observer study by experienced medical imaging specialists and radiologists. This work was carried out in preparation for live patient PCT breast cancer imaging, initially at specialized synchrotron facilities.
Eye-tracking data has been shown to correlate with a user's knowledge level and query formulation behaviour. While previous work has focused primarily on eye gaze fixations for attention analysis, often requiring additional contextual information, our study investigates the memory-related cognitive dimension by relying solely on pupil dilation and gaze velocity to infer users' topic familiarity and query specificity without needing any contextual information. Using eye-tracking data collected via a lab user study (N=18), we achieved a Macro F1 score of 71.25% for predicting topic familiarity with a Gradient Boosting classifier, and a Macro F1 score of 60.54% with a k-nearest neighbours (KNN) classifier for query specificity. Furthermore, we developed a novel annotation guideline -- specifically tailored for question answering -- to manually classify queries as Specific or Non-specific. This study demonstrates the feasibility of eye-tracking to better understand topic familiarity and query specificity in search.
LLMs trained on massive datasets may inadvertently acquire sensitive information such as personal details and potentially harmful content. This risk is further heightened in multimodal LLMs as they integrate information from multiple modalities (image and text). Adversaries can exploit this knowledge through multimodal prompts to extract sensitive details. Evaluating how effectively MLLMs can forget such information (targeted unlearning) necessitates the creation of high-quality, well-annotated image-text pairs. While prior work on unlearning has focused on text, multimodal unlearning remains underexplored. To address this gap, we first introduce a multimodal unlearning benchmark, UnLOK-VQA (Unlearning Outside Knowledge VQA), as well as an attack-and-defense framework to evaluate methods for deleting specific multimodal knowledge from MLLMs. We extend a visual question-answering dataset using an automated pipeline that generates varying-proximity samples for testing generalization and specificity, followed by manual filtering for maintaining high quality. We then evaluate six defense objectives against seven attacks (four whitebox, three blackbox), including a novel whitebox method leveraging interpretability of hidden states. Our results show multimodal attacks outperform text- or image-only ones, and that the most effective defense removes answer information from internal model states. Additionally, larger models exhibit greater post-editing robustness, suggesting that scale enhances safety. UnLOK-VQA provides a rigorous benchmark for advancing unlearning in MLLMs.
Motivated by the emerging demand in the financial industry for the automatic analysis of unstructured and structured data at scale, Question Answering (QA) systems can provide lucrative and competitive advantages to companies by facilitating the decision making of financial advisers. Consequently, we propose a novel financial QA system using the transformer-based pre-trained BERT language model to address the limitations of data scarcity and language specificity in the financial domain. Our system focuses on financial non-factoid answer selection, which retrieves a set of passage-level texts and selects the most relevant as the answer. To increase efficiency, we formulate the answer selection task as a re-ranking problem, in which our system consists of an Answer Retriever using BM25, a simple information retrieval approach, to first return a list of candidate answers, and an Answer Re-ranker built with variants of pre-trained BERT language models to re-rank and select the most relevant answers. We investigate various learning, further pre-training, and fine-tuning approaches for BERT. Our experiments suggest that FinBERT-QA, a model built from applying the Transfer and Adapt further fine-tuning and pointwise learning approach, is the most effective, improving the state-of-the-art results of task 2 of the FiQA dataset by 16% on MRR, 17% on NDCG, and 21% on Precision@1.
While deep learning has shown strong performance in musculoskeletal imaging, existing work has largely focused on pathologies where diagnosis is not a clinical challenge, leaving more difficult problems underexplored, such as detecting Bankart lesions (anterior-inferior glenoid labral tears) on standard MRIs. Diagnosing these lesions is challenging due to their subtle imaging features, often leading to reliance on invasive MRI arthrograms (MRAs). This study introduces ScopeMRI, the first publicly available, expert-annotated dataset for shoulder pathologies, and presents a deep learning (DL) framework for detecting Bankart lesions on both standard MRIs and MRAs. ScopeMRI includes 586 shoulder MRIs (335 standard, 251 MRAs) from 558 patients who underwent arthroscopy. Ground truth labels were derived from intraoperative findings, the gold standard for diagnosis. Separate DL models for MRAs and standard MRIs were trained using a combination of CNNs and transformers. Predictions from sagittal, axial, and coronal views were ensembled to optimize performance. The models were evaluated on a 20% hold-out test set (117 MRIs: 46 MRAs, 71 standard MRIs). The models achieved an AUC of 0.91 and 0.93, sensitivity of 83% and 94%, and specificity of 91% and 86% for standard MRIs and MRAs, respectively. Notably, model performance on non-invasive standard MRIs matched or surpassed radiologists interpreting MRAs. External validation demonstrated initial generalizability across imaging protocols. This study demonstrates that DL models can achieve radiologist-level diagnostic performance on standard MRIs, reducing the need for invasive MRAs. By releasing ScopeMRI and a modular codebase for training and evaluating deep learning models on 3D medical imaging data, we aim to accelerate research in musculoskeletal imaging and support the development of new datasets for clinically challenging diagnostic tasks.
The current study describes a cost-effective method for adapting large language models (LLMs) for academic advising with study-abroad contexts in mind and for application in low-resource methods for acculturation. With the Mistral-7B-Instruct model applied with a Low-Rank Adaptation (LoRA) method and a 4-bit quantization method, the model underwent training in two distinct stages related to this study's purpose to enhance domain specificity while maintaining computational efficiency. In Phase 1, the model was conditioned with a synthetic dataset via the Gemini Pro API, and in Phase 2, it was trained with manually curated datasets from the StudyAbroadGPT project to achieve enhanced, contextualized responses. Technical innovations entailed memory-efficient quantization, parameter-efficient adaptation, and continuous training analytics via Weights & Biases. After training, this study demonstrated a reduction in training loss by 52.7%, 92% accuracy in domain-specific recommendations, achieved 95% markdown-based formatting support, and a median run-rate of 100 samples per second on off-the-shelf GPU equipment. These findings support the effective application of instruction-tuned LLMs within educational advisers, especially in low-resource institutional scenarios. Limitations included decreased generalizability and the application of a synthetically generated dataset, but this framework is scalable for adding new multilingual-augmented and real-time academic advising processes. Future directions may include plans for the integration of retrieval-augmented generation, applying dynamic quantization routines, and connecting to real-time academic databases to increase adaptability and accuracy.
The rapid growth of video-text data presents challenges in storage and computation during training. Online learning, which processes streaming data in real-time, offers a promising solution to these issues while also allowing swift adaptations in scenarios demanding real-time responsiveness. One strategy to enhance the efficiency and effectiveness of learning involves identifying and prioritizing data that enhances performance on target downstream tasks. We propose Relevance and Specificity-based online filtering framework (ReSpec) that selects data based on four criteria: (i) modality alignment for clean data, (ii) task relevance for target focused data, (iii) specificity for informative and detailed data, and (iv) efficiency for low-latency processing. Relevance is determined by the probabilistic alignment of incoming data with downstream tasks, while specificity employs the distance to a root embedding representing the least specific data as an efficient proxy for informativeness. By establishing reference points from target task data, ReSpec filters incoming data in real-time, eliminating the need for extensive storage and compute. Evaluating on large-scale datasets WebVid2M and VideoCC3M, ReSpec attains state-of-the-art performance on five zeroshot video retrieval tasks, using as little as 5% of the data while incurring minimal compute. The source code is available at https://github.com/cdjkim/ReSpec.