Daily Papers

The whole slide image (WSI) classification is often formulated as a multiple instance learning (MIL) problem. Since the positive tissue is only a small fraction of the gigapixel WSI, existing MIL methods intuitively focus on identifying salient instances via attention mechanisms. However, this leads to a bias towards easy-to-classify instances while neglecting hard-to-classify instances. Some literature has revealed that hard examples are beneficial for modeling a discriminative boundary accurately. By applying such an idea at the instance level, we elaborate a novel MIL framework with masked hard instance mining (MHIM-MIL), which uses a Siamese structure (Teacher-Student) with a consistency constraint to explore the potential hard instances. With several instance masking strategies based on attention scores, MHIM-MIL employs a momentum teacher to implicitly mine hard instances for training the student model, which can be any attention-based MIL model. This counter-intuitive strategy essentially enables the student to learn a better discriminating boundary. Moreover, the student is used to update the teacher with an exponential moving average (EMA), which in turn identifies new hard instances for subsequent training iterations and stabilizes the optimization. Experimental results on the CAMELYON-16 and TCGA Lung Cancer datasets demonstrate that MHIM-MIL outperforms other latest methods in terms of performance and training cost. The code is available at: https://github.com/DearCaat/MHIM-MIL.

Whole Slide Image (WSI) classification with multiple instance learning (MIL) in digital pathology faces significant computational challenges. Current methods mostly rely on extensive self-supervised learning (SSL) for satisfactory performance, requiring long training periods and considerable computational resources. At the same time, no pre-training affects performance due to domain shifts from natural images to WSIs. We introduce Snuffy architecture, a novel MIL-pooling method based on sparse transformers that mitigates performance loss with limited pre-training and enables continual few-shot pre-training as a competitive option. Our sparsity pattern is tailored for pathology and is theoretically proven to be a universal approximator with the tightest probabilistic sharp bound on the number of layers for sparse transformers, to date. We demonstrate Snuffy's effectiveness on CAMELYON16 and TCGA Lung cancer datasets, achieving superior WSI and patch-level accuracies. The code is available on https://github.com/jafarinia/snuffy.

Recently, intelligent analysis of lung nodules with the assistant of computer aided detection (CAD) techniques can improve the accuracy rate of lung cancer diagnosis. However, existing CAD systems and pulmonary datasets mainly focus on Computed Tomography (CT) images from one single period, while ignoring the cross spatio-temporal features associated with the progression of nodules contained in imaging data from various captured periods of lung cancer. If the evolution patterns of nodules across various periods in the patients' CT sequences can be explored, it will play a crucial role in guiding the precise screening identification of lung cancer. Therefore, a cross spatio-temporal lung nodule dataset with pathological information for nodule identification and diagnosis is constructed, which contains 328 CT sequences and 362 annotated nodules from 109 patients. This comprehensive database is intended to drive research in the field of CAD towards more practical and robust methods, and also contribute to the further exploration of precision medicine related field. To ensure patient confidentiality, we have removed sensitive information from the dataset.

Recently, Computer-Aided Diagnosis (CAD) systems have emerged as indispensable tools in clinical diagnostic workflows, significantly alleviating the burden on radiologists. Nevertheless, despite their integration into clinical settings, CAD systems encounter limitations. Specifically, while CAD systems can achieve high performance in the detection of lung nodules, they face challenges in accurately predicting multiple cancer types. This limitation can be attributed to the scarcity of publicly available datasets annotated with expert-level cancer type information. This research aims to bridge this gap by providing publicly accessible datasets and reliable tools for medical diagnosis, facilitating a finer categorization of different types of lung diseases so as to offer precise treatment recommendations. To achieve this objective, we curated a diverse dataset of lung Computed Tomography (CT) images, comprising 330 annotated nodules (nodules are labeled as bounding boxes) from 95 distinct patients. The quality of the dataset was evaluated using a variety of classical classification and detection models, and these promising results demonstrate that the dataset has a feasible application and further facilitate intelligent auxiliary diagnosis.

With an estimated 160,000 deaths in 2018, lung cancer is the most common cause of cancer death in the United States. Lung cancer CT screening has been shown to reduce mortality by up to 40% and is now included in US screening guidelines. Reducing the high error rates in lung cancer screening is imperative because of the high clinical and financial costs caused by diagnosis mistakes. Despite the use of standards for radiological diagnosis, persistent inter-grader variability and incomplete characterization of comprehensive imaging findings remain as limitations of current methods. These limitations suggest opportunities for more sophisticated systems to improve performance and inter-reader consistency. In this report, we reproduce a state-of-the-art deep learning algorithm for lung cancer risk prediction. Our model predicts malignancy probability and risk bucket classification from lung CT studies. This allows for risk categorization of patients being screened and suggests the most appropriate surveillance and management. Combining our solution high accuracy, consistency and fully automated nature, our approach may enable highly efficient screening procedures and accelerate the adoption of lung cancer screening.

This paper addresses complex challenges in histopathological image analysis through three key contributions. Firstly, it introduces a fast patch selection method, FPS, for whole-slide image (WSI) analysis, significantly reducing computational cost while maintaining accuracy. Secondly, it presents PathDino, a lightweight histopathology feature extractor with a minimal configuration of five Transformer blocks and only 9 million parameters, markedly fewer than alternatives. Thirdly, it introduces a rotation-agnostic representation learning paradigm using self-supervised learning, effectively mitigating overfitting. We also show that our compact model outperforms existing state-of-the-art histopathology-specific vision transformers on 12 diverse datasets, including both internal datasets spanning four sites (breast, liver, skin, and colorectal) and seven public datasets (PANDA, CAMELYON16, BRACS, DigestPath, Kather, PanNuke, and WSSS4LUAD). Notably, even with a training dataset of 6 million histopathology patches from The Cancer Genome Atlas (TCGA), our approach demonstrates an average 8.5% improvement in patch-level majority vote performance. These contributions provide a robust framework for enhancing image analysis in digital pathology, rigorously validated through extensive evaluation. Project Page: https://rhazeslab.github.io/PathDino-Page/

Feature vectors provided by pre-trained deep artificial neural networks have become a dominant source for image representation in recent literature. Their contribution to the performance of image analysis can be improved through finetuning. As an ultimate solution, one might even train a deep network from scratch with the domain-relevant images, a highly desirable option which is generally impeded in pathology by lack of labeled images and the computational expense. In this study, we propose a new network, namely KimiaNet, that employs the topology of the DenseNet with four dense blocks, fine-tuned and trained with histopathology images in different configurations. We used more than 240,000 image patches with 1000x1000 pixels acquired at 20x magnification through our proposed "highcellularity mosaic" approach to enable the usage of weak labels of 7,126 whole slide images of formalin-fixed paraffin-embedded human pathology samples publicly available through the The Cancer Genome Atlas (TCGA) repository. We tested KimiaNet using three public datasets, namely TCGA, endometrial cancer images, and colorectal cancer images by evaluating the performance of search and classification when corresponding features of different networks are used for image representation. As well, we designed and trained multiple convolutional batch-normalized ReLU (CBR) networks. The results show that KimiaNet provides superior results compared to the original DenseNet and smaller CBR networks when used as feature extractor to represent histopathology images.

To improve the prognosis of patients suffering from pulmonary diseases, such as lung cancer, early diagnosis and treatment are crucial. The analysis of CT images is invaluable for diagnosis, whereas high quality segmentation of the airway tree are required for intervention planning and live guidance during bronchoscopy. Recently, the Multi-domain Airway Tree Modeling (ATM'22) challenge released a large dataset, both enabling training of deep-learning based models and bringing substantial improvement of the state-of-the-art for the airway segmentation task. However, the ATM'22 dataset includes few patients with severe pathologies affecting the airway tree anatomy. In this study, we introduce a new public benchmark dataset (AeroPath), consisting of 27 CT images from patients with pathologies ranging from emphysema to large tumors, with corresponding trachea and bronchi annotations. Second, we present a multiscale fusion design for automatic airway segmentation. Models were trained on the ATM'22 dataset, tested on the AeroPath dataset, and further evaluated against competitive open-source methods. The same performance metrics as used in the ATM'22 challenge were used to benchmark the different considered approaches. Lastly, an open web application is developed, to easily test the proposed model on new data. The results demonstrated that our proposed architecture predicted topologically correct segmentations for all the patients included in the AeroPath dataset. The proposed method is robust and able to handle various anomalies, down to at least the fifth airway generation. In addition, the AeroPath dataset, featuring patients with challenging pathologies, will contribute to development of new state-of-the-art methods. The AeroPath dataset and the web application are made openly available.

Lung cancer stands as the preeminent cause of cancer-related mortality globally. Prompt and precise diagnosis, coupled with effective treatment, is imperative to reduce the fatality rates associated with this formidable disease. This study introduces a cutting-edge deep learning framework for the classification of lung cancer from CT scan imagery. The research encompasses a suite of image pre-processing strategies, notably Canny edge detection, and wavelet transformations, which precede the extraction of salient features and subsequent classification via a Multi-Layer Perceptron (MLP). The optimization process is further refined using the Dragonfly Algorithm (DA). The methodology put forth has attained an impressive training and testing accuracy of 99.82\%, underscoring its efficacy and reliability in the accurate diagnosis of lung cancer.

Understanding how deep learning models predict oncology patient risk can provide critical insights into disease progression, support clinical decision-making, and pave the way for trustworthy and data-driven precision medicine. Building on recent advances in the spatial modeling of the tumor microenvironment using graph neural networks, we present an explainable cell graph (xCG) approach for survival prediction. We validate our model on a public cohort of imaging mass cytometry (IMC) data for 416 cases of lung adenocarcinoma. We explain survival predictions in terms of known phenotypes on the cell level by computing risk attributions over cell graphs, for which we propose an efficient grid-based layer-wise relevance propagation (LRP) method. Our ablation studies highlight the importance of incorporating the cancer stage and model ensembling to improve the quality of risk estimates. Our xCG method, together with the IMC data, is made publicly available to support further research.

Survival risk stratification is an important step in clinical decision making for breast cancer management. We propose a novel deep learning approach for this purpose by integrating histopathological imaging, genetic and clinical data. It employs vision transformers, specifically the MaxViT model, for image feature extraction, and self-attention to capture intricate image relationships at the patient level. A dual cross-attention mechanism fuses these features with genetic data, while clinical data is incorporated at the final layer to enhance predictive accuracy. Experiments on the public TCGA-BRCA dataset show that our model, trained using the negative log likelihood loss function, can achieve superior performance with a mean C-index of 0.64, surpassing existing methods. This advancement facilitates tailored treatment strategies, potentially leading to improved patient outcomes.

To investigate whether the pleurae, airways and vessels surrounding a nodule on non-contrast computed tomography (CT) can discriminate benign and malignant pulmonary nodules. The LIDC-IDRI dataset, one of the largest publicly available CT database, was exploited for study. A total of 1556 nodules from 694 patients were involved in statistical analysis, where nodules with average scorings <3 and >3 were respectively denoted as benign and malignant. Besides, 339 nodules from 113 patients with diagnosis ground-truth were independently evaluated. Computer algorithms were developed to segment pulmonary structures and quantify the distances to pleural surface, airways and vessels, as well as the counting number and normalized volume of airways and vessels near a nodule. Odds ratio (OR) and Chi-square (\chi^2) testing were performed to demonstrate the correlation between features of surrounding structures and nodule malignancy. A non-parametric receiver operating characteristic (ROC) analysis was conducted in logistic regression to evaluate discrimination ability of each structure. For benign and malignant groups, the average distances from nodules to pleural surface, airways and vessels are respectively (6.56, 5.19), (37.08, 26.43) and (1.42, 1.07) mm. The correlation between nodules and the counting number of airways and vessels that contact or project towards nodules are respectively (OR=22.96, \chi^2=105.04) and (OR=7.06, \chi^2=290.11). The correlation between nodules and the volume of airways and vessels are (OR=9.19, \chi^2=159.02) and (OR=2.29, \chi^2=55.89). The areas-under-curves (AUCs) for pleurae, airways and vessels are respectively 0.5202, 0.6943 and 0.6529. Our results show that malignant nodules are often surrounded by more pulmonary structures compared with benign ones, suggesting that features of these structures could be viewed as lung cancer biomarkers.

Background: Cancer remains one of the leading causes of morbidity and mortality worldwide. Comprehensive datasets that combine histopathological images with genetic and survival data across various tumour sites are essential for advancing computational pathology and personalised medicine. Results: We present SurGen, a dataset comprising 1,020 H&E-stained whole slide images (WSIs) from 843 colorectal cancer cases. The dataset includes detailed annotations for key genetic mutations (KRAS, NRAS, BRAF) and mismatch repair status, as well as survival data for 426 cases. To demonstrate SurGen's practical utility, we conducted a proof-of-concept machine learning experiment predicting mismatch repair status from the WSIs, achieving a test AUROC of 0.8316. These preliminary results underscore the dataset's potential to facilitate research in biomarker discovery, prognostic modelling, and advanced machine learning applications in colorectal cancer. Conclusions: SurGen offers a valuable resource for the scientific community, enabling studies that require high-quality WSIs linked with comprehensive clinical and genetic information on colorectal cancer. Our initial findings affirm the dataset's capacity to advance diagnostic precision and foster the development of personalised treatment strategies in colorectal oncology. Data available online at https://doi.org/10.6019/S-BIAD1285.

Metadata are general characteristics of the data in a well-curated and condensed format, and have been proven to be useful for decision making, knowledge discovery, and also heterogeneous data organization of biobank. Among all data types in the biobank, pathology is the key component of the biobank and also serves as the gold standard of diagnosis. To maximize the utility of biobank and allow the rapid progress of biomedical science, it is essential to organize the data with well-populated pathology metadata. However, manual annotation of such information is tedious and time-consuming. In the study, we develop a multimodal multitask learning framework to predict four major slide-level metadata of pathology images. The framework learns generalizable representations across tissue slides, pathology reports, and case-level structured data. We demonstrate improved performance across all four tasks with the proposed method compared to a single modal single task baseline on two test sets, one external test set from a distinct data source (TCGA) and one internal held-out test set (TTH). In the test sets, the performance improvements on the averaged area under receiver operating characteristic curve across the four tasks are 16.48% and 9.05% on TCGA and TTH, respectively. Such pathology metadata prediction system may be adopted to mitigate the effort of expert annotation and ultimately accelerate the data-driven research by better utilization of the pathology biobank.

Pretraining a deep learning model on large image datasets is a standard step before fine-tuning the model on small targeted datasets. The large dataset is usually general images (e.g. imagenet2012) while the small dataset can be specialized datasets that have different distributions from the large dataset. However, this 'large-to-small' strategy is not well-validated when the large dataset is specialized and has a similar distribution to small datasets. We newly compiled three hematoxylin and eosin-stained image datasets, one large (PTCGA200) and two magnification-adjusted small datasets (PCam200 and segPANDA200). Major deep learning models were trained with supervised and self-supervised learning methods and fine-tuned on the small datasets for tumor classification and tissue segmentation benchmarks. ResNet50 pretrained with MoCov2, SimCLR, and BYOL on PTCGA200 was better than imagenet2012 pretraining when fine-tuned on PTCGA200 (accuracy of 83.94%, 86.41%, 84.91%, and 82.72%, respectively). ResNet50 pre-trained on PTCGA200 with MoCov2 exceeded the COCOtrain2017-pretrained baseline and was the best in ResNet50 for the tissue segmentation benchmark (mIoU of 63.53% and 63.22%). We found re-training imagenet-pretrained models (ResNet50, BiT-M-R50x1, and ViT-S/16) on PTCGA200 improved downstream benchmarks.

The field of Machine Learning, a subset of Artificial Intelligence, has led to remarkable advancements in many areas, including medicine. Machine Learning algorithms require large datasets to train computer models successfully. Although there are medical image datasets available, more image datasets are needed from a variety of medical entities, especially cancer pathology. Even more scarce are ML-ready image datasets. To address this need, we created an image dataset (LC25000) with 25,000 color images in 5 classes. Each class contains 5,000 images of the following histologic entities: colon adenocarcinoma, benign colonic tissue, lung adenocarcinoma, lung squamous cell carcinoma, and benign lung tissue. All images are de-identified, HIPAA compliant, validated, and freely available for download to AI researchers.

Considering the increased workload in pathology laboratories today, automated tools such as artificial intelligence models can help pathologists with their tasks and ease the workload. In this paper, we are proposing a segmentation model (DRU-Net) that can provide a delineation of human non-small cell lung carcinomas and an augmentation method that can improve classification results. The proposed model is a fused combination of truncated pre-trained DenseNet201 and ResNet101V2 as a patch-wise classifier followed by a lightweight U-Net as a refinement model. We have used two datasets (Norwegian Lung Cancer Biobank and Haukeland University Hospital lung cancer cohort) to create our proposed model. The DRU-Net model achieves an average of 0.91 Dice similarity coefficient. The proposed spatial augmentation method (multi-lens distortion) improved the network performance by 3%. Our findings show that choosing image patches that specifically include regions of interest leads to better results for the patch-wise classifier compared to other sampling methods. The qualitative analysis showed that the DRU-Net model is generally successful in detecting the tumor. On the test set, some of the cases showed areas of false positive and false negative segmentation in the periphery, particularly in tumors with inflammatory and reactive changes.

Purpose: Automating tasks such as lung tumor localization and segmentation in radiological images can free valuable time for radiologists and other clinical personnel. Convolutional neural networks may be suited for such tasks, but require substantial amounts of labeled data to train. Obtaining labeled data is a challenge, especially in the medical domain. Methods: This paper investigates the use of a teacher-student design to utilize datasets with different types of supervision to train an automatic model performing pulmonary tumor segmentation on computed tomography images. The framework consists of two models: the student that performs end-to-end automatic tumor segmentation and the teacher that supplies the student additional pseudo-annotated data during training. Results: Using only a small proportion of semantically labeled data and a large number of bounding box annotated data, we achieved competitive performance using a teacher-student design. Models trained on larger amounts of semantic annotations did not perform better than those trained on teacher-annotated data. Conclusions: Our results demonstrate the potential of utilizing teacher-student designs to reduce the annotation load, as less supervised annotation schemes may be performed, without any real degradation in segmentation accuracy.

Magnetic resonance imaging (MRI) is a cornerstone of modern medical imaging. However, long image acquisition times, the need for qualitative expert analysis, and the lack of (and difficulty extracting) quantitative indicators that are sensitive to tissue health have curtailed widespread clinical and research studies. While recent machine learning methods for MRI reconstruction and analysis have shown promise for reducing this burden, these techniques are primarily validated with imperfect image quality metrics, which are discordant with clinically-relevant measures that ultimately hamper clinical deployment and clinician trust. To mitigate this challenge, we present the Stanford Knee MRI with Multi-Task Evaluation (SKM-TEA) dataset, a collection of quantitative knee MRI (qMRI) scans that enables end-to-end, clinically-relevant evaluation of MRI reconstruction and analysis tools. This 1.6TB dataset consists of raw-data measurements of ~25,000 slices (155 patients) of anonymized patient MRI scans, the corresponding scanner-generated DICOM images, manual segmentations of four tissues, and bounding box annotations for sixteen clinically relevant pathologies. We provide a framework for using qMRI parameter maps, along with image reconstructions and dense image labels, for measuring the quality of qMRI biomarker estimates extracted from MRI reconstruction, segmentation, and detection techniques. Finally, we use this framework to benchmark state-of-the-art baselines on this dataset. We hope our SKM-TEA dataset and code can enable a broad spectrum of research for modular image reconstruction and image analysis in a clinically informed manner. Dataset access, code, and benchmarks are available at https://github.com/StanfordMIMI/skm-tea.

The emerging area of computational pathology (CPath) is ripe ground for the application of deep learning (DL) methods to healthcare due to the sheer volume of raw pixel data in whole-slide images (WSIs) of cancerous tissue slides. However, it is imperative for the DL algorithms relying on nuclei-level details to be able to cope with data from `the clinical wild', which tends to be quite challenging. We study, and extend recently released PanNuke dataset consisting of ~200,000 nuclei categorized into 5 clinically important classes for the challenging tasks of segmenting and classifying nuclei in WSIs. Previous pan-cancer datasets consisted of only up to 9 different tissues and up to 21,000 unlabeled nuclei and just over 24,000 labeled nuclei with segmentation masks. PanNuke consists of 19 different tissue types that have been semi-automatically annotated and quality controlled by clinical pathologists, leading to a dataset with statistics similar to the clinical wild and with minimal selection bias. We study the performance of segmentation and classification models when applied to the proposed dataset and demonstrate the application of models trained on PanNuke to whole-slide images. We provide comprehensive statistics about the dataset and outline recommendations and research directions to address the limitations of existing DL tools when applied to real-world CPath applications.

With the rapid advances in high-throughput sequencing technologies, the focus of survival analysis has shifted from examining clinical indicators to incorporating genomic profiles with pathological images. However, existing methods either directly adopt a straightforward fusion of pathological features and genomic profiles for survival prediction, or take genomic profiles as guidance to integrate the features of pathological images. The former would overlook intrinsic cross-modal correlations. The latter would discard pathological information irrelevant to gene expression. To address these issues, we present a Cross-Modal Translation and Alignment (CMTA) framework to explore the intrinsic cross-modal correlations and transfer potential complementary information. Specifically, we construct two parallel encoder-decoder structures for multi-modal data to integrate intra-modal information and generate cross-modal representation. Taking the generated cross-modal representation to enhance and recalibrate intra-modal representation can significantly improve its discrimination for comprehensive survival analysis. To explore the intrinsic crossmodal correlations, we further design a cross-modal attention module as the information bridge between different modalities to perform cross-modal interactions and transfer complementary information. Our extensive experiments on five public TCGA datasets demonstrate that our proposed framework outperforms the state-of-the-art methods.

We present a labeled large-scale, high resolution chest x-ray dataset for the automated exploration of medical images along with their associated reports. This dataset includes more than 160,000 images obtained from 67,000 patients that were interpreted and reported by radiologists at Hospital San Juan Hospital (Spain) from 2009 to 2017, covering six different position views and additional information on image acquisition and patient demography. The reports were labeled with 174 different radiographic findings, 19 differential diagnoses and 104 anatomic locations organized as a hierarchical taxonomy and mapped onto standard Unified Medical Language System (UMLS) terminology. Of these reports, 27% were manually annotated by trained physicians and the remaining set was labeled using a supervised method based on a recurrent neural network with attention mechanisms. The labels generated were then validated in an independent test set achieving a 0.93 Micro-F1 score. To the best of our knowledge, this is one of the largest public chest x-ray database suitable for training supervised models concerning radiographs, and the first to contain radiographic reports in Spanish. The PadChest dataset can be downloaded from http://bimcv.cipf.es/bimcv-projects/padchest/.

Vision Language Models (VLMs) like CLIP have attracted substantial attention in pathology, serving as backbones for applications such as zero-shot image classification and Whole Slide Image (WSI) analysis. Additionally, they can function as vision encoders when combined with large language models (LLMs) to support broader capabilities. Current efforts to train pathology VLMs rely on pathology image-text pairs from platforms like PubMed, YouTube, and Twitter, which provide limited, unscalable data with generally suboptimal image quality. In this work, we leverage large-scale WSI datasets like TCGA to extract numerous high-quality image patches. We then train a large multimodal model to generate captions for these images, creating PathGen-1.6M, a dataset containing 1.6 million high-quality image-caption pairs. Our approach involves multiple agent models collaborating to extract representative WSI patches, generating and refining captions to obtain high-quality image-text pairs. Extensive experiments show that integrating these generated pairs with existing datasets to train a pathology-specific CLIP model, PathGen-CLIP, significantly enhances its ability to analyze pathological images, with substantial improvements across nine pathology-related zero-shot image classification tasks and three whole-slide image tasks. Furthermore, we construct 200K instruction-tuning data based on PathGen-1.6M and integrate PathGen-CLIP with the Vicuna LLM to create more powerful multimodal models through instruction tuning. Overall, we provide a scalable pathway for high-quality data generation in pathology, paving the way for next-generation general pathology models.

With over 85 million CT scans performed annually in the United States, creating tumor-related reports is a challenging and time-consuming task for radiologists. To address this need, we present RadGPT, an Anatomy-Aware Vision-Language AI Agent for generating detailed reports from CT scans. RadGPT first segments tumors, including benign cysts and malignant tumors, and their surrounding anatomical structures, then transforms this information into both structured reports and narrative reports. These reports provide tumor size, shape, location, attenuation, volume, and interactions with surrounding blood vessels and organs. Extensive evaluation on unseen hospitals shows that RadGPT can produce accurate reports, with high sensitivity/specificity for small tumor (<2 cm) detection: 80/73% for liver tumors, 92/78% for kidney tumors, and 77/77% for pancreatic tumors. For large tumors, sensitivity ranges from 89% to 97%. The results significantly surpass the state-of-the-art in abdominal CT report generation. RadGPT generated reports for 17 public datasets. Through radiologist review and refinement, we have ensured the reports' accuracy, and created the first publicly available image-text 3D medical dataset, comprising over 1.8 million text tokens and 2.7 million images from 9,262 CT scans, including 2,947 tumor scans/reports of 8,562 tumor instances. Our reports can: (1) localize tumors in eight liver sub-segments and three pancreatic sub-segments annotated per-voxel; (2) determine pancreatic tumor stage (T1-T4) in 260 reports; and (3) present individual analyses of multiple tumors--rare in human-made reports. Importantly, 948 of the reports are for early-stage tumors.

The development of successful artificial intelligence models for chest X-ray analysis relies on large, diverse datasets with high-quality annotations. While several databases of chest X-ray images have been released, most include disease diagnosis labels but lack detailed pixel-level anatomical segmentation labels. To address this gap, we introduce an extensive chest X-ray multi-center segmentation dataset with uniform and fine-grain anatomical annotations for images coming from six well-known publicly available databases: CANDID-PTX, ChestX-ray8, Chexpert, MIMIC-CXR-JPG, Padchest, and VinDr-CXR, resulting in 676,803 segmentation masks. Our methodology utilizes the HybridGNet model to ensure consistent and high-quality segmentations across all datasets. Rigorous validation, including expert physician evaluation and automatic quality control, was conducted to validate the resulting masks. Additionally, we provide individualized quality indices per mask and an overall quality estimation per dataset. This dataset serves as a valuable resource for the broader scientific community, streamlining the development and assessment of innovative methodologies in chest X-ray analysis. The CheXmask dataset is publicly available at: https://physionet.org/content/chexmask-cxr-segmentation-data/.

Chest radiography is an extremely powerful imaging modality, allowing for a detailed inspection of a patient's thorax, but requiring specialized training for proper interpretation. With the advent of high performance general purpose computer vision algorithms, the accurate automated analysis of chest radiographs is becoming increasingly of interest to researchers. However, a key challenge in the development of these techniques is the lack of sufficient data. Here we describe MIMIC-CXR-JPG v2.0.0, a large dataset of 377,110 chest x-rays associated with 227,827 imaging studies sourced from the Beth Israel Deaconess Medical Center between 2011 - 2016. Images are provided with 14 labels derived from two natural language processing tools applied to the corresponding free-text radiology reports. MIMIC-CXR-JPG is derived entirely from the MIMIC-CXR database, and aims to provide a convenient processed version of MIMIC-CXR, as well as to provide a standard reference for data splits and image labels. All images have been de-identified to protect patient privacy. The dataset is made freely available to facilitate and encourage a wide range of research in medical computer vision.

Robust and accurate detection and segmentation of heterogenous tumors appearing in different anatomical organs with supervised methods require large-scale labeled datasets covering all possible types of diseases. Due to the unavailability of such rich datasets and the high cost of annotations, unsupervised anomaly detection (UAD) methods have been developed aiming to detect the pathologies as deviation from the normality by utilizing the unlabeled healthy image data. However, developed UAD models are often trained with an incomplete distribution of healthy anatomies and have difficulties in preserving anatomical constraints. This work intends to, first, propose a robust inpainting model to learn the details of healthy anatomies and reconstruct high-resolution images by preserving anatomical constraints. Second, we propose an autoinpainting pipeline to automatically detect tumors, replace their appearance with the learned healthy anatomies, and based on that segment the tumoral volumes in a purely unsupervised fashion. Three imaging datasets, including PET, CT, and PET-CT scans of lung tumors and head and neck tumors, are studied as benchmarks for evaluation. Experimental results demonstrate the significant superiority of the proposed method over a wide range of state-of-the-art UAD methods. Moreover, the unsupervised method we propose produces comparable results to a robust supervised segmentation method when applied to multimodal images.

Prediction sets capture uncertainty by predicting sets of labels rather than individual labels, enabling downstream decisions to conservatively account for all plausible outcomes. Conformal inference algorithms construct prediction sets guaranteed to contain the true label with high probability. These guarantees fail to hold in the face of distribution shift, which is precisely when reliable uncertainty quantification can be most useful. We propose a novel algorithm for constructing prediction sets with PAC guarantees in the label shift setting. This method estimates the predicted probabilities of the classes in a target domain, as well as the confusion matrix, then propagates uncertainty in these estimates through a Gaussian elimination algorithm to compute confidence intervals for importance weights. Finally, it uses these intervals to construct prediction sets. We evaluate our approach on five datasets: the CIFAR-10, ChestX-Ray and Entity-13 image datasets, the tabular CDC Heart dataset, and the AGNews text dataset. Our algorithm satisfies the PAC guarantee while producing smaller, more informative, prediction sets compared to several baselines.

The chest X-ray is one of the most commonly accessible radiological examinations for screening and diagnosis of many lung diseases. A tremendous number of X-ray imaging studies accompanied by radiological reports are accumulated and stored in many modern hospitals' Picture Archiving and Communication Systems (PACS). On the other side, it is still an open question how this type of hospital-size knowledge database containing invaluable imaging informatics (i.e., loosely labeled) can be used to facilitate the data-hungry deep learning paradigms in building truly large-scale high precision computer-aided diagnosis (CAD) systems. In this paper, we present a new chest X-ray database, namely "ChestX-ray8", which comprises 108,948 frontal-view X-ray images of 32,717 unique patients with the text-mined eight disease image labels (where each image can have multi-labels), from the associated radiological reports using natural language processing. Importantly, we demonstrate that these commonly occurring thoracic diseases can be detected and even spatially-located via a unified weakly-supervised multi-label image classification and disease localization framework, which is validated using our proposed dataset. Although the initial quantitative results are promising as reported, deep convolutional neural network based "reading chest X-rays" (i.e., recognizing and locating the common disease patterns trained with only image-level labels) remains a strenuous task for fully-automated high precision CAD systems. Data download link: https://nihcc.app.box.com/v/ChestXray-NIHCC

The gigapixel scale of whole slide images (WSIs) poses a challenge for histopathology multi-modal chatbots, requiring a global WSI analysis for diagnosis, compounding evidence from different WSI patches. Current visual instruction datasets, generated through large language models, focus on creating question/answer pairs for individual image patches, which may lack diagnostic capacity on their own in histopathology, further complicated by the absence of spatial grounding in histopathology image captions. To bridge this gap, we introduce Quilt-Instruct, a large-scale dataset of 107,131 histopathology-specific instruction question/answer pairs, that is collected by leveraging educational histopathology videos from YouTube, which provides spatial localization of captions by automatically extracting narrators' cursor movements. In addition, we provide contextual reasoning by extracting diagnosis and supporting facts from the entire video content to guide the extrapolative reasoning of GPT-4. Using Quilt-Instruct, we train Quilt-LLaVA, which can reason beyond the given single image patch, enabling diagnostic reasoning and the capability of spatial awareness. To evaluate Quilt-LLaVA, we propose a comprehensive evaluation dataset created from 985 images and 1283 human-generated question-answers. We also thoroughly evaluate Quilt-LLaVA using public histopathology datasets, where Quilt-LLaVA significantly outperforms SOTA by over 10% on relative GPT-4 score and 4% and 9% on open and closed set VQA. Our code, data, and model are publicly available at quilt-llava.github.io.

Extracting structured clinical information from free-text radiology reports can enable the use of radiology report information for a variety of critical healthcare applications. In our work, we present RadGraph, a dataset of entities and relations in full-text chest X-ray radiology reports based on a novel information extraction schema we designed to structure radiology reports. We release a development dataset, which contains board-certified radiologist annotations for 500 radiology reports from the MIMIC-CXR dataset (14,579 entities and 10,889 relations), and a test dataset, which contains two independent sets of board-certified radiologist annotations for 100 radiology reports split equally across the MIMIC-CXR and CheXpert datasets. Using these datasets, we train and test a deep learning model, RadGraph Benchmark, that achieves a micro F1 of 0.82 and 0.73 on relation extraction on the MIMIC-CXR and CheXpert test sets respectively. Additionally, we release an inference dataset, which contains annotations automatically generated by RadGraph Benchmark across 220,763 MIMIC-CXR reports (around 6 million entities and 4 million relations) and 500 CheXpert reports (13,783 entities and 9,908 relations) with mappings to associated chest radiographs. Our freely available dataset can facilitate a wide range of research in medical natural language processing, as well as computer vision and multi-modal learning when linked to chest radiographs.

The availability of large public datasets and the increased amount of computing power have shifted the interest of the medical community to high-performance algorithms. However, little attention is paid to the quality of the data and their annotations. High performance on benchmark datasets may be reported without considering possible shortcuts or artifacts in the data, besides, models are not tested on subpopulation groups. With this work, we aim to raise awareness about shortcuts problems. We validate previous findings, and present a case study on chest X-rays using two publicly available datasets. We share annotations for a subset of pneumothorax images with drains. We conclude with general recommendations for medical image classification.

The way in which data are shared can affect their utility and reusability. Here, we demonstrate how data that we had previously shared in bulk can be mobilized further through a knowledge graph that allows for much more granular exploration and interrogation. The original dataset is about the computational reproducibility of GitHub-hosted Jupyter notebooks associated with biomedical publications. It contains rich metadata about the publications, associated GitHub repositories and Jupyter notebooks, and the notebooks' reproducibility. We took this dataset, converted it into semantic triples and loaded these into a triple store to create a knowledge graph, FAIR Jupyter, that we made accessible via a web service. This enables granular data exploration and analysis through queries that can be tailored to specific use cases. Such queries may provide details about any of the variables from the original dataset, highlight relationships between them or combine some of the graph's content with materials from corresponding external resources. We provide a collection of example queries addressing a range of use cases in research and education. We also outline how sets of such queries can be used to profile specific content types, either individually or by class. We conclude by discussing how such a semantically enhanced sharing of complex datasets can both enhance their FAIRness, i.e., their findability, accessibility, interoperability, and reusability, and help identify and communicate best practices, particularly with regards to data quality, standardization, automation and reproducibility.

Multi-modality magnetic resonance imaging data with various sequences facilitate the early diagnosis, tumor segmentation, and disease staging in the management of nasopharyngeal carcinoma (NPC). The lack of publicly available, comprehensive datasets limits advancements in diagnosis, treatment planning, and the development of machine learning algorithms for NPC. Addressing this critical need, we introduce the first comprehensive NPC MRI dataset, encompassing MR axial imaging of 277 primary NPC patients. This dataset includes T1-weighted, T2-weighted, and contrast-enhanced T1-weighted sequences, totaling 831 scans. In addition to the corresponding clinical data, manually annotated and labeled segmentations by experienced radiologists offer high-quality data resources from untreated primary NPC.

Recent advances in multi-modal algorithms have driven and been driven by the increasing availability of large image-text datasets, leading to significant strides in various fields, including computational pathology. However, in most existing medical image-text datasets, the text typically provides high-level summaries that may not sufficiently describe sub-tile regions within a large pathology image. For example, an image might cover an extensive tissue area containing cancerous and healthy regions, but the accompanying text might only specify that this image is a cancer slide, lacking the nuanced details needed for in-depth analysis. In this study, we introduce STimage-1K4M, a novel dataset designed to bridge this gap by providing genomic features for sub-tile images. STimage-1K4M contains 1,149 images derived from spatial transcriptomics data, which captures gene expression information at the level of individual spatial spots within a pathology image. Specifically, each image in the dataset is broken down into smaller sub-image tiles, with each tile paired with 15,000-30,000 dimensional gene expressions. With 4,293,195 pairs of sub-tile images and gene expressions, STimage-1K4M offers unprecedented granularity, paving the way for a wide range of advanced research in multi-modal data analysis an innovative applications in computational pathology, and beyond.

Recent accelerations in multi-modal applications have been made possible with the plethora of image and text data available online. However, the scarcity of analogous data in the medical field, specifically in histopathology, has halted comparable progress. To enable similar representation learning for histopathology, we turn to YouTube, an untapped resource of videos, offering 1,087 hours of valuable educational histopathology videos from expert clinicians. From YouTube, we curate Quilt: a large-scale vision-language dataset consisting of 768,826 image and text pairs. Quilt was automatically curated using a mixture of models, including large language models, handcrafted algorithms, human knowledge databases, and automatic speech recognition. In comparison, the most comprehensive datasets curated for histopathology amass only around 200K samples. We combine Quilt with datasets from other sources, including Twitter, research papers, and the internet in general, to create an even larger dataset: Quilt-1M, with 1M paired image-text samples, marking it as the largest vision-language histopathology dataset to date. We demonstrate the value of Quilt-1M by fine-tuning a pre-trained CLIP model. Our model outperforms state-of-the-art models on both zero-shot and linear probing tasks for classifying new histopathology images across 13 diverse patch-level datasets of 8 different sub-pathologies and cross-modal retrieval tasks.

The performance on deep learning is significantly affected by volume of training data. Models pre-trained from massive dataset such as ImageNet become a powerful weapon for speeding up training convergence and improving accuracy. Similarly, models based on large dataset are important for the development of deep learning in 3D medical images. However, it is extremely challenging to build a sufficiently large dataset due to difficulty of data acquisition and annotation in 3D medical imaging. We aggregate the dataset from several medical challenges to build 3DSeg-8 dataset with diverse modalities, target organs, and pathologies. To extract general medical three-dimension (3D) features, we design a heterogeneous 3D network called Med3D to co-train multi-domain 3DSeg-8 so as to make a series of pre-trained models. We transfer Med3D pre-trained models to lung segmentation in LIDC dataset, pulmonary nodule classification in LIDC dataset and liver segmentation on LiTS challenge. Experiments show that the Med3D can accelerate the training convergence speed of target 3D medical tasks 2 times compared with model pre-trained on Kinetics dataset, and 10 times compared with training from scratch as well as improve accuracy ranging from 3% to 20%. Transferring our Med3D model on state-the-of-art DenseASPP segmentation network, in case of single model, we achieve 94.6\% Dice coefficient which approaches the result of top-ranged algorithms on the LiTS challenge.

The recent introduction of synthetic correlated diffusion (CDI^s) imaging has demonstrated significant potential in the realm of clinical decision support for prostate cancer (PCa). CDI^s is a new form of magnetic resonance imaging (MRI) designed to characterize tissue characteristics through the joint correlation of diffusion signal attenuation across different Brownian motion sensitivities. Despite the performance improvement, the CDI^s data for PCa has not been previously made publicly available. In our commitment to advance research efforts for PCa, we introduce Cancer-Net PCa-Data, an open-source benchmark dataset of volumetric CDI^s imaging data of PCa patients. Cancer-Net PCa-Data consists of CDI^s volumetric images from a patient cohort of 200 patient cases, along with full annotations (gland masks, tumor masks, and PCa diagnosis for each tumor). We also analyze the demographic and label region diversity of Cancer-Net PCa-Data for potential biases. Cancer-Net PCa-Data is the first-ever public dataset of CDI^s imaging data for PCa, and is a part of the global open-source initiative dedicated to advancement in machine learning and imaging research to aid clinicians in the global fight against cancer.

Quantitative tools are increasingly appealing for decision support in healthcare, driven by the growing capabilities of advanced AI systems. However, understanding the predictive uncertainties surrounding a tool's output is crucial for decision-makers to ensure reliable and transparent decisions. In this paper, we present a case study on pulmonary nodule detection for lung cancer screening, enhancing an advanced detection model with an uncertainty quantification technique called conformal risk control (CRC). We demonstrate that prediction sets with conformal guarantees are attractive measures of predictive uncertainty in the safety-critical healthcare domain, allowing end-users to achieve arbitrary validity by trading off false positives and providing formal statistical guarantees on model performance. Among ground-truth nodules annotated by at least three radiologists, our model achieves a sensitivity that is competitive with that generally achieved by individual radiologists, with a slight increase in false positives. Furthermore, we illustrate the risks of using off-the-shelve prediction models when faced with ontological uncertainty, such as when radiologists disagree on what constitutes the ground truth on pulmonary nodules.

Multiple Instance learning (MIL) models have been extensively used in pathology to predict biomarkers and risk-stratify patients from gigapixel-sized images. Machine learning problems in medical imaging often deal with rare diseases, making it important for these models to work in a label-imbalanced setting. In pathology images, there is another level of imbalance, where given a positively labeled Whole Slide Image (WSI), only a fraction of pixels within it contribute to the positive label. This compounds the severity of imbalance and makes imbalanced classification in pathology challenging. Furthermore, these imbalances can occur in out-of-distribution (OOD) datasets when the models are deployed in the real-world. We leverage the idea that decoupling feature and classifier learning can lead to improved decision boundaries for label imbalanced datasets. To this end, we investigate the integration of supervised contrastive learning with multiple instance learning (SC-MIL). Specifically, we propose a joint-training MIL framework in the presence of label imbalance that progressively transitions from learning bag-level representations to optimal classifier learning. We perform experiments with different imbalance settings for two well-studied problems in cancer pathology: subtyping of non-small cell lung cancer and subtyping of renal cell carcinoma. SC-MIL provides large and consistent improvements over other techniques on both in-distribution (ID) and OOD held-out sets across multiple imbalanced settings.

Polyps in the colon are widely known cancer precursors identified by colonoscopy. Whilst most polyps are benign, the polyp's number, size and surface structure are linked to the risk of colon cancer. Several methods have been developed to automate polyp detection and segmentation. However, the main issue is that they are not tested rigorously on a large multicentre purpose-built dataset, one reason being the lack of a comprehensive public dataset. As a result, the developed methods may not generalise to different population datasets. To this extent, we have curated a dataset from six unique centres incorporating more than 300 patients. The dataset includes both single frame and sequence data with 3762 annotated polyp labels with precise delineation of polyp boundaries verified by six senior gastroenterologists. To our knowledge, this is the most comprehensive detection and pixel-level segmentation dataset (referred to as PolypGen) curated by a team of computational scientists and expert gastroenterologists. The paper provides insight into data construction and annotation strategies, quality assurance, and technical validation. Our dataset can be downloaded from https://doi.org/10.7303/syn26376615.

In clinical radiology reports, doctors capture important information about the patient's health status. They convey their observations from raw medical imaging data about the inner structures of a patient. As such, formulating reports requires medical experts to possess wide-ranging knowledge about anatomical regions with their normal, healthy appearance as well as the ability to recognize abnormalities. This explicit grasp on both the patient's anatomy and their appearance is missing in current medical image-processing systems as annotations are especially difficult to gather. This renders the models to be narrow experts e.g. for identifying specific diseases. In this work, we recover this missing link by adding human anatomy into the mix and enable the association of content in medical reports to their occurrence in associated imagery (medical phrase grounding). To exploit anatomical structures in this scenario, we present a sophisticated automatic pipeline to gather and integrate human bodily structures from computed tomography datasets, which we incorporate in our PAXRay: A Projected dataset for the segmentation of Anatomical structures in X-Ray data. Our evaluation shows that methods that take advantage of anatomical information benefit heavily in visually grounding radiologists' findings, as our anatomical segmentations allow for up to absolute 50% better grounding results on the OpenI dataset as compared to commonly used region proposals. The PAXRay dataset is available at https://constantinseibold.github.io/paxray/.

We introduce Kvasir-VQA, an extended dataset derived from the HyperKvasir and Kvasir-Instrument datasets, augmented with question-and-answer annotations to facilitate advanced machine learning tasks in Gastrointestinal (GI) diagnostics. This dataset comprises 6,500 annotated images spanning various GI tract conditions and surgical instruments, and it supports multiple question types including yes/no, choice, location, and numerical count. The dataset is intended for applications such as image captioning, Visual Question Answering (VQA), text-based generation of synthetic medical images, object detection, and classification. Our experiments demonstrate the dataset's effectiveness in training models for three selected tasks, showcasing significant applications in medical image analysis and diagnostics. We also present evaluation metrics for each task, highlighting the usability and versatility of our dataset. The dataset and supporting artifacts are available at https://datasets.simula.no/kvasir-vqa.

Curating a large scale medical imaging dataset for machine learning applications is both time consuming and expensive. Balancing the workload between model development, data collection and annotations is difficult for machine learning practitioners, especially under time constraints. Causal analysis is often used in medicine and economics to gain insights about the effects of actions and policies. In this paper we explore the effect of dataset interventions on the output of image classification models. Through a causal approach we investigate the effects of the quantity and type of data we need to incorporate in a dataset to achieve better performance for specific subtasks. The main goal of this paper is to highlight the potential of causal analysis as a tool for resource optimization for developing medical imaging ML applications. We explore this concept with a synthetic dataset and an exemplary use-case for Diabetic Retinopathy image analysis.

Gene expression can be used to subtype breast cancer with improved prediction of risk of recurrence and treatment responsiveness over that obtained using routine immunohistochemistry (IHC). However, in the clinic, molecular profiling is primarily used for ER+ breast cancer, which is costly, tissue destructive, requires specialized platforms and takes several weeks to obtain a result. Deep learning algorithms can effectively extract morphological patterns in digital histopathology images to predict molecular phenotypes quickly and cost-effectively. We propose a new, computationally efficient approach called hist2RNA inspired by bulk RNA-sequencing techniques to predict the expression of 138 genes (incorporated from six commercially available molecular profiling tests), including luminal PAM50 subtype, from hematoxylin and eosin (H&E) stained whole slide images (WSIs). The training phase involves the aggregation of extracted features for each patient from a pretrained model to predict gene expression at the patient level using annotated H&E images from The Cancer Genome Atlas (TCGA, n=335). We demonstrate successful gene prediction on a held-out test set (n = 160, corr = 0.82 across patients, corr = 0.29 across genes) and perform exploratory analysis on an external tissue microarray (TMA) dataset (n = 498) with known IHC and survival information. Our model is able to predict gene expression and luminal PAM50 subtype (Luminal A versus Luminal B) on the TMA dataset with prognostic significance for overall survival in univariate analysis (c-index = 0.56, hazard ratio = 2.16 (95% CI 1.12-3.06), p < 5 x 10-3), and independent significance in multivariate analysis incorporating standard clinicopathological variables (c-index = 0.65, hazard ratio = 1.85 (95% CI 1.30-2.68), p < 5 x 10-3).

Pancreatic NEuroendocrine Tumors (pNETs) are very rare endocrine neoplasms that account for less than 5% of all pancreatic malignancies, with an incidence of only 1-1.5 cases per 100,000. Early detection of pNETs is critical for improving patient survival, but the rarity of pNETs makes segmenting them from CT a very challenging problem. So far, there has not been a dataset specifically for pNETs available to researchers. To address this issue, we propose a pNETs dataset, a well-annotated Contrast-Enhanced Computed Tomography (CECT) dataset focused exclusively on Pancreatic Neuroendocrine Tumors, containing data from 469 patients. This is the first dataset solely dedicated to pNETs, distinguishing it from previous collections. Additionally, we provide the baseline detection networks with a new slice-wise weight loss function designed for the UNet-based model, improving the overall pNET segmentation performance. We hope that our dataset can enhance the understanding and diagnosis of pNET Tumors within the medical community, facilitate the development of more accurate diagnostic tools, and ultimately improve patient outcomes and advance the field of oncology.

The rise of large language models (LLMs) has driven significant progress in medical applications, including traditional Chinese medicine (TCM). However, current medical LLMs struggle with TCM diagnosis and syndrome differentiation due to substantial differences between TCM and modern medical theory, and the scarcity of specialized, high-quality corpora. This paper addresses these challenges by proposing BianCang, a TCM-specific LLM, using a two-stage training process that first injects domain-specific knowledge and then aligns it through targeted stimulation. To enhance diagnostic and differentiation capabilities, we constructed pre-training corpora, instruction-aligned datasets based on real hospital records, and the ChP-TCM dataset derived from the Pharmacopoeia of the People's Republic of China. We compiled extensive TCM and medical corpora for continuous pre-training and supervised fine-tuning, building a comprehensive dataset to refine the model's understanding of TCM. Evaluations across 11 test sets involving 29 models and 4 tasks demonstrate the effectiveness of BianCang, offering valuable insights for future research. Code, datasets, and models are available at https://github.com/QLU-NLP/BianCang.

Developing accurate machine learning models for oncology requires large-scale, high-quality multimodal datasets. However, creating such datasets remains challenging due to the complexity and heterogeneity of medical data. To address this challenge, we introduce HoneyBee, a scalable modular framework for building multimodal oncology datasets that leverages foundational models to generate representative embeddings. HoneyBee integrates various data modalities, including clinical records, imaging data, and patient outcomes. It employs data preprocessing techniques and transformer-based architectures to generate embeddings that capture the essential features and relationships within the raw medical data. The generated embeddings are stored in a structured format using Hugging Face datasets and PyTorch dataloaders for accessibility. Vector databases enable efficient querying and retrieval for machine learning applications. We demonstrate the effectiveness of HoneyBee through experiments assessing the quality and representativeness of the embeddings. The framework is designed to be extensible to other medical domains and aims to accelerate oncology research by providing high-quality, machine learning-ready datasets. HoneyBee is an ongoing open-source effort, and the code, datasets, and models are available at the project repository.

Scarcity of large publicly available retinal fundus image datasets for automated glaucoma detection has been the bottleneck for successful application of artificial intelligence towards practical Computer-Aided Diagnosis (CAD). A few small datasets that are available for research community usually suffer from impractical image capturing conditions and stringent inclusion criteria. These shortcomings in already limited choice of existing datasets make it challenging to mature a CAD system so that it can perform in real-world environment. In this paper we present a large publicly available retinal fundus image dataset for glaucoma classification called G1020. The dataset is curated by conforming to standard practices in routine ophthalmology and it is expected to serve as standard benchmark dataset for glaucoma detection. This database consists of 1020 high resolution colour fundus images and provides ground truth annotations for glaucoma diagnosis, optic disc and optic cup segmentation, vertical cup-to-disc ratio, size of neuroretinal rim in inferior, superior, nasal and temporal quadrants, and bounding box location for optic disc. We also report baseline results by conducting extensive experiments for automated glaucoma diagnosis and segmentation of optic disc and optic cup.

Purpose: In radiology, large language models (LLMs), including ChatGPT, have recently gained attention, and their utility is being rapidly evaluated. However, concerns have emerged regarding their reliability in clinical applications due to limitations such as hallucinations and insufficient referencing. To address these issues, we focus on the latest technology, retrieval-augmented generation (RAG), which enables LLMs to reference reliable external knowledge (REK). Specifically, this study examines the utility and reliability of a recently released RAG-equipped LLM (RAG-LLM), NotebookLM, for staging lung cancer. Materials and methods: We summarized the current lung cancer staging guideline in Japan and provided this as REK to NotebookLM. We then tasked NotebookLM with staging 100 fictional lung cancer cases based on CT findings and evaluated its accuracy. For comparison, we performed the same task using a gold-standard LLM, GPT-4 Omni (GPT-4o), both with and without the REK. Results: NotebookLM achieved 86% diagnostic accuracy in the lung cancer staging experiment, outperforming GPT-4o, which recorded 39% accuracy with the REK and 25% without it. Moreover, NotebookLM demonstrated 95% accuracy in searching reference locations within the REK. Conclusion: NotebookLM successfully performed lung cancer staging by utilizing the REK, demonstrating superior performance compared to GPT-4o. Additionally, it provided highly accurate reference locations within the REK, allowing radiologists to efficiently evaluate the reliability of NotebookLM's responses and detect possible hallucinations. Overall, this study highlights the potential of NotebookLM, a RAG-LLM, in image diagnosis.

In this brief technical report we introduce the CINIC-10 dataset as a plug-in extended alternative for CIFAR-10. It was compiled by combining CIFAR-10 with images selected and downsampled from the ImageNet database. We present the approach to compiling the dataset, illustrate the example images for different classes, give pixel distributions for each part of the repository, and give some standard benchmarks for well known models. Details for download, usage, and compilation can be found in the associated github repository.

We present a deep learning segmentation model that can automatically and robustly segment all major anatomical structures in body CT images. In this retrospective study, 1204 CT examinations (from the years 2012, 2016, and 2020) were used to segment 104 anatomical structures (27 organs, 59 bones, 10 muscles, 8 vessels) relevant for use cases such as organ volumetry, disease characterization, and surgical or radiotherapy planning. The CT images were randomly sampled from routine clinical studies and thus represent a real-world dataset (different ages, pathologies, scanners, body parts, sequences, and sites). The authors trained an nnU-Net segmentation algorithm on this dataset and calculated Dice similarity coefficients (Dice) to evaluate the model's performance. The trained algorithm was applied to a second dataset of 4004 whole-body CT examinations to investigate age dependent volume and attenuation changes. The proposed model showed a high Dice score (0.943) on the test set, which included a wide range of clinical data with major pathologies. The model significantly outperformed another publicly available segmentation model on a separate dataset (Dice score, 0.932 versus 0.871, respectively). The aging study demonstrated significant correlations between age and volume and mean attenuation for a variety of organ groups (e.g., age and aortic volume; age and mean attenuation of the autochthonous dorsal musculature). The developed model enables robust and accurate segmentation of 104 anatomical structures. The annotated dataset (https://doi.org/10.5281/zenodo.6802613) and toolkit (https://www.github.com/wasserth/TotalSegmentator) are publicly available.

In this work, we report the set-up and results of the Liver Tumor Segmentation Benchmark (LiTS), which was organized in conjunction with the IEEE International Symposium on Biomedical Imaging (ISBI) 2017 and the International Conferences on Medical Image Computing and Computer-Assisted Intervention (MICCAI) 2017 and 2018. The image dataset is diverse and contains primary and secondary tumors with varied sizes and appearances with various lesion-to-background levels (hyper-/hypo-dense), created in collaboration with seven hospitals and research institutions. Seventy-five submitted liver and liver tumor segmentation algorithms were trained on a set of 131 computed tomography (CT) volumes and were tested on 70 unseen test images acquired from different patients. We found that not a single algorithm performed best for both liver and liver tumors in the three events. The best liver segmentation algorithm achieved a Dice score of 0.963, whereas, for tumor segmentation, the best algorithms achieved Dices scores of 0.674 (ISBI 2017), 0.702 (MICCAI 2017), and 0.739 (MICCAI 2018). Retrospectively, we performed additional analysis on liver tumor detection and revealed that not all top-performing segmentation algorithms worked well for tumor detection. The best liver tumor detection method achieved a lesion-wise recall of 0.458 (ISBI 2017), 0.515 (MICCAI 2017), and 0.554 (MICCAI 2018), indicating the need for further research. LiTS remains an active benchmark and resource for research, e.g., contributing the liver-related segmentation tasks in http://medicaldecathlon.com/. In addition, both data and online evaluation are accessible via www.lits-challenge.com.

Artificial intelligence-assisted imaging analysis has made substantial strides in tumor diagnosis and management. Here we present PASTA, a pan-tumor CT foundation model that achieves state-of-the-art performance on 45 of 46 representative oncology tasks -- including lesion segmentation, tumor detection in plain CT, tumor staging, survival prediction, structured report generation, and cross-modality transfer learning, significantly outperforming the second-best models on 35 tasks. This remarkable advancement is driven by our development of PASTA-Gen, an innovative synthetic tumor generation framework that produces a comprehensive dataset of 30,000 CT scans with pixel-level annotated lesions and paired structured reports, encompassing malignancies across ten organs and five benign lesion types. By leveraging this rich, high-quality synthetic data, we overcome a longstanding bottleneck in the development of CT foundation models -- specifically, the scarcity of publicly available, high-quality annotated datasets due to privacy constraints and the substantial labor required for scaling precise data annotation. Encouragingly, PASTA demonstrates exceptional data efficiency with promising practical value, markedly improving performance on various tasks with only a small amount of real-world data. The open release of both the synthetic dataset and PASTA foundation model effectively addresses the challenge of data scarcity, thereby advancing oncological research and clinical translation.

Deep learning has enabled the development of highly robust foundation models for various pathological tasks across diverse diseases and patient cohorts. Among these models, vision-language pre-training, which leverages large-scale paired data to align pathology image and text embedding spaces, and provides a novel zero-shot paradigm for downstream tasks. However, existing models have been primarily data-driven and lack the incorporation of domain-specific knowledge, which limits their performance in cancer diagnosis, especially for rare tumor subtypes. To address this limitation, we establish a Knowledge-enhanced Pathology (KEEP) foundation model that harnesses disease knowledge to facilitate vision-language pre-training. Specifically, we first construct a disease knowledge graph (KG) that covers 11,454 human diseases with 139,143 disease attributes, including synonyms, definitions, and hypernym relations. We then systematically reorganize the millions of publicly available noisy pathology image-text pairs, into 143K well-structured semantic groups linked through the hierarchical relations of the disease KG. To derive more nuanced image and text representations, we propose a novel knowledge-enhanced vision-language pre-training approach that integrates disease knowledge into the alignment within hierarchical semantic groups instead of unstructured image-text pairs. Validated on 18 diverse benchmarks with more than 14,000 whole slide images (WSIs), KEEP achieves state-of-the-art performance in zero-shot cancer diagnostic tasks. Notably, for cancer detection, KEEP demonstrates an average sensitivity of 89.8% at a specificity of 95.0% across 7 cancer types. For cancer subtyping, KEEP achieves a median balanced accuracy of 0.456 in subtyping 30 rare brain cancers, indicating strong generalizability for diagnosing rare tumors.

Developing generalist foundation model has recently attracted tremendous attention among researchers in the field of AI for Medicine (AI4Medicine). A pivotal insight in developing these models is their reliance on dataset scaling, which emphasizes the requirements on developing open-source medical image datasets that incorporate diverse supervision signals across various imaging modalities. In this paper, we introduce RadGenome-Chest CT, a comprehensive, large-scale, region-guided 3D chest CT interpretation dataset based on CT-RATE. Specifically, we leverage the latest powerful universal segmentation and large language models, to extend the original datasets (over 25,692 non-contrast 3D chest CT volume and reports from 20,000 patients) from the following aspects: (i) organ-level segmentation masks covering 197 categories, which provide intermediate reasoning visual clues for interpretation; (ii) 665 K multi-granularity grounded reports, where each sentence of the report is linked to the corresponding anatomical region of CT volume in the form of a segmentation mask; (iii) 1.3 M grounded VQA pairs, where questions and answers are all linked with reference segmentation masks, enabling models to associate visual evidence with textual explanations. All grounded reports and VQA pairs in the validation set have gone through manual verification to ensure dataset quality. We believe that RadGenome-Chest CT can significantly advance the development of multimodal medical foundation models, by training to generate texts based on given segmentation regions, which is unattainable with previous relevant datasets. We will release all segmentation masks, grounded reports, and VQA pairs to facilitate further research and development in this field.

Smoke generated by surgical instruments during laparoscopic surgery can obscure the visual field, impairing surgeons' ability to perform operations accurately and safely. Thus, smoke removal task for laparoscopic images is highly desirable. Despite laparoscopic image desmoking has attracted the attention of researchers in recent years and several algorithms have emerged, the lack of publicly available high-quality benchmark datasets is the main bottleneck to hamper the development progress of this task. To advance this field, we construct a new high-quality dataset for Laparoscopic Surgery image Desmoking, named LSD3K, consisting of 3,000 paired synthetic non-homogeneous smoke images. In this paper, we provide a dataset generation pipeline, which includes modeling smoke shape using Blender, collecting ground-truth images from the Cholec80 dataset, random sampling of smoke masks and etc. Based on the proposed benchmark, we further conducted a comprehensive evaluation of the existing representative desmoking algorithms. The proposed dataset is publicly available at https://drive.google.com/file/d/1v0U5_3S4nJpaUiP898Q0pc-MfEAtnbOq/view?usp=sharing

Deep neural networks have introduced significant advancements in the field of machine learning-based analysis of digital pathology images including prostate tissue images. With the help of transfer learning, classification and segmentation performance of neural network models have been further increased. However, due to the absence of large, extensively annotated, publicly available prostate histopathology datasets, several previous studies employ datasets from well-studied computer vision tasks such as ImageNet dataset. In this work, we propose a transfer learning scheme from breast histopathology images to improve prostate cancer detection performance. We validate our approach on annotated prostate whole slide images by using a publicly available breast histopathology dataset as pre-training. We show that the proposed cross-cancer approach outperforms transfer learning from ImageNet dataset.

Is it possible to develop an "AI Pathologist" to pass the board-certified examination of the American Board of Pathology? To achieve this goal, the first step is to create a visual question answering (VQA) dataset where the AI agent is presented with a pathology image together with a question and is asked to give the correct answer. Our work makes the first attempt to build such a dataset. Different from creating general-domain VQA datasets where the images are widely accessible and there are many crowdsourcing workers available and capable of generating question-answer pairs, developing a medical VQA dataset is much more challenging. First, due to privacy concerns, pathology images are usually not publicly available. Second, only well-trained pathologists can understand pathology images, but they barely have time to help create datasets for AI research. To address these challenges, we resort to pathology textbooks and online digital libraries. We develop a semi-automated pipeline to extract pathology images and captions from textbooks and generate question-answer pairs from captions using natural language processing. We collect 32,799 open-ended questions from 4,998 pathology images where each question is manually checked to ensure correctness. To our best knowledge, this is the first dataset for pathology VQA. Our dataset will be released publicly to promote research in medical VQA.

The recent surge in performance for image analysis of digitised pathology slides can largely be attributed to the advances in deep learning. Deep models can be used to initially localise various structures in the tissue and hence facilitate the extraction of interpretable features for biomarker discovery. However, these models are typically trained for a single task and therefore scale poorly as we wish to adapt the model for an increasing number of different tasks. Also, supervised deep learning models are very data hungry and therefore rely on large amounts of training data to perform well. In this paper, we present a multi-task learning approach for segmentation and classification of nuclei, glands, lumina and different tissue regions that leverages data from multiple independent data sources. While ensuring that our tasks are aligned by the same tissue type and resolution, we enable meaningful simultaneous prediction with a single network. As a result of feature sharing, we also show that the learned representation can be used to improve the performance of additional tasks via transfer learning, including nuclear classification and signet ring cell detection. As part of this work, we train our developed Cerberus model on a huge amount of data, consisting of over 600K objects for segmentation and 440K patches for classification. We use our approach to process 599 colorectal whole-slide images from TCGA, where we localise 377 million, 900K and 2.1 million nuclei, glands and lumina, respectively and make the results available to the community for downstream analysis.

The article presents a new multi-label comprehensive image dataset from flexible endoscopy, colonoscopy and capsule endoscopy, named ERS. The collection has been labeled according to the full medical specification of 'Minimum Standard Terminology 3.0' (MST 3.0), describing all possible findings in the gastrointestinal tract (104 possible labels), extended with an additional 19 labels useful in common machine learning applications. The dataset contains around 6000 precisely and 115,000 approximately labeled frames from endoscopy videos, 3600 precise and 22,600 approximate segmentation masks, and 1.23 million unlabeled frames from flexible and capsule endoscopy videos. The labeled data cover almost entirely the MST 3.0 standard. The data came from 1520 videos of 1135 patients. Additionally, this paper proposes and describes four exemplary experiments in gastrointestinal image classification task performed using the created dataset. The obtained results indicate the high usefulness and flexibility of the dataset in training and testing machine learning algorithms in the field of endoscopic data analysis.

The visual examination of tissue biopsy sections is fundamental for cancer diagnosis, with pathologists analyzing sections at multiple magnifications to discern tumor cells and their subtypes. However, existing attention-based multiple instance learning (MIL) models, used for analyzing Whole Slide Images (WSIs) in cancer diagnostics, often overlook the contextual information of tumor and neighboring tiles, leading to misclassifications. To address this, we propose the Context-Aware Multiple Instance Learning (CAMIL) architecture. CAMIL incorporates neighbor-constrained attention to consider dependencies among tiles within a WSI and integrates contextual constraints as prior knowledge into the MIL model. We evaluated CAMIL on subtyping non-small cell lung cancer (TCGA-NSCLC) and detecting lymph node (CAMELYON16) metastasis, achieving test AUCs of 0.959\% and 0.975\%, respectively, outperforming other state-of-the-art methods. Additionally, CAMIL enhances model interpretability by identifying regions of high diagnostic value.

Prenatal ultrasound imaging is the first-choice modality to assess fetal health. Medical image datasets for AI and ML methods must be diverse (i.e. diagnoses, diseases, pathologies, scanners, demographics, etc), however there are few public ultrasound fetal imaging datasets due to insufficient amounts of clinical data, patient privacy, rare occurrence of abnormalities in general practice, and limited experts for data collection and validation. To address such data scarcity, we proposed generative adversarial networks (GAN)-based models, diffusion-super-resolution-GAN and transformer-based-GAN, to synthesise images of fetal ultrasound brain planes from one public dataset. We reported that GAN-based methods can generate 256x256 pixel size of fetal ultrasound trans-cerebellum brain image plane with stable training losses, resulting in lower FID values for diffusion-super-resolution-GAN (average 7.04 and lower FID 5.09 at epoch 10) than the FID values of transformer-based-GAN (average 36.02 and lower 28.93 at epoch 60). The results of this work illustrate the potential of GAN-based methods to synthesise realistic high-resolution ultrasound images, leading to future work with other fetal brain planes, anatomies, devices and the need of a pool of experts to evaluate synthesised images. Code, data and other resources to reproduce this work are available at https://github.com/budai4medtech/midl2023.

We present an end-to-end deep learning segmentation method by combining a 3D UNet architecture with a graph neural network (GNN) model. In this approach, the convolutional layers at the deepest level of the UNet are replaced by a GNN-based module with a series of graph convolutions. The dense feature maps at this level are transformed into a graph input to the GNN module. The incorporation of graph convolutions in the UNet provides nodes in the graph with information that is based on node connectivity, in addition to the local features learnt through the downsampled paths. This information can help improve segmentation decisions. By stacking several graph convolution layers, the nodes can access higher order neighbourhood information without substantial increase in computational expense. We propose two types of node connectivity in the graph adjacency: i) one predefined and based on a regular node neighbourhood, and ii) one dynamically computed during training and using the nearest neighbour nodes in the feature space. We have applied this method to the task of segmenting the airway tree from chest CT scans. Experiments have been performed on 32 CTs from the Danish Lung Cancer Screening Trial dataset. We evaluate the performance of the UNet-GNN models with two types of graph adjacency and compare it with the baseline UNet.

Background: Health datasets from clinical sources do not reflect the breadth and diversity of disease in the real world, impacting research, medical education, and artificial intelligence (AI) tool development. Dermatology is a suitable area to develop and test a new and scalable method to create representative health datasets. Methods: We used Google Search advertisements to invite contributions to an open access dataset of images of dermatology conditions, demographic and symptom information. With informed contributor consent, we describe and release this dataset containing 10,408 images from 5,033 contributions from internet users in the United States over 8 months starting March 2023. The dataset includes dermatologist condition labels as well as estimated Fitzpatrick Skin Type (eFST) and Monk Skin Tone (eMST) labels for the images. Results: We received a median of 22 submissions/day (IQR 14-30). Female (66.72%) and younger (52% < age 40) contributors had a higher representation in the dataset compared to the US population, and 32.6% of contributors reported a non-White racial or ethnic identity. Over 97.5% of contributions were genuine images of skin conditions. Dermatologist confidence in assigning a differential diagnosis increased with the number of available variables, and showed a weaker correlation with image sharpness (Spearman's P values <0.001 and 0.01 respectively). Most contributions were short-duration (54% with onset < 7 days ago ) and 89% were allergic, infectious, or inflammatory conditions. eFST and eMST distributions reflected the geographical origin of the dataset. The dataset is available at github.com/google-research-datasets/scin . Conclusion: Search ads are effective at crowdsourcing images of health conditions. The SCIN dataset bridges important gaps in the availability of representative images of common skin conditions.

Background: Recent advances in large language models highlight the need for high-quality multilingual medical datasets. While Japan leads globally in CT scanner deployment and utilization, the lack of large-scale Japanese radiology datasets has hindered the development of specialized language models for medical imaging analysis. Objective: To develop a comprehensive Japanese CT report dataset through machine translation and establish a specialized language model for structured finding classification. Additionally, to create a rigorously validated evaluation dataset through expert radiologist review. Methods: We translated the CT-RATE dataset (24,283 CT reports from 21,304 patients) into Japanese using GPT-4o mini. The training dataset consisted of 22,778 machine-translated reports, while the validation dataset included 150 radiologist-revised reports. We developed CT-BERT-JPN based on "tohoku-nlp/bert-base-japanese-v3" architecture for extracting 18 structured findings from Japanese radiology reports. Results: Translation metrics showed strong performance with BLEU scores of 0.731 and 0.690, and ROUGE scores ranging from 0.770 to 0.876 for Findings and from 0.748 to 0.857 for Impression sections. CT-BERT-JPN demonstrated superior performance compared to GPT-4o in 11 out of 18 conditions, including lymphadenopathy (+14.2%), interlobular septal thickening (+10.9%), and atelectasis (+7.4%). The model maintained F1 scores exceeding 0.95 in 14 out of 18 conditions and achieved perfect scores in four conditions. Conclusions: Our study establishes a robust Japanese CT report dataset and demonstrates the effectiveness of a specialized language model for structured finding classification. The hybrid approach of machine translation and expert validation enables the creation of large-scale medical datasets while maintaining high quality.

Artificial intelligence has significantly advanced skin cancer diagnosis by enabling rapid and accurate detection of malignant lesions. In this domain, most publicly available image datasets consist of single, isolated skin lesions positioned at the center of the image. While these lesion-centric datasets have been fundamental for developing diagnostic algorithms, they lack the context of the surrounding skin, which is critical for improving lesion detection. The iToBoS dataset was created to address this challenge. It includes 16,954 images of skin regions from 100 participants, captured using 3D total body photography. Each image roughly corresponds to a 7 times 9 cm section of skin with all suspicious lesions annotated using bounding boxes. Additionally, the dataset provides metadata such as anatomical location, age group, and sun damage score for each image. This dataset aims to facilitate training and benchmarking of algorithms, with the goal of enabling early detection of skin cancer and deployment of this technology in non-clinical environments.

High-throughput screening techniques are commonly used to obtain large quantities of data in many fields of biology. It is well known that artifacts arising from variability in the technical execution of different experimental batches within such screens confound these observations and can lead to invalid biological conclusions. It is therefore necessary to account for these batch effects when analyzing outcomes. In this paper we describe RxRx1, a biological dataset designed specifically for the systematic study of batch effect correction methods. The dataset consists of 125,510 high-resolution fluorescence microscopy images of human cells under 1,138 genetic perturbations in 51 experimental batches across 4 cell types. Visual inspection of the images alone clearly demonstrates significant batch effects. We propose a classification task designed to evaluate the effectiveness of experimental batch correction methods on these images and examine the performance of a number of correction methods on this task. Our goal in releasing RxRx1 is to encourage the development of effective experimental batch correction methods that generalize well to unseen experimental batches. The dataset can be downloaded at https://rxrx.ai.

The advancements in data acquisition, storage, and processing techniques have resulted in the rapid growth of heterogeneous medical data. Integrating radiological scans, histopathology images, and molecular information with clinical data is essential for developing a holistic understanding of the disease and optimizing treatment. The need for integrating data from multiple sources is further pronounced in complex diseases such as cancer for enabling precision medicine and personalized treatments. This work proposes Multimodal Integration of Oncology Data System (MINDS) - a flexible, scalable, and cost-effective metadata framework for efficiently fusing disparate data from public sources such as the Cancer Research Data Commons (CRDC) into an interconnected, patient-centric framework. MINDS offers an interface for exploring relationships across data types and building cohorts for developing large-scale multimodal machine learning models. By harmonizing multimodal data, MINDS aims to potentially empower researchers with greater analytical ability to uncover diagnostic and prognostic insights and enable evidence-based personalized care. MINDS tracks granular end-to-end data provenance, ensuring reproducibility and transparency. The cloud-native architecture of MINDS can handle exponential data growth in a secure, cost-optimized manner while ensuring substantial storage optimization, replication avoidance, and dynamic access capabilities. Auto-scaling, access controls, and other mechanisms guarantee pipelines' scalability and security. MINDS overcomes the limitations of existing biomedical data silos via an interoperable metadata-driven approach that represents a pivotal step toward the future of oncology data integration.

The increasing interest in developing Artificial Intelligence applications in the medical domain, suffers from the lack of high-quality dataset, mainly due to privacy-related issues. Moreover, the recent rising of Multimodal Large Language Models (MLLM) leads to a need for multimodal medical datasets, where clinical reports and findings are attached to the corresponding CT or MR scans. This paper illustrates the entire workflow for building the data set MedPix 2.0. Starting from the well-known multimodal dataset MedPix\textregistered, mainly used by physicians, nurses and healthcare students for Continuing Medical Education purposes, a semi-automatic pipeline was developed to extract visual and textual data followed by a manual curing procedure where noisy samples were removed, thus creating a MongoDB database. Along with the dataset, we developed a GUI aimed at navigating efficiently the MongoDB instance, and obtaining the raw data that can be easily used for training and/or fine-tuning MLLMs. To enforce this point, we also propose a CLIP-based model trained on MedPix 2.0 for scan classification tasks.

Recent advancements in digital pathology have led to the development of numerous foundational models that utilize self-supervised learning on patches extracted from gigapixel whole slide images (WSIs). While this approach leverages vast amounts of unlabeled data, we have discovered a significant issue: features extracted from these self-supervised models tend to cluster by individual WSIs, a phenomenon we term WSI-specific feature collapse. This problem can potentially limit the model's generalization ability and performance on various downstream tasks. To address this issue, we introduce Stain Normalized Pathology Foundational Model, a novel foundational model trained on patches that have undergone stain normalization. Stain normalization helps reduce color variability arising from different laboratories and scanners, enabling the model to learn more consistent features. Stain Normalized Pathology Foundational Model is trained using 285,153,903 patches extracted from a total of 34,795 WSIs, combining data from The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) project. Our experiments demonstrate that Stain Normalized Pathology Foundational Model significantly mitigates the feature collapse problem, indicating that the model has learned more generalized features rather than overfitting to individual WSI characteristics. We compared Stain Normalized Pathology Foundational Model with state-of-the-art models across six downstream task datasets, and our results show that Stain Normalized Pathology Foundational Model achieves excellent performance relative to the number of WSIs used and the model's parameter count. This suggests that the application of stain normalization has substantially improved the model's efficiency and generalization capabilities.

Coronary artery disease (CAD) remains the leading cause of death globally and invasive coronary angiography (ICA) is considered the gold standard of anatomical imaging evaluation when CAD is suspected. However, risk evaluation based on ICA has several limitations, such as visual assessment of stenosis severity, which has significant interobserver variability. This motivates to development of a lesion classification system that can support specialists in their clinical procedures. Although deep learning classification methods are well-developed in other areas of medical imaging, ICA image classification is still at an early stage. One of the most important reasons is the lack of available and high-quality open-access datasets. In this paper, we reported a new annotated ICA images dataset, CADICA, to provide the research community with a comprehensive and rigorous dataset of coronary angiography consisting of a set of acquired patient videos and associated disease-related metadata. This dataset can be used by clinicians to train their skills in angiographic assessment of CAD severity and by computer scientists to create computer-aided diagnostic systems to help in such assessment. In addition, baseline classification methods are proposed and analyzed, validating the functionality of CADICA and giving the scientific community a starting point to improve CAD detection.

Recent advances in methods focused on the grounding problem have resulted in techniques that can be used to construct a symbolic language associated with a specific domain. Inspired by how humans communicate complex ideas through language, we developed a generalized Symbolic Semantic (S^2) framework for interpretable segmentation. Unlike adversarial models (e.g., GANs), we explicitly model cooperation between two agents, a Sender and a Receiver, that must cooperate to achieve a common goal. The Sender receives information from a high layer of a segmentation network and generates a symbolic sentence derived from a categorical distribution. The Receiver obtains the symbolic sentences and co-generates the segmentation mask. In order for the model to converge, the Sender and Receiver must learn to communicate using a private language. We apply our architecture to segment tumors in the TCGA dataset. A UNet-like architecture is used to generate input to the Sender network which produces a symbolic sentence, and a Receiver network co-generates the segmentation mask based on the sentence. Our Segmentation framework achieved similar or better performance compared with state-of-the-art segmentation methods. In addition, our results suggest direct interpretation of the symbolic sentences to discriminate between normal and tumor tissue, tumor morphology, and other image characteristics.

The morphometry of a kidney tumor revealed by contrast-enhanced Computed Tomography (CT) imaging is an important factor in clinical decision making surrounding the lesion's diagnosis and treatment. Quantitative study of the relationship between kidney tumor morphology and clinical outcomes is difficult due to data scarcity and the laborious nature of manually quantifying imaging predictors. Automatic semantic segmentation of kidneys and kidney tumors is a promising tool towards automatically quantifying a wide array of morphometric features, but no sizeable annotated dataset is currently available to train models for this task. We present the KiTS19 challenge dataset: A collection of multi-phase CT imaging, segmentation masks, and comprehensive clinical outcomes for 300 patients who underwent nephrectomy for kidney tumors at our center between 2010 and 2018. 210 (70%) of these patients were selected at random as the training set for the 2019 MICCAI KiTS Kidney Tumor Segmentation Challenge and have been released publicly. With the presence of clinical context and surgical outcomes, this data can serve not only for benchmarking semantic segmentation models, but also for developing and studying biomarkers which make use of the imaging and semantic segmentation masks.

Recently, there has been an increasing interest in (supervised) learning with graph data, especially using graph neural networks. However, the development of meaningful benchmark datasets and standardized evaluation procedures is lagging, consequently hindering advancements in this area. To address this, we introduce the TUDataset for graph classification and regression. The collection consists of over 120 datasets of varying sizes from a wide range of applications. We provide Python-based data loaders, kernel and graph neural network baseline implementations, and evaluation tools. Here, we give an overview of the datasets, standardized evaluation procedures, and provide baseline experiments. All datasets are available at www.graphlearning.io. The experiments are fully reproducible from the code available at www.github.com/chrsmrrs/tudataset.

We present a new challenging dataset, CPPE - 5 (Medical Personal Protective Equipment), with the goal to allow the study of subordinate categorization of medical personal protective equipments, which is not possible with other popular data sets that focus on broad-level categories (such as PASCAL VOC, ImageNet, Microsoft COCO, OpenImages, etc). To make it easy for models trained on this dataset to be used in practical scenarios in complex scenes, our dataset mainly contains images that show complex scenes with several objects in each scene in their natural context. The image collection for this dataset focuses on: obtaining as many non-iconic images as possible and making sure all the images are real-life images, unlike other existing datasets in this area. Our dataset includes 5 object categories (coveralls, face shields, gloves, masks, and goggles), and each image is annotated with a set of bounding boxes and positive labels. We present a detailed analysis of the dataset in comparison to other popular broad category datasets as well as datasets focusing on personal protective equipments, we also find that at present there exist no such publicly available datasets. Finally, we also analyze performance and compare model complexities on baseline and state-of-the-art models for bounding box results. Our code, data, and trained models are available at https://git.io/cppe5-dataset.

Resection and whole brain radiotherapy (WBRT) are the standards of care for the treatment of patients with brain metastases (BM) but are often associated with cognitive side effects. Stereotactic radiosurgery (SRS) involves a more targeted treatment approach and has been shown to avoid the side effects associated with WBRT. However, SRS requires precise identification and delineation of BM. While many AI algorithms have been developed for this purpose, their clinical adoption has been limited due to poor model performance in the clinical setting. Major reasons for non-generalizable algorithms are the limitations in the datasets used for training the AI network. The purpose of this study was to create a large, heterogenous, annotated BM dataset for training and validation of AI models to improve generalizability. We present a BM dataset of 200 patients with pretreatment T1, T1 post-contrast, T2, and FLAIR MR images. The dataset includes contrast-enhancing and necrotic 3D segmentations on T1 post-contrast and whole tumor (including peritumoral edema) 3D segmentations on FLAIR. Our dataset contains 975 contrast-enhancing lesions, many of which are sub centimeter, along with clinical and imaging feature information. We used a streamlined approach to database-building leveraging a PACS-integrated segmentation workflow.

Computational microscopy, in which hardware and algorithms of an imaging system are jointly designed, shows promise for making imaging systems that cost less, perform more robustly, and collect new types of information. Often, the performance of computational imaging systems, especially those that incorporate machine learning, is sample-dependent. Thus, standardized datasets are an essential tool for comparing the performance of different approaches. Here, we introduce the Berkeley Single Cell Computational Microscopy (BSCCM) dataset, which contains over ~12,000,000 images of 400,000 of individual white blood cells. The dataset contains images captured with multiple illumination patterns on an LED array microscope and fluorescent measurements of the abundance of surface proteins that mark different cell types. We hope this dataset will provide a valuable resource for the development and testing of new algorithms in computational microscopy and computer vision with practical biomedical applications.

Multimodal learning significantly benefits cancer survival prediction, especially the integration of pathological images and genomic data. Despite advantages of multimodal learning for cancer survival prediction, massive redundancy in multimodal data prevents it from extracting discriminative and compact information: (1) An extensive amount of intra-modal task-unrelated information blurs discriminability, especially for gigapixel whole slide images (WSIs) with many patches in pathology and thousands of pathways in genomic data, leading to an ``intra-modal redundancy" issue. (2) Duplicated information among modalities dominates the representation of multimodal data, which makes modality-specific information prone to being ignored, resulting in an ``inter-modal redundancy" issue. To address these, we propose a new framework, Prototypical Information Bottlenecking and Disentangling (PIBD), consisting of Prototypical Information Bottleneck (PIB) module for intra-modal redundancy and Prototypical Information Disentanglement (PID) module for inter-modal redundancy. Specifically, a variant of information bottleneck, PIB, is proposed to model prototypes approximating a bunch of instances for different risk levels, which can be used for selection of discriminative instances within modality. PID module decouples entangled multimodal data into compact distinct components: modality-common and modality-specific knowledge, under the guidance of the joint prototypical distribution. Extensive experiments on five cancer benchmark datasets demonstrated our superiority over other methods.

This paper proposes one of the first clinical applications of multimodal large language models (LLMs) as an assistant for radiologists to check errors in their reports. We created an evaluation dataset from two real-world radiology datasets (MIMIC-CXR and IU-Xray), with 1,000 subsampled reports each. A subset of original reports was modified to contain synthetic errors by introducing various type of mistakes. The evaluation contained two difficulty levels: SIMPLE for binary error-checking and COMPLEX for identifying error types. LLaVA (Large Language and Visual Assistant) variant models, including our instruction-tuned model, were used for the evaluation. Additionally, a domain expert evaluation was conducted on a small test set. At the SIMPLE level, the LLaVA v1.5 model outperformed other publicly available models. Instruction tuning significantly enhanced performance by 47.4% and 25.4% on MIMIC-CXR and IU-Xray data, respectively. The model also surpassed the domain experts accuracy in the MIMIC-CXR dataset by 1.67%. Notably, among the subsets (N=21) of the test set where a clinician did not achieve the correct conclusion, the LLaVA ensemble mode correctly identified 71.4% of these cases. This study marks a promising step toward utilizing multi-modal LLMs to enhance diagnostic accuracy in radiology. The ensemble model demonstrated comparable performance to clinicians, even capturing errors overlooked by humans. Nevertheless, future work is needed to improve the model ability to identify the types of inconsistency.

Tissue phenotyping is a fundamental computational pathology (CPath) task in learning objective characterizations of histopathologic biomarkers in anatomic pathology. However, whole-slide imaging (WSI) poses a complex computer vision problem in which the large-scale image resolutions of WSIs and the enormous diversity of morphological phenotypes preclude large-scale data annotation. Current efforts have proposed using pretrained image encoders with either transfer learning from natural image datasets or self-supervised pretraining on publicly-available histopathology datasets, but have not been extensively developed and evaluated across diverse tissue types at scale. We introduce UNI, a general-purpose self-supervised model for pathology, pretrained using over 100 million tissue patches from over 100,000 diagnostic haematoxylin and eosin-stained WSIs across 20 major tissue types, and evaluated on 33 representative CPath clinical tasks in CPath of varying diagnostic difficulties. In addition to outperforming previous state-of-the-art models, we demonstrate new modeling capabilities in CPath such as resolution-agnostic tissue classification, slide classification using few-shot class prototypes, and disease subtyping generalization in classifying up to 108 cancer types in the OncoTree code classification system. UNI advances unsupervised representation learning at scale in CPath in terms of both pretraining data and downstream evaluation, enabling data-efficient AI models that can generalize and transfer to a gamut of diagnostically-challenging tasks and clinical workflows in anatomic pathology.

Survival prediction is a complicated ordinal regression task that aims to predict the ranking risk of death, which generally benefits from the integration of histology and genomic data. Despite the progress in joint learning from pathology and genomics, existing methods still suffer from challenging issues: 1) Due to the large size of pathological images, it is difficult to effectively represent the gigapixel whole slide images (WSIs). 2) Interactions within tumor microenvironment (TME) in histology are essential for survival analysis. Although current approaches attempt to model these interactions via co-attention between histology and genomic data, they focus on only dense local similarity across modalities, which fails to capture global consistency between potential structures, i.e. TME-related interactions of histology and co-expression of genomic data. To address these challenges, we propose a Multimodal Optimal Transport-based Co-Attention Transformer framework with global structure consistency, in which optimal transport (OT) is applied to match patches of a WSI and genes embeddings for selecting informative patches to represent the gigapixel WSI. More importantly, OT-based co-attention provides a global awareness to effectively capture structural interactions within TME for survival prediction. To overcome high computational complexity of OT, we propose a robust and efficient implementation over micro-batch of WSI patches by approximating the original OT with unbalanced mini-batch OT. Extensive experiments show the superiority of our method on five benchmark datasets compared to the state-of-the-art methods. The code is released.

Pathology text mining is a challenging task given the reporting variability and constant new findings in cancer sub-type definitions. However, successful text mining of a large pathology database can play a critical role to advance 'big data' cancer research like similarity-based treatment selection, case identification, prognostication, surveillance, clinical trial screening, risk stratification, and many others. While there is a growing interest in developing language models for more specific clinical domains, no pathology-specific language space exist to support the rapid data-mining development in pathology space. In literature, a few approaches fine-tuned general transformer models on specialized corpora while maintaining the original tokenizer, but in fields requiring specialized terminology, these models often fail to perform adequately. We propose PathologyBERT - a pre-trained masked language model which was trained on 347,173 histopathology specimen reports and publicly released in the Huggingface repository. Our comprehensive experiments demonstrate that pre-training of transformer model on pathology corpora yields performance improvements on Natural Language Understanding (NLU) and Breast Cancer Diagnose Classification when compared to nonspecific language models.

Cancer is a complex disease, the understanding and treatment of which are being aided through increases in the volume of collected data and in the scale of deployed computing power. Consequently, there is a growing need for the development of data-driven and, in particular, deep learning methods for various tasks such as cancer diagnosis, detection, prognosis, and prediction. Despite recent successes, however, designing high-performing deep learning models for nonimage and nontext cancer data is a time-consuming, trial-and-error, manual task that requires both cancer domain and deep learning expertise. To that end, we develop a reinforcement-learning-based neural architecture search to automate deep-learning-based predictive model development for a class of representative cancer data. We develop custom building blocks that allow domain experts to incorporate the cancer-data-specific characteristics. We show that our approach discovers deep neural network architectures that have significantly fewer trainable parameters, shorter training time, and accuracy similar to or higher than those of manually designed architectures. We study and demonstrate the scalability of our approach on up to 1,024 Intel Knights Landing nodes of the Theta supercomputer at the Argonne Leadership Computing Facility.

While machine learning is currently transforming the field of histopathology, the domain lacks a comprehensive evaluation of state-of-the-art models based on essential but complementary quality requirements beyond a mere classification accuracy. In order to fill this gap, we developed a new methodology to extensively evaluate a wide range of classification models, including recent vision transformers, and convolutional neural networks such as: ConvNeXt, ResNet (BiT), Inception, ViT and Swin transformer, with and without supervised or self-supervised pretraining. We thoroughly tested the models on five widely used histopathology datasets containing whole slide images of breast, gastric, and colorectal cancer and developed a novel approach using an image-to-image translation model to assess the robustness of a cancer classification model against stain variations. Further, we extended existing interpretability methods to previously unstudied models and systematically reveal insights of the models' classifications strategies that can be transferred to future model architectures.

Clinical gait analysis (CGA) using computer vision is an emerging field in artificial intelligence that faces barriers of accessible, real-world data, and clear task objectives. This paper lays the foundation for current developments in CGA as well as vision-based methods and datasets suitable for gait analysis. We introduce The Gait Abnormality in Video Dataset (GAVD) in response to our review of over 150 current gait-related computer vision datasets, which highlighted the need for a large and accessible gait dataset clinically annotated for CGA. GAVD stands out as the largest video gait dataset, comprising 1874 sequences of normal, abnormal and pathological gaits. Additionally, GAVD includes clinically annotated RGB data sourced from publicly available content on online platforms. It also encompasses over 400 subjects who have undergone clinical grade visual screening to represent a diverse range of abnormal gait patterns, captured in various settings, including hospital clinics and urban uncontrolled outdoor environments. We demonstrate the validity of the dataset and utility of action recognition models for CGA using pretrained models Temporal Segment Networks(TSN) and SlowFast network to achieve video abnormality detection of 94% and 92% respectively when tested on GAVD dataset. A GitHub repository https://github.com/Rahmyyy/GAVD consisting of convenient URL links, and clinically relevant annotation for CGA is provided for over 450 online videos, featuring diverse subjects performing a range of normal, pathological, and abnormal gait patterns.

Computed tomography (CT) serves as an effective tool for lung cancer screening, diagnosis, treatment, and prognosis, providing a rich source of features to quantify temporal and spatial tumor changes. Nonetheless, the diversity of CT scanners and customized acquisition protocols can introduce significant inconsistencies in texture features, even when assessing the same patient. This variability poses a fundamental challenge for subsequent research that relies on consistent image features. Existing CT image standardization models predominantly utilize GAN-based supervised or semi-supervised learning, but their performance remains limited. We present DiffusionCT, an innovative score-based DDPM model that operates in the latent space to transform disparate non-standard distributions into a standardized form. The architecture comprises a U-Net-based encoder-decoder, augmented by a DDPM model integrated at the bottleneck position. First, the encoder-decoder is trained independently, without embedding DDPM, to capture the latent representation of the input data. Second, the latent DDPM model is trained while keeping the encoder-decoder parameters fixed. Finally, the decoder uses the transformed latent representation to generate a standardized CT image, providing a more consistent basis for downstream analysis. Empirical tests on patient CT images indicate notable improvements in image standardization using DiffusionCT. Additionally, the model significantly reduces image noise in SPAD images, further validating the effectiveness of DiffusionCT for advanced imaging tasks.

Fairness in artificial intelligence models has gained significantly more attention in recent years, especially in the area of medicine, as fairness in medical models is critical to people's well-being and lives. High-quality medical fairness datasets are needed to promote fairness learning research. Existing medical fairness datasets are all for classification tasks, and no fairness datasets are available for medical segmentation, while medical segmentation is an equally important clinical task as classifications, which can provide detailed spatial information on organ abnormalities ready to be assessed by clinicians. In this paper, we propose the first fairness dataset for medical segmentation named Harvard-FairSeg with 10,000 subject samples. In addition, we propose a fair error-bound scaling approach to reweight the loss function with the upper error-bound in each identity group, using the segment anything model (SAM). We anticipate that the segmentation performance equity can be improved by explicitly tackling the hard cases with high training errors in each identity group. To facilitate fair comparisons, we utilize a novel equity-scaled segmentation performance metric to compare segmentation metrics in the context of fairness, such as the equity-scaled Dice coefficient. Through comprehensive experiments, we demonstrate that our fair error-bound scaling approach either has superior or comparable fairness performance to the state-of-the-art fairness learning models. The dataset and code are publicly accessible via https://ophai.hms.harvard.edu/datasets/harvard-fairseg10k.

With the rapid development of computational pathology, many AI-assisted diagnostic tasks have emerged. Cellular nuclei segmentation can segment various types of cells for downstream analysis, but it relies on predefined categories and lacks flexibility. Moreover, pathology visual question answering can perform image-level understanding but lacks region-level detection capability. To address this, we propose a new benchmark called Pathology Visual Grounding (PathVG), which aims to detect regions based on expressions with different attributes. To evaluate PathVG, we create a new dataset named RefPath which contains 27,610 images with 33,500 language-grounded boxes. Compared to visual grounding in other domains, PathVG presents pathological images at multi-scale and contains expressions with pathological knowledge. In the experimental study, we found that the biggest challenge was the implicit information underlying the pathological expressions. Based on this, we proposed Pathology Knowledge-enhanced Network (PKNet) as the baseline model for PathVG. PKNet leverages the knowledge-enhancement capabilities of Large Language Models (LLMs) to convert pathological terms with implicit information into explicit visual features, and fuses knowledge features with expression features through the designed Knowledge Fusion Module (KFM). The proposed method achieves state-of-the-art performance on the PathVG benchmark.

Whole slide image (WSI) analysis has become increasingly important in the medical imaging community, enabling automated and objective diagnosis, prognosis, and therapeutic-response prediction. However, in clinical practice, the ever-evolving environment hamper the utility of WSI analysis models. In this paper, we propose the FIRST continual learning framework for WSI analysis, named ConSlide, to tackle the challenges of enormous image size, utilization of hierarchical structure, and catastrophic forgetting by progressive model updating on multiple sequential datasets. Our framework contains three key components. The Hierarchical Interaction Transformer (HIT) is proposed to model and utilize the hierarchical structural knowledge of WSI. The Breakup-Reorganize (BuRo) rehearsal method is developed for WSI data replay with efficient region storing buffer and WSI reorganizing operation. The asynchronous updating mechanism is devised to encourage the network to learn generic and specific knowledge respectively during the replay stage, based on a nested cross-scale similarity learning (CSSL) module. We evaluated the proposed ConSlide on four public WSI datasets from TCGA projects. It performs best over other state-of-the-art methods with a fair WSI-based continual learning setting and achieves a better trade-off of the overall performance and forgetting on previous task

Previous research on radiology report generation has made significant progress in terms of increasing the clinical accuracy of generated reports. In this paper, we emphasize another crucial quality that it should possess, i.e., inter-report consistency, which refers to the capability of generating consistent reports for semantically equivalent radiographs. This quality is even of greater significance than the overall report accuracy in terms of ensuring the system's credibility, as a system prone to providing conflicting results would severely erode users' trust. Regrettably, existing approaches struggle to maintain inter-report consistency, exhibiting biases towards common patterns and susceptibility to lesion variants. To address this issue, we propose ICON, which improves the inter-report consistency of radiology report generation. Aiming at enhancing the system's ability to capture the similarities in semantically equivalent lesions, our approach involves first extracting lesions from input images and examining their characteristics. Then, we introduce a lesion-aware mix-up augmentation technique to ensure that the representations of the semantically equivalent lesions align with the same attributes, by linearly interpolating them during the training phase. Extensive experiments on three publicly available chest X-ray datasets verify the effectiveness of our approach, both in terms of improving the consistency and accuracy of the generated reports.

The global ramifications of the COVID-19 pandemic remain significant, exerting persistent pressure on nations even three years after its initial outbreak. Deep learning models have shown promise in improving COVID-19 diagnostics but require diverse and larger-scale datasets to improve performance. In this paper, we introduce COVIDx CXR-4, an expanded multi-institutional open-source benchmark dataset for chest X-ray image-based computer-aided COVID-19 diagnostics. COVIDx CXR-4 expands significantly on the previous COVIDx CXR-3 dataset by increasing the total patient cohort size by greater than 2.66 times, resulting in 84,818 images from 45,342 patients across multiple institutions. We provide extensive analysis on the diversity of the patient demographic, imaging metadata, and disease distributions to highlight potential dataset biases. To the best of the authors' knowledge, COVIDx CXR-4 is the largest and most diverse open-source COVID-19 CXR dataset and is made publicly available as part of an open initiative to advance research to aid clinicians against the COVID-19 disease.

Fairness or equity in machine learning is profoundly important for societal well-being, but limited public datasets hinder its progress, especially in the area of medicine. It is undeniable that fairness in medicine is one of the most important areas for fairness learning's applications. Currently, no large-scale public medical datasets with 3D imaging data for fairness learning are available, while 3D imaging data in modern clinics are standard tests for disease diagnosis. In addition, existing medical fairness datasets are actually repurposed datasets, and therefore they typically have limited demographic identity attributes with at most three identity attributes of age, gender, and race for fairness modeling. To address this gap, we introduce our Eye Fairness dataset with 30,000 subjects (Harvard-EF) covering three major eye diseases including age-related macular degeneration, diabetic retinopathy, and glaucoma affecting 380 million patients globally. Our Harvard-EF dataset includes both 2D fundus photos and 3D optical coherence tomography scans with six demographic identity attributes including age, gender, race, ethnicity, preferred language, and marital status. We also propose a fair identity scaling (FIS) approach combining group and individual scaling together to improve model fairness. Our FIS approach is compared with various state-of-the-art fairness learning methods with superior performance in the racial, gender, and ethnicity fairness tasks with 2D and 3D imaging data, which demonstrate the utilities of our Harvard-EF dataset for fairness learning. To facilitate fairness comparisons between different models, we propose performance-scaled disparity measures, which can be used to compare model fairness accounting for overall performance levels. The dataset and code are publicly accessible via https://ophai.hms.harvard.edu/datasets/harvard-ef30k.

Contrastive pretraining on parallel image-text data has attained great success in vision-language processing (VLP), as exemplified by CLIP and related methods. However, prior explorations tend to focus on general domains in the web. Biomedical images and text are rather different, but publicly available datasets are small and skew toward chest X-ray, thus severely limiting progress. In this paper, we conducted by far the largest study on biomedical VLP, using 15 million figure-caption pairs extracted from biomedical research articles in PubMed Central. Our dataset (PMC-15M) is two orders of magnitude larger than existing biomedical image-text datasets such as MIMIC-CXR, and spans a diverse range of biomedical images. The standard CLIP method is suboptimal for the biomedical domain. We propose BiomedCLIP with domain-specific adaptations tailored to biomedical VLP. We conducted extensive experiments and ablation studies on standard biomedical imaging tasks from retrieval to classification to visual question-answering (VQA). BiomedCLIP established new state of the art in a wide range of standard datasets, substantially outperformed prior VLP approaches. Surprisingly, BiomedCLIP even outperformed radiology-specific state-of-the-art models such as BioViL on radiology-specific tasks such as RSNA pneumonia detection, thus highlighting the utility in large-scale pretraining across all biomedical image types. We will release our models at https://aka.ms/biomedclip to facilitate future research in biomedical VLP.

In this paper, we release a largest ever medical Question Answering (QA) dataset with 26 million QA pairs. We benchmark many existing approaches in our dataset in terms of both retrieval and generation. Experimental results show that the existing models perform far lower than expected and the released dataset is still challenging in the pre-trained language model era. Moreover, we also experimentally show the benefit of the proposed dataset in many aspects: (i) trained models for other QA datasets in a zero-shot fashion; and (ii) as external knowledge for retrieval-augmented generation (RAG); and (iii) improving existing pre-trained language models by using the QA pairs as a pre-training corpus in continued training manner. We believe that this dataset will not only contribute to medical research but also facilitate both the patients and clinical doctors. See https://github.com/FreedomIntelligence/Huatuo-26M.

Digital pathology enables automatic analysis of histopathological sections using artificial intelligence (AI). Automatic evaluation could improve diagnostic efficiency and help find associations between morphological features and clinical outcome. For development of such prediction models, identifying invasive epithelial cells, and separating these from benign epithelial cells and in situ lesions would be the first step. In this study, we aimed to develop an AI model for segmentation of epithelial cells in sections from breast cancer. We generated epithelial ground truth masks by restaining hematoxylin and eosin (HE) sections with cytokeratin (CK) AE1/AE3, and by pathologists' annotations. HE/CK image pairs were used to train a convolutional neural network, and data augmentation was used to make the model more robust. Tissue microarrays (TMAs) from 839 patients, and whole slide images from two patients were used for training and evaluation of the models. The sections were derived from four cohorts of breast cancer patients. TMAs from 21 patients from a fifth cohort was used as a second test set. In quantitative evaluation, a mean Dice score of 0.70, 0.79, and 0.75 for invasive epithelial cells, benign epithelial cells, and in situ lesions, respectively, were achieved. In qualitative scoring (0-5) by pathologists, results were best for all epithelium and invasive epithelium, with scores of 4.7 and 4.4. Scores for benign epithelium and in situ lesions were 3.7 and 2.0. The proposed model segmented epithelial cells in HE stained breast cancer slides well, but further work is needed for accurate division between the classes. Immunohistochemistry, together with pathologists' annotations, enabled the creation of accurate ground truths. The model is made freely available in FastPathology and the code is available at https://github.com/AICAN-Research/breast-epithelium-segmentation

Histopathological cancer diagnostics has become more complex, and the increasing number of biopsies is a challenge for most pathology laboratories. Thus, development of automatic methods for evaluation of histopathological cancer sections would be of value. In this study, we used 624 whole slide images (WSIs) of breast cancer from a Norwegian cohort. We propose a cascaded convolutional neural network design, called H2G-Net, for semantic segmentation of gigapixel histopathological images. The design involves a detection stage using a patch-wise method, and a refinement stage using a convolutional autoencoder. To validate the design, we conducted an ablation study to assess the impact of selected components in the pipeline on tumour segmentation. Guiding segmentation, using hierarchical sampling and deep heatmap refinement, proved to be beneficial when segmenting the histopathological images. We found a significant improvement when using a refinement network for postprocessing the generated tumour segmentation heatmaps. The overall best design achieved a Dice score of 0.933 on an independent test set of 90 WSIs. The design outperformed single-resolution approaches, such as cluster-guided, patch-wise high-resolution classification using MobileNetV2 (0.872) and a low-resolution U-Net (0.874). In addition, segmentation on a representative x400 WSI took ~58 seconds, using only the CPU. The findings demonstrate the potential of utilizing a refinement network to improve patch-wise predictions. The solution is efficient and does not require overlapping patch inference or ensembling. Furthermore, we showed that deep neural networks can be trained using a random sampling scheme that balances on multiple different labels simultaneously, without the need of storing patches on disk. Future work should involve more efficient patch generation and sampling, as well as improved clustering.

The burgeoning integration of 3D medical imaging into healthcare has led to a substantial increase in the workload of medical professionals. To assist clinicians in their diagnostic processes and alleviate their workload, the development of a robust system for retrieving similar case studies presents a viable solution. While the concept holds great promise, the field of 3D medical text-image retrieval is currently limited by the absence of robust evaluation benchmarks and curated datasets. To remedy this, our study presents a groundbreaking dataset, BIMCV-R (This dataset will be released upon acceptance.), which includes an extensive collection of 8,069 3D CT volumes, encompassing over 2 million slices, paired with their respective radiological reports. Expanding upon the foundational work of our dataset, we craft a retrieval strategy, MedFinder. This approach employs a dual-stream network architecture, harnessing the potential of large language models to advance the field of medical image retrieval beyond existing text-image retrieval solutions. It marks our preliminary step towards developing a system capable of facilitating text-to-image, image-to-text, and keyword-based retrieval tasks.

Recently, pre-trained foundation models have enabled significant advancements in multiple fields. In molecular machine learning, however, where datasets are often hand-curated, and hence typically small, the lack of datasets with labeled features, and codebases to manage those datasets, has hindered the development of foundation models. In this work, we present seven novel datasets categorized by size into three distinct categories: ToyMix, LargeMix and UltraLarge. These datasets push the boundaries in both the scale and the diversity of supervised labels for molecular learning. They cover nearly 100 million molecules and over 3000 sparsely defined tasks, totaling more than 13 billion individual labels of both quantum and biological nature. In comparison, our datasets contain 300 times more data points than the widely used OGB-LSC PCQM4Mv2 dataset, and 13 times more than the quantum-only QM1B dataset. In addition, to support the development of foundational models based on our proposed datasets, we present the Graphium graph machine learning library which simplifies the process of building and training molecular machine learning models for multi-task and multi-level molecular datasets. Finally, we present a range of baseline results as a starting point of multi-task and multi-level training on these datasets. Empirically, we observe that performance on low-resource biological datasets show improvement by also training on large amounts of quantum data. This indicates that there may be potential in multi-task and multi-level training of a foundation model and fine-tuning it to resource-constrained downstream tasks.

Electronic Health Records (EHRs), which contain patients' medical histories in various multi-modal formats, often overlook the potential for joint reasoning across imaging and table modalities underexplored in current EHR Question Answering (QA) systems. In this paper, we introduce EHRXQA, a novel multi-modal question answering dataset combining structured EHRs and chest X-ray images. To develop our dataset, we first construct two uni-modal resources: 1) The MIMIC- CXR-VQA dataset, our newly created medical visual question answering (VQA) benchmark, specifically designed to augment the imaging modality in EHR QA, and 2) EHRSQL (MIMIC-IV), a refashioned version of a previously established table-based EHR QA dataset. By integrating these two uni-modal resources, we successfully construct a multi-modal EHR QA dataset that necessitates both uni-modal and cross-modal reasoning. To address the unique challenges of multi-modal questions within EHRs, we propose a NeuralSQL-based strategy equipped with an external VQA API. This pioneering endeavor enhances engagement with multi-modal EHR sources and we believe that our dataset can catalyze advances in real-world medical scenarios such as clinical decision-making and research. EHRXQA is available at https://github.com/baeseongsu/ehrxqa.

Pathology diagnosis based on EEG signals and decoding brain activity holds immense importance in understanding neurological disorders. With the advancement of artificial intelligence methods and machine learning techniques, the potential for accurate data-driven diagnoses and effective treatments has grown significantly. However, applying machine learning algorithms to real-world datasets presents diverse challenges at multiple levels. The scarcity of labelled data, especially in low regime scenarios with limited availability of real patient cohorts due to high costs of recruitment, underscores the vital deployment of scaling and transfer learning techniques. In this study, we explore a real-world pathology classification task to highlight the effectiveness of data and model scaling and cross-dataset knowledge transfer. As such, we observe varying performance improvements through data scaling, indicating the need for careful evaluation and labelling. Additionally, we identify the challenges of possible negative transfer and emphasize the significance of some key components to overcome distribution shifts and potential spurious correlations and achieve positive transfer. We see improvement in the performance of the target model on the target (NMT) datasets by using the knowledge from the source dataset (TUAB) when a low amount of labelled data was available. Our findings indicate a small and generic model (e.g. ShallowNet) performs well on a single dataset, however, a larger model (e.g. TCN) performs better on transfer and learning from a larger and diverse dataset.

Colorectal Cancer(CRC) poses a great risk to public health. It is the third most common cause of cancer in the US. Development of colorectal polyps is one of the earliest signs of cancer. Early detection and resection of polyps can greatly increase survival rate to 90%. Manual inspection can cause misdetections because polyps vary in color, shape, size and appearance. To this end, Computer-Aided Diagnosis systems(CADx) has been proposed that detect polyps by processing the colonoscopic videos. The system acts a secondary check to help clinicians reduce misdetections so that polyps may be resected before they transform to cancer. Polyps vary in color, shape, size, texture and appearance. As a result, the miss rate of polyps is between 6% and 27% despite the prominence of CADx solutions. Furthermore, sessile and flat polyps which have diameter less than 10 mm are more likely to be undetected. Convolutional Neural Networks(CNN) have shown promising results in polyp segmentation. However, all of these works have a supervised approach and are limited by the size of the dataset. It was observed that smaller datasets reduce the segmentation accuracy of ResUNet++. We train a U-Net to inpaint randomly dropped out pixels in the image as a proxy task. The dataset we use for pre-training is Kvasir-SEG dataset. This is followed by a supervised training on the limited Kvasir-Sessile dataset. Our experimental results demonstrate that with limited annotated dataset and a larger unlabeled dataset, self-supervised approach is a better alternative than fully supervised approach. Specifically, our self-supervised U-Net performs better than five segmentation models which were trained in supervised manner on the Kvasir-Sessile dataset.

The objective of Radiology Report Generation (RRG) is to automatically generate coherent textual analyses of diseases based on radiological images, thereby alleviating the workload of radiologists. Current AI-based methods for RRG primarily focus on modifications to the encoder-decoder model architecture. To advance these approaches, this paper introduces an Organ-Regional Information Driven (ORID) framework which can effectively integrate multi-modal information and reduce the influence of noise from unrelated organs. Specifically, based on the LLaVA-Med, we first construct an RRG-related instruction dataset to improve organ-regional diagnosis description ability and get the LLaVA-Med-RRG. After that, we propose an organ-based cross-modal fusion module to effectively combine the information from the organ-regional diagnosis description and radiology image. To further reduce the influence of noise from unrelated organs on the radiology report generation, we introduce an organ importance coefficient analysis module, which leverages Graph Neural Network (GNN) to examine the interconnections of the cross-modal information of each organ region. Extensive experiments an1d comparisons with state-of-the-art methods across various evaluation metrics demonstrate the superior performance of our proposed method.

Lack of large expert annotated MR datasets makes training deep learning models difficult. Therefore, a cross-modality (MR-CT) deep learning segmentation approach that augments training data using pseudo MR images produced by transforming expert-segmented CT images was developed. Eighty-One T2-weighted MRI scans from 28 patients with non-small cell lung cancers were analyzed. Cross-modality prior encoding the transformation of CT to pseudo MR images resembling T2w MRI was learned as a generative adversarial deep learning model. This model augmented training data arising from 6 expert-segmented T2w MR patient scans with 377 pseudo MRI from non-small cell lung cancer CT patient scans with obtained from the Cancer Imaging Archive. A two-dimensional Unet implemented with batch normalization was trained to segment the tumors from T2w MRI. This method was benchmarked against (a) standard data augmentation and two state-of-the art cross-modality pseudo MR-based augmentation and (b) two segmentation networks. Segmentation accuracy was computed using Dice similarity coefficient (DSC), Hausdroff distance metrics, and volume ratio. The proposed approach produced the lowest statistical variability in the intensity distribution between pseudo and T2w MR images measured as Kullback-Leibler divergence of 0.069. This method produced the highest segmentation accuracy with a DSC of 0.75 and the lowest Hausdroff distance on the test dataset. This approach produced highly similar estimations of tumor growth as an expert (P = 0.37). A novel deep learning MR segmentation was developed that overcomes the limitation of learning robust models from small datasets by leveraging learned cross-modality priors to augment training. The results show the feasibility of the approach and the corresponding improvement over the state-of-the-art methods.

Automated medical image analysis systems often require large amounts of training data with high quality labels, which are difficult and time consuming to generate. This paper introduces Radiology Object in COntext version 2 (ROCOv2), a multimodal dataset consisting of radiological images and associated medical concepts and captions extracted from the PMC Open Access subset. It is an updated version of the ROCO dataset published in 2018, and adds 35,705 new images added to PMC since 2018. It further provides manually curated concepts for imaging modalities with additional anatomical and directional concepts for X-rays. The dataset consists of 79,789 images and has been used, with minor modifications, in the concept detection and caption prediction tasks of ImageCLEFmedical Caption 2023. The dataset is suitable for training image annotation models based on image-caption pairs, or for multi-label image classification using Unified Medical Language System (UMLS) concepts provided with each image. In addition, it can serve for pre-training of medical domain models, and evaluation of deep learning models for multi-task learning.

The global cost of drug discovery and development exceeds $200 billion annually. The main results of drug discovery and development are the outcomes of clinical trials, which directly influence the regulatory approval of new drug candidates and ultimately affect patient outcomes. Despite their significance, large-scale, high-quality clinical trial outcome data are not readily available to the public. Suppose a large clinical trial outcome dataset is provided; machine learning researchers can potentially develop accurate prediction models using past trials and outcome labels, which could help prioritize and optimize therapeutic programs, ultimately benefiting patients. This paper introduces Clinical Trial Outcome (CTO) dataset, the largest trial outcome dataset with around 479K clinical trials, aggregating outcomes from multiple sources of weakly supervised labels, minimizing the noise from individual sources, and eliminating the need for human annotation. These sources include large language model (LLM) decisions on trial-related documents, news headline sentiments, stock prices of trial sponsors, trial linkages across phases, and other signals such as patient dropout rates and adverse events. CTO's labels show unprecedented agreement with supervised clinical trial outcome labels from test split of the supervised TOP dataset, with a 91 F1.

Short-video platforms show an increasing impact on people's daily lives nowadays, with billions of active users spending plenty of time each day. The interactions between users and online platforms give rise to many scientific problems across computational social science and artificial intelligence. However, despite the rapid development of short-video platforms, currently there are serious shortcomings in existing relevant datasets on three aspects: inadequate user-video feedback, limited user attributes and lack of video content. To address these problems, we provide a large-scale dataset with rich user behavior, attributes and video content from a real mobile short-video platform. This dataset covers 10,000 voluntary users and 153,561 videos, and we conduct four-fold technical validations of the dataset. First, we verify the richness of the behavior and attribute data. Second, we confirm the representing ability of the content features. Third, we provide benchmarking results on recommendation algorithms with our dataset. Finally, we explore the filter bubble phenomenon on the platform using the dataset. We believe the dataset could support the broad research community, including but not limited to user modeling, social science, human behavior understanding, etc. The dataset and code is available at https://github.com/tsinghua-fib-lab/ShortVideo_dataset.

This technical report provides a detailed overview of Endoscapes, a dataset of laparoscopic cholecystectomy (LC) videos with highly intricate annotations targeted at automated assessment of the Critical View of Safety (CVS). Endoscapes comprises 201 LC videos with frames annotated sparsely but regularly with segmentation masks, bounding boxes, and CVS assessment by three different clinical experts. Altogether, there are 11090 frames annotated with CVS and 1933 frames annotated with tool and anatomy bounding boxes from the 201 videos, as well as an additional 422 frames from 50 of the 201 videos annotated with tool and anatomy segmentation masks. In this report, we provide detailed dataset statistics (size, class distribution, dataset splits, etc.) and a comprehensive performance benchmark for instance segmentation, object detection, and CVS prediction. The dataset and model checkpoints are publically available at https://github.com/CAMMA-public/Endoscapes.

Chest X-rays (CXRs) are the most frequently performed imaging test in clinical practice. Recent advances in the development of vision-language foundation models (FMs) give rise to the possibility of performing automated CXR interpretation, which can assist physicians with clinical decision-making and improve patient outcomes. However, developing FMs that can accurately interpret CXRs is challenging due to the (1) limited availability of large-scale vision-language datasets in the medical image domain, (2) lack of vision and language encoders that can capture the complexities of medical data, and (3) absence of evaluation frameworks for benchmarking the abilities of FMs on CXR interpretation. In this work, we address these challenges by first introducing CheXinstruct - a large-scale instruction-tuning dataset curated from 28 publicly-available datasets. We then present CheXagent - an instruction-tuned FM capable of analyzing and summarizing CXRs. To build CheXagent, we design a clinical large language model (LLM) for parsing radiology reports, a vision encoder for representing CXR images, and a network to bridge the vision and language modalities. Finally, we introduce CheXbench - a novel benchmark designed to systematically evaluate FMs across 8 clinically-relevant CXR interpretation tasks. Extensive quantitative evaluations and qualitative reviews with five expert radiologists demonstrate that CheXagent outperforms previously-developed general- and medical-domain FMs on CheXbench tasks. Furthermore, in an effort to improve model transparency, we perform a fairness evaluation across factors of sex, race and age to highlight potential performance disparities. Our project is at https://stanford-aimi.github.io/chexagent.html.

The scaling laws and extraordinary performance of large foundation models motivate the development and utilization of such models in biomedicine. However, despite early promising results on some biomedical benchmarks, there are still major challenges that need to be addressed before these models can be used in real-world clinics. Frontier general-domain models such as GPT-4V still have significant performance gaps in multimodal biomedical applications. More importantly, less-acknowledged pragmatic issues, including accessibility, model cost, and tedious manual evaluation make it hard for clinicians to use state-of-the-art large models directly on private patient data. Here, we explore training open-source small multimodal models (SMMs) to bridge competency gaps for unmet clinical needs in radiology. To maximize data efficiency, we adopt a modular approach by incorporating state-of-the-art pre-trained models for image and text modalities, and focusing on training a lightweight adapter to ground each modality to the text embedding space, as exemplified by LLaVA-Med. For training, we assemble a large dataset of over 697 thousand radiology image-text pairs. For evaluation, we propose CheXprompt, a GPT-4-based metric for factuality evaluation, and demonstrate its parity with expert evaluation. For best practice, we conduct a systematic ablation study on various choices in data engineering and multimodal training. The resulting LlaVA-Rad (7B) model attains state-of-the-art results on standard radiology tasks such as report generation and cross-modal retrieval, even outperforming much larger models such as GPT-4V and Med-PaLM M (84B). The inference of LlaVA-Rad is fast and can be performed on a single V100 GPU in private settings, offering a promising state-of-the-art tool for real-world clinical applications.

Lung diseases remain a critical global health concern, and it's crucial to have accurate and quick ways to diagnose them. This work focuses on classifying different lung diseases into five groups: viral pneumonia, bacterial pneumonia, COVID, tuberculosis, and normal lungs. Employing advanced deep learning techniques, we explore a diverse range of models including CNN, hybrid models, ensembles, transformers, and Big Transfer. The research encompasses comprehensive methodologies such as hyperparameter tuning, stratified k-fold cross-validation, and transfer learning with fine-tuning.Remarkably, our findings reveal that the Xception model, fine-tuned through 5-fold cross-validation, achieves the highest accuracy of 96.21\%. This success shows that our methods work well in accurately identifying different lung diseases. The exploration of explainable artificial intelligence (XAI) methodologies further enhances our understanding of the decision-making processes employed by these models, contributing to increased trust in their clinical applications.

Medical Visual Question Answering (MedVQA), which offers language responses to image-based medical inquiries, represents a challenging task and significant advancement in healthcare. It assists medical experts to swiftly interpret medical images, thereby enabling faster and more accurate diagnoses. However, the model interpretability and transparency of existing MedVQA solutions are often limited, posing challenges in understanding their decision-making processes. To address this issue, we devise a semi-automated annotation process to streamline data preparation and build new benchmark MedVQA datasets R-RAD, R-SLAKE and R-Path. These datasets provide intermediate medical decision-making rationales generated by multimodal large language models and human annotations for question-answering pairs in existing MedVQA datasets, i.e., VQA-RAD, SLAKE and PathVQA. Moreover, we design a novel framework, MedThink, which finetunes lightweight pretrained generative models by incorporating medical decision-making rationales. MedThink includes three distinct strategies to generate decision outcomes and corresponding rationales, thereby clearly showcasing the medical decision-making process during reasoning. Our comprehensive experiments show that our method achieves an accuracy of 83.5% on R-RAD, 86.3% on R-SLAKE and 87.2% on R-Path. These results significantly exceed those of existing state-of-the-art models with comparable parameters. Datasets and code will be released.

We present the Temporal Graph Benchmark (TGB), a collection of challenging and diverse benchmark datasets for realistic, reproducible, and robust evaluation of machine learning models on temporal graphs. TGB datasets are of large scale, spanning years in duration, incorporate both node and edge-level prediction tasks and cover a diverse set of domains including social, trade, transaction, and transportation networks. For both tasks, we design evaluation protocols based on realistic use-cases. We extensively benchmark each dataset and find that the performance of common models can vary drastically across datasets. In addition, on dynamic node property prediction tasks, we show that simple methods often achieve superior performance compared to existing temporal graph models. We believe that these findings open up opportunities for future research on temporal graphs. Finally, TGB provides an automated machine learning pipeline for reproducible and accessible temporal graph research, including data loading, experiment setup and performance evaluation. TGB will be maintained and updated on a regular basis and welcomes community feedback. TGB datasets, data loaders, example codes, evaluation setup, and leaderboards are publicly available at https://tgb.complexdatalab.com/.

We present the RODEM Jet Datasets, a comprehensive collection of simulated large-radius jets designed to support the development and evaluation of machine-learning algorithms in particle physics. These datasets encompass a diverse range of jet sources, including quark/gluon jets, jets from the decay of W bosons, top quarks, and heavy new-physics particles. The datasets provide detailed substructure information, including jet kinematics, constituent kinematics, and track displacement details, enabling a wide range of applications in jet tagging, anomaly detection, and generative modelling.

An increasing number of public datasets have shown a marked impact on automated organ segmentation and tumor detection. However, due to the small size and partially labeled problem of each dataset, as well as a limited investigation of diverse types of tumors, the resulting models are often limited to segmenting specific organs/tumors and ignore the semantics of anatomical structures, nor can they be extended to novel domains. To address these issues, we propose the CLIP-Driven Universal Model, which incorporates text embedding learned from Contrastive Language-Image Pre-training (CLIP) to segmentation models. This CLIP-based label encoding captures anatomical relationships, enabling the model to learn a structured feature embedding and segment 25 organs and 6 types of tumors. The proposed model is developed from an assembly of 14 datasets, using a total of 3,410 CT scans for training and then evaluated on 6,162 external CT scans from 3 additional datasets. We rank first on the Medical Segmentation Decathlon (MSD) public leaderboard and achieve state-of-the-art results on Beyond The Cranial Vault (BTCV). Additionally, the Universal Model is computationally more efficient (6x faster) compared with dataset-specific models, generalized better to CT scans from varying sites, and shows stronger transfer learning performance on novel tasks.

Due to the cost of developing and training deep learning models from scratch, machine learning engineers have begun to reuse pre-trained models (PTMs) and fine-tune them for downstream tasks. PTM registries known as "model hubs" support engineers in distributing and reusing deep learning models. PTM packages include pre-trained weights, documentation, model architectures, datasets, and metadata. Mining the information in PTM packages will enable the discovery of engineering phenomena and tools to support software engineers. However, accessing this information is difficult - there are many PTM registries, and both the registries and the individual packages may have rate limiting for accessing the data. We present an open-source dataset, PTMTorrent, to facilitate the evaluation and understanding of PTM packages. This paper describes the creation, structure, usage, and limitations of the dataset. The dataset includes a snapshot of 5 model hubs and a total of 15,913 PTM packages. These packages are represented in a uniform data schema for cross-hub mining. We describe prior uses of this data and suggest research opportunities for mining using our dataset. The PTMTorrent dataset (v1) is available at: https://app.globus.org/file-manager?origin_id=55e17a6e-9d8f-11ed-a2a2-8383522b48d9&origin_path=%2F~%2F. Our dataset generation tools are available on GitHub: https://doi.org/10.5281/zenodo.7570357.

Small sample sizes are common in many disciplines, which necessitates pooling roughly similar datasets across multiple institutions to study weak but relevant associations between images and disease outcomes. Such data often manifest shift/imbalance in covariates (i.e., secondary non-imaging data). Controlling for such nuisance variables is common within standard statistical analysis, but the ideas do not directly apply to overparameterized models. Consequently, recent work has shown how strategies from invariant representation learning provides a meaningful starting point, but the current repertoire of methods is limited to accounting for shifts/imbalances in just a couple of covariates at a time. In this paper, we show how viewing this problem from the perspective of Category theory provides a simple and effective solution that completely avoids elaborate multi-stage training pipelines that would otherwise be needed. We show the effectiveness of this approach via extensive experiments on real datasets. Further, we discuss how this style of formulation offers a unified perspective on at least 5+ distinct problem settings, from self-supervised learning to matching problems in 3D reconstruction.

Radiotherapy (RT) planning is complex, subjective, and time-intensive. Advances in artificial intelligence (AI) promise to improve its precision, efficiency, and consistency, but progress is often limited by the scarcity of large, standardized datasets. To address this, we introduce the Automated Iterative RT Planning (AIRTP) system, a scalable solution for generating high-quality treatment plans. This scalable solution is designed to generate substantial volumes of consistently high-quality treatment plans, overcoming a key obstacle in the advancement of AI-driven RT planning. Our AIRTP pipeline adheres to clinical guidelines and automates essential steps, including organ-at-risk (OAR) contouring, helper structure creation, beam setup, optimization, and plan quality improvement, using AI integrated with RT planning software like Eclipse of Varian. Furthermore, a novel approach for determining optimization parameters to reproduce 3D dose distributions, i.e. a method to convert dose predictions to deliverable treatment plans constrained by machine limitations. A comparative analysis of plan quality reveals that our automated pipeline produces treatment plans of quality comparable to those generated manually, which traditionally require several hours of labor per plan. Committed to public research, the first data release of our AIRTP pipeline includes nine cohorts covering head-and-neck and lung cancer sites to support an AAPM 2025 challenge. This data set features more than 10 times the number of plans compared to the largest existing well-curated public data set to our best knowledge. Repo:{https://github.com/RiqiangGao/GDP-HMM_AAPMChallenge}

Systematic literature reviews (SLRs) play an essential role in summarising, synthesising and validating scientific evidence. In recent years, there has been a growing interest in using machine learning techniques to automate the identification of relevant studies for SLRs. However, the lack of standardised evaluation datasets makes comparing the performance of such automated literature screening systems difficult. In this paper, we analyse the citation screening evaluation datasets, revealing that many of the available datasets are either too small, suffer from data leakage or have limited applicability to systems treating automated literature screening as a classification task, as opposed to, for example, a retrieval or question-answering task. To address these challenges, we introduce CSMeD, a meta-dataset consolidating nine publicly released collections, providing unified access to 325 SLRs from the fields of medicine and computer science. CSMeD serves as a comprehensive resource for training and evaluating the performance of automated citation screening models. Additionally, we introduce CSMeD-FT, a new dataset designed explicitly for evaluating the full text publication screening task. To demonstrate the utility of CSMeD, we conduct experiments and establish baselines on new datasets.

Complex prediction models such as deep learning are the output from fitting machine learning, neural networks, or AI models to a set of training data. These are now standard tools in science. A key challenge with the current generation of models is that they are highly parameterized, which makes describing and interpreting the prediction strategies difficult. We use topological data analysis to transform these complex prediction models into pictures representing a topological view. The result is a map of the predictions that enables inspection. The methods scale up to large datasets across different domains and enable us to detect labeling errors in training data, understand generalization in image classification, and inspect predictions of likely pathogenic mutations in the BRCA1 gene.

Tuberculosis (TB) is caused by the bacterium Mycobacterium tuberculosis, primarily affecting the lungs. Early detection is crucial for improving treatment effectiveness and reducing transmission risk. Artificial intelligence (AI), particularly through image classification of chest X-rays, can assist in TB detection. However, class imbalance in TB chest X-ray datasets presents a challenge for accurate classification. In this paper, we propose a few-shot learning (FSL) approach using the Prototypical Network algorithm to address this issue. We compare the performance of ResNet-18, ResNet-50, and VGG16 in feature extraction from the TBX11K Chest X-ray dataset. Experimental results demonstrate classification accuracies of 98.93% for ResNet-18, 98.60% for ResNet-50, and 33.33% for VGG16. These findings indicate that the proposed method outperforms others in mitigating data imbalance, which is particularly beneficial for disease classification applications.

Driven by the recent advances in deep learning methods and, in particular, by the development of modern self-supervised learning algorithms, increased interest and efforts have been devoted to build foundation models (FMs) for medical images. In this work, we present our scalable training pipeline for large pathology imaging data, and a comprehensive analysis of various hyperparameter choices and training techniques for building pathology FMs. We release and make publicly available the first batch of our pathology FMs (https://github.com/kaiko-ai/towards_large_pathology_fms) trained on open-access TCGA whole slide images, a commonly used collection of pathology images. The experimental evaluation shows that our models reach state-of-the-art performance on various patch-level downstream tasks, ranging from breast cancer subtyping to colorectal nuclear segmentation. Finally, to unify the evaluation approaches used in the field and to simplify future comparisons of different FMs, we present an open-source framework (https://github.com/kaiko-ai/eva) designed for the consistent evaluation of pathology FMs across various downstream tasks.

Radiology report generation (RRG) has attracted significant attention due to its potential to reduce the workload of radiologists. Current RRG approaches are still unsatisfactory against clinical standards. This paper introduces a novel RRG method, LM-RRG, that integrates large models (LMs) with clinical quality reinforcement learning to generate accurate and comprehensive chest X-ray radiology reports. Our method first designs a large language model driven feature extractor to analyze and interpret different regions of the chest X-ray image, emphasizing specific regions with medical significance. Next, based on the large model's decoder, we develop a multimodal report generator that leverages multimodal prompts from visual features and textual instruction to produce the radiology report in an auto-regressive way. Finally, to better reflect the clinical significant and insignificant errors that radiologists would normally assign in the report, we introduce a novel clinical quality reinforcement learning strategy. It utilizes the radiology report clinical quality (RadCliQ) metric as a reward function in the learning process. Extensive experiments on the MIMIC-CXR and IU-Xray datasets demonstrate the superiority of our method over the state of the art.

Obtaining text datasets with semantic annotations is an effortful process, yet crucial for supervised training in natural language processsing (NLP). In general, developing and applying new NLP pipelines in domain-specific contexts for tasks often requires custom designed datasets to address NLP tasks in supervised machine learning fashion. When operating in non-English languages for medical data processing, this exposes several minor and major, interconnected problems such as lack of task-matching datasets as well as task-specific pre-trained models. In our work we suggest to leverage pretrained language models for training data acquisition in order to retrieve sufficiently large datasets for training smaller and more efficient models for use-case specific tasks. To demonstrate the effectiveness of your approach, we create a custom dataset which we use to train a medical NER model for German texts, GPTNERMED, yet our method remains language-independent in principle. Our obtained dataset as well as our pre-trained models are publicly available at: https://github.com/frankkramer-lab/GPTNERMED

Despite the progress made by multimodal large language models (MLLMs) in computational pathology, they remain limited by a predominant focus on patch-level analysis, missing essential contextual information at the whole-slide level. The lack of large-scale instruction datasets and the gigapixel scale of whole slide images (WSIs) pose significant developmental challenges. In this paper, we present SlideChat, the first vision-language assistant capable of understanding gigapixel whole-slide images, exhibiting excellent multimodal conversational capability and response complex instruction across diverse pathology scenarios. To support its development, we created SlideInstruction, the largest instruction-following dataset for WSIs consisting of 4.2K WSI captions and 176K VQA pairs with multiple categories. Furthermore, we propose SlideBench, a multimodal benchmark that incorporates captioning and VQA tasks to assess SlideChat's capabilities in varied clinical settings such as microscopy, diagnosis. Compared to both general and specialized MLLMs, SlideChat exhibits exceptional capabilities achieving state-of-the-art performance on 18 of 22 tasks. For example, it achieved an overall accuracy of 81.17% on SlideBench-VQA (TCGA), and 54.15% on SlideBench-VQA (BCNB). We will fully release SlideChat, SlideInstruction and SlideBench as open-source resources to facilitate research and development in computational pathology.

Generating Natural Language Explanations (NLEs) for model predictions on medical images, particularly those depicting thoracic pathologies, remains a critical and challenging task. Existing methodologies often struggle due to general models' insufficient domain-specific medical knowledge and privacy concerns associated with retrieval-based augmentation techniques. To address these issues, we propose a novel Vision-Language framework augmented with a Knowledge Graph (KG)-based datastore, which enhances the model's understanding by incorporating additional domain-specific medical knowledge essential for generating accurate and informative NLEs. Our framework employs a KG-based retrieval mechanism that not only improves the precision of the generated explanations but also preserves data privacy by avoiding direct data retrieval. The KG datastore is designed as a plug-and-play module, allowing for seamless integration with various model architectures. We introduce and evaluate three distinct frameworks within this paradigm: KG-LLaVA, which integrates the pre-trained LLaVA model with KG-RAG; Med-XPT, a custom framework combining MedCLIP, a transformer-based projector, and GPT-2; and Bio-LLaVA, which adapts LLaVA by incorporating the Bio-ViT-L vision model. These frameworks are validated on the MIMIC-NLE dataset, where they achieve state-of-the-art results, underscoring the effectiveness of KG augmentation in generating high-quality NLEs for thoracic pathologies.

Photovoltaic (PV) energy generation plays a crucial role in the energy transition. Small-scale PV installations are deployed at an unprecedented pace, and their integration into the grid can be challenging since public authorities often lack quality data about them. Overhead imagery is increasingly used to improve the knowledge of residential PV installations with machine learning models capable of automatically mapping these installations. However, these models cannot be easily transferred from one region or data source to another due to differences in image acquisition. To address this issue known as domain shift and foster the development of PV array mapping pipelines, we propose a dataset containing aerial images, annotations, and segmentation masks. We provide installation metadata for more than 28,000 installations. We provide ground truth segmentation masks for 13,000 installations, including 7,000 with annotations for two different image providers. Finally, we provide installation metadata that matches the annotation for more than 8,000 installations. Dataset applications include end-to-end PV registry construction, robust PV installations mapping, and analysis of crowdsourced datasets.

Instance level detection and segmentation of thoracic diseases or abnormalities are crucial for automatic diagnosis in chest X-ray images. Leveraging on constant structure and disease relations extracted from domain knowledge, we propose a structure-aware relation network (SAR-Net) extending Mask R-CNN. The SAR-Net consists of three relation modules: 1. the anatomical structure relation module encoding spatial relations between diseases and anatomical parts. 2. the contextual relation module aggregating clues based on query-key pair of disease RoI and lung fields. 3. the disease relation module propagating co-occurrence and causal relations into disease proposals. Towards making a practical system, we also provide ChestX-Det, a chest X-Ray dataset with instance-level annotations (boxes and masks). ChestX-Det is a subset of the public dataset NIH ChestX-ray14. It contains ~3500 images of 13 common disease categories labeled by three board-certified radiologists. We evaluate our SAR-Net on it and another dataset DR-Private. Experimental results show that it can enhance the strong baseline of Mask R-CNN with significant improvements. The ChestX-Det is released at https://github.com/Deepwise-AILab/ChestX-Det-Dataset.

Cancer has relational information residing at varying scales, modalities, and resolutions of the acquired data, such as radiology, pathology, genomics, proteomics, and clinical records. Integrating diverse data types can improve the accuracy and reliability of cancer diagnosis and treatment. There can be disease-related information that is too subtle for humans or existing technological tools to discern visually. Traditional methods typically focus on partial or unimodal information about biological systems at individual scales and fail to encapsulate the complete spectrum of the heterogeneous nature of data. Deep neural networks have facilitated the development of sophisticated multimodal data fusion approaches that can extract and integrate relevant information from multiple sources. Recent deep learning frameworks such as Graph Neural Networks (GNNs) and Transformers have shown remarkable success in multimodal learning. This review article provides an in-depth analysis of the state-of-the-art in GNNs and Transformers for multimodal data fusion in oncology settings, highlighting notable research studies and their findings. We also discuss the foundations of multimodal learning, inherent challenges, and opportunities for integrative learning in oncology. By examining the current state and potential future developments of multimodal data integration in oncology, we aim to demonstrate the promising role that multimodal neural networks can play in cancer prevention, early detection, and treatment through informed oncology practices in personalized settings.

Synthetic medical data generation has opened up new possibilities in the healthcare domain, offering a powerful tool for simulating clinical scenarios, enhancing diagnostic and treatment quality, gaining granular medical knowledge, and accelerating the development of unbiased algorithms. In this context, we present a novel approach called ViewXGen, designed to overcome the limitations of existing methods that rely on general domain pipelines using only radiology reports to generate frontal-view chest X-rays. Our approach takes into consideration the diverse view positions found in the dataset, enabling the generation of chest X-rays with specific views, which marks a significant advancement in the field. To achieve this, we introduce a set of specially designed tokens for each view position, tailoring the generation process to the user's preferences. Furthermore, we leverage multi-view chest X-rays as input, incorporating valuable information from different views within the same study. This integration rectifies potential errors and contributes to faithfully capturing abnormal findings in chest X-ray generation. To validate the effectiveness of our approach, we conducted statistical analyses, evaluating its performance in a clinical efficacy metric on the MIMIC-CXR dataset. Also, human evaluation demonstrates the remarkable capabilities of ViewXGen, particularly in producing realistic view-specific X-rays that closely resemble the original images.

Plant diseases pose significant threats to agriculture. It necessitates proper diagnosis and effective treatment to safeguard crop yields. To automate the diagnosis process, image segmentation is usually adopted for precisely identifying diseased regions, thereby advancing precision agriculture. Developing robust image segmentation models for plant diseases demands high-quality annotations across numerous images. However, existing plant disease datasets typically lack segmentation labels and are often confined to controlled laboratory settings, which do not adequately reflect the complexity of natural environments. Motivated by this fact, we established PlantSeg, a large-scale segmentation dataset for plant diseases. PlantSeg distinguishes itself from existing datasets in three key aspects. (1) Annotation type: Unlike the majority of existing datasets that only contain class labels or bounding boxes, each image in PlantSeg includes detailed and high-quality segmentation masks, associated with plant types and disease names. (2) Image source: Unlike typical datasets that contain images from laboratory settings, PlantSeg primarily comprises in-the-wild plant disease images. This choice enhances the practical applicability, as the trained models can be applied for integrated disease management. (3) Scale: PlantSeg is extensive, featuring 11,400 images with disease segmentation masks and an additional 8,000 healthy plant images categorized by plant type. Extensive technical experiments validate the high quality of PlantSeg's annotations. This dataset not only allows researchers to evaluate their image classification methods but also provides a critical foundation for developing and benchmarking advanced plant disease segmentation algorithms.

One fundamental limitation to the research of bird strike prevention is the lack of a large-scale dataset taken directly from real-world airports. Existing relevant datasets are either small in size or not dedicated for this purpose. To advance the research and practical solutions for bird strike prevention, in this paper, we present a large-scale challenging dataset AirBirds that consists of 118,312 time-series images, where a total of 409,967 bounding boxes of flying birds are manually, carefully annotated. The average size of all annotated instances is smaller than 10 pixels in 1920x1080 images. Images in the dataset are captured over 4 seasons of a whole year by a network of cameras deployed at a real-world airport, covering diverse bird species, lighting conditions and 13 meteorological scenarios. To the best of our knowledge, it is the first large-scale image dataset that directly collects flying birds in real-world airports for bird strike prevention. This dataset is publicly available at https://airbirdsdata.github.io/.

In order to fully harness the potential of machine learning, it is crucial to establish a system that renders the field more accessible and less daunting for individuals who may not possess a comprehensive understanding of its intricacies. The paper describes the design of a system that integrates AutoML, XAI, and synthetic data generation to provide a great UX design for users. The system allows users to navigate and harness the power of machine learning while abstracting its complexities and providing high usability. The paper proposes two novel classifiers, Logistic Regression Forest and Support Vector Tree, for enhanced model performance, achieving 96\% accuracy on a diabetes dataset and 93\% on a survey dataset. The paper also introduces a model-dependent local interpreter called MEDLEY and evaluates its interpretation against LIME, Greedy, and Parzen. Additionally, the paper introduces LLM-based synthetic data generation, library-based data generation, and enhancing the original dataset with GAN. The findings on synthetic data suggest that enhancing the original dataset with GAN is the most reliable way to generate synthetic data, as evidenced by KS tests, standard deviation, and feature importance. The authors also found that GAN works best for quantitative datasets.

This paper describes EMBER: a labeled benchmark dataset for training machine learning models to statically detect malicious Windows portable executable files. The dataset includes features extracted from 1.1M binary files: 900K training samples (300K malicious, 300K benign, 300K unlabeled) and 200K test samples (100K malicious, 100K benign). To accompany the dataset, we also release open source code for extracting features from additional binaries so that additional sample features can be appended to the dataset. This dataset fills a void in the information security machine learning community: a benign/malicious dataset that is large, open and general enough to cover several interesting use cases. We enumerate several use cases that we considered when structuring the dataset. Additionally, we demonstrate one use case wherein we compare a baseline gradient boosted decision tree model trained using LightGBM with default settings to MalConv, a recently published end-to-end (featureless) deep learning model for malware detection. Results show that even without hyper-parameter optimization, the baseline EMBER model outperforms MalConv. The authors hope that the dataset, code and baseline model provided by EMBER will help invigorate machine learning research for malware detection, in much the same way that benchmark datasets have advanced computer vision research.

Automated slice classification is clinically relevant since it can be incorporated into medical image segmentation workflows as a preprocessing step that would flag slices with a higher probability of containing tumors, thereby directing physicians attention to the important slices. In this work, we train a ResNet-18 network to classify axial slices of lymphoma PET/CT images (collected from two institutions) depending on whether the slice intercepted a tumor (positive slice) in the 3D image or if the slice did not (negative slice). Various instances of the network were trained on 2D axial datasets created in different ways: (i) slice-level split and (ii) patient-level split; inputs of different types were used: (i) only PET slices and (ii) concatenated PET and CT slices; and different training strategies were employed: (i) center-aware (CAW) and (ii) center-agnostic (CAG). Model performances were compared using the area under the receiver operating characteristic curve (AUROC) and the area under the precision-recall curve (AUPRC), and various binary classification metrics. We observe and describe a performance overestimation in the case of slice-level split as compared to the patient-level split training. The model trained using patient-level split data with the network input containing only PET slices in the CAG training regime was the best performing/generalizing model on a majority of metrics. Our models were additionally more closely compared using the sensitivity metric on the positive slices from their respective test sets.

Medical image classification in radiology faces significant challenges, particularly in generalizing to unseen pathologies. In contrast, CLIP offers a promising solution by leveraging multimodal learning to improve zero-shot classification performance. However, in the medical domain, lesions can be small and might not be well represented in the embedding space. Therefore, in this paper, we explore the potential of visual prompt engineering to enhance the capabilities of Vision Language Models (VLMs) in radiology. Leveraging BiomedCLIP, trained on extensive biomedical image-text pairs, we investigate the impact of embedding visual markers directly within radiological images to guide the model's attention to critical regions. Our evaluation on the JSRT dataset, focusing on lung nodule malignancy classification, demonstrates that incorporating visual prompts x2013 such as arrows, circles, and contours x2013 significantly improves classification metrics including AUROC, AUPRC, F1 score, and accuracy. Moreover, the study provides attention maps, showcasing enhanced model interpretability and focus on clinically relevant areas. These findings underscore the efficacy of visual prompt engineering as a straightforward yet powerful approach to advance VLM performance in medical image analysis.

This paper presents a differentially private approach to Kaplan-Meier estimation that achieves accurate survival probability estimates while safeguarding individual privacy. The Kaplan-Meier estimator is widely used in survival analysis to estimate survival functions over time, yet applying it to sensitive datasets, such as clinical records, risks revealing private information. To address this, we introduce a novel algorithm that applies time-indexed Laplace noise, dynamic clipping, and smoothing to produce a privacy-preserving survival curve while maintaining the cumulative structure of the Kaplan-Meier estimator. By scaling noise over time, the algorithm accounts for decreasing sensitivity as fewer individuals remain at risk, while dynamic clipping and smoothing prevent extreme values and reduce fluctuations, preserving the natural shape of the survival curve. Our results, evaluated on the NCCTG lung cancer dataset, show that the proposed method effectively lowers root mean squared error (RMSE) and enhances accuracy across privacy budgets (epsilon). At epsilon = 10, the algorithm achieves an RMSE as low as 0.04, closely approximating non-private estimates. Additionally, membership inference attacks reveal that higher epsilon values (e.g., epsilon geq 6) significantly reduce influential points, particularly at higher thresholds, lowering susceptibility to inference attacks. These findings confirm that our approach balances privacy and utility, advancing privacy-preserving survival analysis.

Addressing the critical theme of recycling electronic waste (E-waste), this contribution is dedicated to developing advanced automated data processing pipelines as a basis for decision-making and process control. Aligning with the broader goals of the circular economy and the United Nations (UN) Sustainable Development Goals (SDG), our work leverages non-invasive analysis methods utilizing RGB and hyperspectral imaging data to provide both quantitative and qualitative insights into the E-waste stream composition for optimizing recycling efficiency. In this paper, we introduce 'PCB-Vision'; a pioneering RGB-hyperspectral printed circuit board (PCB) benchmark dataset, comprising 53 RGB images of high spatial resolution paired with their corresponding high spectral resolution hyperspectral data cubes in the visible and near-infrared (VNIR) range. Grounded in open science principles, our dataset provides a comprehensive resource for researchers through high-quality ground truths, focusing on three primary PCB components: integrated circuits (IC), capacitors, and connectors. We provide extensive statistical investigations on the proposed dataset together with the performance of several state-of-the-art (SOTA) models, including U-Net, Attention U-Net, Residual U-Net, LinkNet, and DeepLabv3+. By openly sharing this multi-scene benchmark dataset along with the baseline codes, we hope to foster transparent, traceable, and comparable developments of advanced data processing across various scientific communities, including, but not limited to, computer vision and remote sensing. Emphasizing our commitment to supporting a collaborative and inclusive scientific community, all materials, including code, data, ground truth, and masks, will be accessible at https://github.com/hifexplo/PCBVision.

The previous advancements in pathology image understanding primarily involved developing models tailored to specific tasks. Recent studies has demonstrated that the large vision-language model can enhance the performance of various downstream tasks in medical image understanding. In this study, we developed a domain-specific large language-vision assistant (PA-LLaVA) for pathology image understanding. Specifically, (1) we first construct a human pathology image-text dataset by cleaning the public medical image-text data for domain-specific alignment; (2) Using the proposed image-text data, we first train a pathology language-image pretraining (PLIP) model as the specialized visual encoder for pathology image, and then we developed scale-invariant connector to avoid the information loss caused by image scaling; (3) We adopt two-stage learning to train PA-LLaVA, first stage for domain alignment, and second stage for end to end visual question \& answering (VQA) task. In experiments, we evaluate our PA-LLaVA on both supervised and zero-shot VQA datasets, our model achieved the best overall performance among multimodal models of similar scale. The ablation experiments also confirmed the effectiveness of our design. We posit that our PA-LLaVA model and the datasets presented in this work can promote research in field of computational pathology. All codes are available at: https://github.com/ddw2AIGROUP2CQUPT/PA-LLaVA}{https://github.com/ddw2AIGROUP2CQUPT/PA-LLaVA

Background. Fully automatic analysis of myocardial perfusion MRI datasets enables rapid and objective reporting of stress/rest studies in patients with suspected ischemic heart disease. Developing deep learning techniques that can analyze multi-center datasets despite limited training data and variations in software and hardware is an ongoing challenge. Methods. Datasets from 3 medical centers acquired at 3T (n = 150 subjects) were included: an internal dataset (inD; n = 95) and two external datasets (exDs; n = 55) used for evaluating the robustness of the trained deep neural network (DNN) models against differences in pulse sequence (exD-1) and scanner vendor (exD-2). A subset of inD (n = 85) was used for training/validation of a pool of DNNs for segmentation, all using the same spatiotemporal U-Net architecture and hyperparameters but with different parameter initializations. We employed a space-time sliding-patch analysis approach that automatically yields a pixel-wise "uncertainty map" as a byproduct of the segmentation process. In our approach, a given test case is segmented by all members of the DNN pool and the resulting uncertainty maps are leveraged to automatically select the "best" one among the pool of solutions. Results. The proposed DAUGS analysis approach performed similarly to the established approach on the internal dataset (p = n.s.) whereas it significantly outperformed on the external datasets (p < 0.005 for exD-1 and exD-2). Moreover, the number of image series with "failed" segmentation was significantly lower for the proposed vs. the established approach (4.3% vs. 17.1%, p < 0.0005). Conclusions. The proposed DAUGS analysis approach has the potential to improve the robustness of deep learning methods for segmentation of multi-center stress perfusion datasets with variations in the choice of pulse sequence, site location or scanner vendor.

Objective: Data unavailability has been one of the biggest barriers in clinical natural language processing. This paper is aimed at providing a large-scale and publicly available patient note dataset, named PMC-Patients, with relevant articles and similar patients annotations. The ultimate goal of PMC-Patients is to facilitate the development of retrieval-based clinical decision support systems. Materials and Methods: To collect PMC-Patients, we extract patient notes from case reports in PubMed Central by recognizing certain section patterns. Patient-article relevance and patient-patient similarity are annotated by citation relationships in PubMed. In addition, we perform three tasks with PMC-Patients to demonstrate its utility in providing clinical decision support for a given patient, including (1) classifying whether another patient is similar, (2) retrieving similar patients in PMC-Patients, and (3) retrieving relevant articles in PubMed. Results: We collect and release PMC-Patients under the CC BY-NC-SA license, which becomes the largest publicly available patient note dataset so far. PMC-Patients contains 167k patient notes that are annotated with 3.1M relevant articles and 293k similar patients. Qualitative and quantitative analyses reveal the high quality and richness of our dataset. Experiments show that classifying the similarity of patient pairs is relatively easy, but it is hard to retrieve similar patients or relevant articles for a given patient from a large set of candidates. Conclusion: We present PMC-Patients, a large-scale dataset of patient notes with high quality, easy access, diverse conditions, and rich annotations. The proposed dataset can also serve as a hard benchmark for evaluating retrieval-based clinical decision support systems.

Modern machine learning relies on datasets to develop and validate research ideas. Given the growth of publicly available data, finding the right dataset to use is increasingly difficult. Any research question imposes explicit and implicit constraints on how well a given dataset will enable researchers to answer this question, such as dataset size, modality, and domain. We operationalize the task of recommending datasets given a short natural language description of a research idea, to help people find relevant datasets for their needs. Dataset recommendation poses unique challenges as an information retrieval problem; datasets are hard to directly index for search and there are no corpora readily available for this task. To facilitate this task, we build the DataFinder Dataset which consists of a larger automatically-constructed training set (17.5K queries) and a smaller expert-annotated evaluation set (392 queries). Using this data, we compare various information retrieval algorithms on our test set and present a superior bi-encoder retriever for text-based dataset recommendation. This system, trained on the DataFinder Dataset, finds more relevant search results than existing third-party dataset search engines. To encourage progress on dataset recommendation, we release our dataset and models to the public.

Stroke remains a leading cause of global morbidity and mortality, placing a heavy socioeconomic burden. Over the past decade, advances in endovascular reperfusion therapy and the use of CT and MRI imaging for treatment guidance have significantly improved patient outcomes and are now standard in clinical practice. To develop machine learning algorithms that can extract meaningful and reproducible models of brain function for both clinical and research purposes from stroke images - particularly for lesion identification, brain health quantification, and prognosis - large, diverse, and well-annotated public datasets are essential. While only a few datasets with (sub-)acute stroke data were previously available, several large, high-quality datasets have recently been made publicly accessible. However, these existing datasets include only MRI data. In contrast, our dataset is the first to offer comprehensive longitudinal stroke data, including acute CT imaging with angiography and perfusion, follow-up MRI at 2-9 days, as well as acute and longitudinal clinical data up to a three-month outcome. The dataset includes a training dataset of n = 150 and a test dataset of n = 100 scans. Training data is publicly available, while test data will be used exclusively for model validation. We are making this dataset available as part of the 2024 edition of the Ischemic Stroke Lesion Segmentation (ISLES) challenge (https://www.isles-challenge.org/), which continuously aims to establish benchmark methods for acute and sub-acute ischemic stroke lesion segmentation, aiding in creating open stroke imaging datasets and evaluating cutting-edge image processing algorithms.

In this paper, we introduce DRR-RATE, a large-scale synthetic chest X-ray dataset derived from the recently released CT-RATE dataset. DRR-RATE comprises of 50,188 frontal Digitally Reconstructed Radiographs (DRRs) from 21,304 unique patients. Each image is paired with a corresponding radiology text report and binary labels for 18 pathology classes. Given the controllable nature of DRR generation, it facilitates the inclusion of lateral view images and images from any desired viewing position. This opens up avenues for research into new and novel multimodal applications involving paired CT, X-ray images from various views, text, and binary labels. We demonstrate the applicability of DRR-RATE alongside existing large-scale chest X-ray resources, notably the CheXpert dataset and CheXnet model. Experiments demonstrate that CheXnet, when trained and tested on the DRR-RATE dataset, achieves sufficient to high AUC scores for the six common pathologies cited in common literature: Atelectasis, Cardiomegaly, Consolidation, Lung Lesion, Lung Opacity, and Pleural Effusion. Additionally, CheXnet trained on the CheXpert dataset can accurately identify several pathologies, even when operating out of distribution. This confirms that the generated DRR images effectively capture the essential pathology features from CT images. The dataset and labels are publicly accessible at https://huggingface.co/datasets/farrell236/DRR-RATE.

Accurately segmenting different organs from medical images is a critical prerequisite for computer-assisted diagnosis and intervention planning. This study proposes a deep learning-based approach for segmenting various organs from CT and MRI scans and classifying diseases. Our study introduces a novel technique integrating momentum within residual blocks for enhanced training dynamics in medical image analysis. We applied our method in two distinct tasks: segmenting liver, lung, & colon data and classifying abdominal pelvic CT and MRI scans. The proposed approach has shown promising results, outperforming state-of-the-art methods on publicly available benchmarking datasets. For instance, in the lung segmentation dataset, our approach yielded significant enhancements over the TransNetR model, including a 5.72% increase in dice score, a 5.04% improvement in mean Intersection over Union (mIoU), an 8.02% improvement in recall, and a 4.42% improvement in precision. Hence, incorporating momentum led to state-of-the-art performance in both segmentation and classification tasks, representing a significant advancement in the field of medical imaging.

Large multimodal datasets have been instrumental in recent breakthroughs such as CLIP, Stable Diffusion, and GPT-4. At the same time, datasets rarely receive the same research attention as model architectures or training algorithms. To address this shortcoming in the machine learning ecosystem, we introduce DataComp, a benchmark where the training code is fixed and researchers innovate by proposing new training sets. We provide a testbed for dataset experiments centered around a new candidate pool of 12.8B image-text pairs from Common Crawl. Participants in our benchmark design new filtering techniques or curate new data sources and then evaluate their new dataset by running our standardized CLIP training code and testing on 38 downstream test sets. Our benchmark consists of multiple scales, with four candidate pool sizes and associated compute budgets ranging from 12.8M to 12.8B samples seen during training. This multi-scale design facilitates the study of scaling trends and makes the benchmark accessible to researchers with varying resources. Our baseline experiments show that the DataComp workflow is a promising way of improving multimodal datasets. We introduce DataComp-1B, a dataset created by applying a simple filtering algorithm to the 12.8B candidate pool. The resulting 1.4B subset enables training a CLIP ViT-L/14 from scratch to 79.2% zero-shot accuracy on ImageNet. Our new ViT-L/14 model outperforms a larger ViT-g/14 trained on LAION-2B by 0.7 percentage points while requiring 9x less training compute. We also outperform OpenAI's CLIP ViT-L/14 by 3.7 percentage points, which is trained with the same compute budget as our model. These gains highlight the potential for improving model performance by carefully curating training sets. We view DataComp-1B as only the first step and hope that DataComp paves the way toward the next generation of multimodal datasets.

The success of Deep Learning applications critically depends on the quality and scale of the underlying training data. Generative adversarial networks (GANs) can generate arbitrary large datasets, but diversity and fidelity are limited, which has recently been addressed by denoising diffusion probabilistic models (DDPMs) whose superiority has been demonstrated on natural images. In this study, we propose Medfusion, a conditional latent DDPM for medical images. We compare our DDPM-based model against GAN-based models, which constitute the current state-of-the-art in the medical domain. Medfusion was trained and compared with (i) StyleGan-3 on n=101,442 images from the AIROGS challenge dataset to generate fundoscopies with and without glaucoma, (ii) ProGAN on n=191,027 from the CheXpert dataset to generate radiographs with and without cardiomegaly and (iii) wGAN on n=19,557 images from the CRCMS dataset to generate histopathological images with and without microsatellite stability. In the AIROGS, CRMCS, and CheXpert datasets, Medfusion achieved lower (=better) FID than the GANs (11.63 versus 20.43, 30.03 versus 49.26, and 17.28 versus 84.31). Also, fidelity (precision) and diversity (recall) were higher (=better) for Medfusion in all three datasets. Our study shows that DDPM are a superior alternative to GANs for image synthesis in the medical domain.

Semantic segmentation of medical images aims to associate a pixel with a label in a medical image without human initialization. The success of semantic segmentation algorithms is contingent on the availability of high-quality imaging data with corresponding labels provided by experts. We sought to create a large collection of annotated medical image datasets of various clinically relevant anatomies available under open source license to facilitate the development of semantic segmentation algorithms. Such a resource would allow: 1) objective assessment of general-purpose segmentation methods through comprehensive benchmarking and 2) open and free access to medical image data for any researcher interested in the problem domain. Through a multi-institutional effort, we generated a large, curated dataset representative of several highly variable segmentation tasks that was used in a crowd-sourced challenge - the Medical Segmentation Decathlon held during the 2018 Medical Image Computing and Computer Aided Interventions Conference in Granada, Spain. Here, we describe these ten labeled image datasets so that these data may be effectively reused by the research community.

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.

Histopathology plays a central role in clinical medicine and biomedical research. While artificial intelligence shows promising results on many pathological tasks, generalization and dealing with rare diseases, where training data is scarce, remains a challenge. Distilling knowledge from unlabeled data into a foundation model before learning from, potentially limited, labeled data provides a viable path to address these challenges. In this work, we extend the state of the art of foundation models for digital pathology whole slide images by semi-automated data curation and incorporating pathologist domain knowledge. Specifically, we combine computational and pathologist domain knowledge (1) to curate a diverse dataset of 103k slides corresponding to 750 million image patches covering data from different fixation, staining, and scanning protocols as well as data from different indications and labs across the EU and US, (2) for grouping semantically similar slides and tissue patches, and (3) to augment the input images during training. We evaluate the resulting model on a set of public and internal benchmarks and show that although our foundation model is trained with an order of magnitude less slides, it performs on par or better than competing models. We expect that scaling our approach to more data and larger models will further increase its performance and capacity to deal with increasingly complex real world tasks in diagnostics and biomedical research.

The digitization of medical records ushered in a new era of big data to clinical science, and with it the possibility that data could be shared, to multiply insights beyond what investigators could abstract from paper records. The need to share individual-level medical data to accelerate innovation in precision medicine continues to grow, and has never been more urgent, as scientists grapple with the COVID-19 pandemic. However, enthusiasm for the use of big data has been tempered by a fully appropriate concern for patient autonomy and privacy. That is, the ability to extract private or confidential information about an individual, in practice, renders it difficult to share data, since significant infrastructure and data governance must be established before data can be shared. Although HIPAA provided de-identification as an approved mechanism for data sharing, linkage attacks were identified as a major vulnerability. A variety of mechanisms have been established to avoid leaking private information, such as field suppression or abstraction, strictly limiting the amount of information that can be shared, or employing mathematical techniques such as differential privacy. Another approach, which we focus on here, is creating synthetic data that mimics the underlying data. For synthetic data to be a useful mechanism in support of medical innovation and a proxy for real-world evidence, one must demonstrate two properties of the synthetic dataset: (1) any analysis on the real data must be matched by analysis of the synthetic data (statistical fidelity) and (2) the synthetic data must preserve privacy, with minimal risk of re-identification (privacy guarantee). In this paper we propose a framework for quantifying the statistical fidelity and privacy preservation properties of synthetic datasets and demonstrate these metrics for synthetic data generated by Syntegra technology.

Automatic medical report generation (MRG), which possesses significant research value as it can aid radiologists in clinical diagnosis and report composition, has garnered increasing attention. Despite recent progress, generating accurate reports remains arduous due to the requirement for precise clinical comprehension and disease diagnosis inference. Furthermore, owing to the limited accessibility of medical data and the imbalanced distribution of diseases, the underrepresentation of rare diseases in training data makes large-scale medical visual language models (LVLMs) prone to hallucinations, such as omissions or fabrications, severely undermining diagnostic performance and further intensifying the challenges for MRG in practice. In this study, to effectively mitigate hallucinations in medical report generation, we propose a chain-of-medical-thought approach (CoMT), which intends to imitate the cognitive process of human doctors by decomposing diagnostic procedures. The radiological features with different importance are structured into fine-grained medical thought chains to enhance the inferential ability during diagnosis, thereby alleviating hallucination problems and enhancing the diagnostic accuracy of MRG. The code and dataset have been released at https://github.com/FRENKIE-CHIANG/CoMT.

There has been a rapidly growing interest in Automatic Symptom Detection (ASD) and Automatic Diagnosis (AD) systems in the machine learning research literature, aiming to assist doctors in telemedicine services. These systems are designed to interact with patients, collect evidence about their symptoms and relevant antecedents, and possibly make predictions about the underlying diseases. Doctors would review the interactions, including the evidence and the predictions, collect if necessary additional information from patients, before deciding on next steps. Despite recent progress in this area, an important piece of doctors' interactions with patients is missing in the design of these systems, namely the differential diagnosis. Its absence is largely due to the lack of datasets that include such information for models to train on. In this work, we present a large-scale synthetic dataset of roughly 1.3 million patients that includes a differential diagnosis, along with the ground truth pathology, symptoms and antecedents for each patient. Unlike existing datasets which only contain binary symptoms and antecedents, this dataset also contains categorical and multi-choice symptoms and antecedents useful for efficient data collection. Moreover, some symptoms are organized in a hierarchy, making it possible to design systems able to interact with patients in a logical way. As a proof-of-concept, we extend two existing AD and ASD systems to incorporate the differential diagnosis, and provide empirical evidence that using differentials as training signals is essential for the efficiency of such systems or for helping doctors better understand the reasoning of those systems.

This paper introduces MedTrinity-25M, a comprehensive, large-scale multimodal dataset for medicine, covering over 25 million images across 10 modalities, with multigranular annotations for more than 65 diseases. These enriched annotations encompass both global textual information, such as disease/lesion type, modality, region-specific descriptions, and inter-regional relationships, as well as detailed local annotations for regions of interest (ROIs), including bounding boxes, segmentation masks. Unlike existing approach which is limited by the availability of image-text pairs, we have developed the first automated pipeline that scales up multimodal data by generating multigranular visual and texual annotations (in the form of image-ROI-description triplets) without the need for any paired text descriptions. Specifically, data from over 90 different sources have been collected, preprocessed, and grounded using domain-specific expert models to identify ROIs related to abnormal regions. We then build a comprehensive knowledge base and prompt multimodal large language models to perform retrieval-augmented generation with the identified ROIs as guidance, resulting in multigranular texual descriptions. Compared to existing datasets, MedTrinity-25M provides the most enriched annotations, supporting a comprehensive range of multimodal tasks such as captioning and report generation, as well as vision-centric tasks like classification and segmentation. Pretraining on MedTrinity-25M, our model achieves state-of-the-art performance on VQA-RAD and PathVQA, surpassing both multimodal large language models and other representative SoTA approaches. This dataset can also be utilized to support large-scale pre-training of multimodal medical AI models, contributing to the development of future foundation models in the medical domain.

Pancreatic cancer is one of the leading causes of cancer-related death. Accurate detection, segmentation, and differential diagnosis of the full taxonomy of pancreatic lesions, i.e., normal, seven major types of lesions, and other lesions, is critical to aid the clinical decision-making of patient management and treatment. However, existing works focus on segmentation and classification for very specific lesion types (PDAC) or groups. Moreover, none of the previous work considers using lesion prevalence-related non-imaging patient information to assist the differential diagnosis. To this end, we develop a meta-information-aware dual-path transformer and exploit the feasibility of classification and segmentation of the full taxonomy of pancreatic lesions. Specifically, the proposed method consists of a CNN-based segmentation path (S-path) and a transformer-based classification path (C-path). The S-path focuses on initial feature extraction by semantic segmentation using a UNet-based network. The C-path utilizes both the extracted features and meta-information for patient-level classification based on stacks of dual-path transformer blocks that enhance the modeling of global contextual information. A large-scale multi-phase CT dataset of 3,096 patients with pathology-confirmed pancreatic lesion class labels, voxel-wise manual annotations of lesions from radiologists, and patient meta-information, was collected for training and evaluations. Our results show that our method can enable accurate classification and segmentation of the full taxonomy of pancreatic lesions, approaching the accuracy of the radiologist's report and significantly outperforming previous baselines. Results also show that adding the common meta-information, i.e., gender and age, can boost the model's performance, thus demonstrating the importance of meta-information for aiding pancreatic disease diagnosis.

Biomedical imaging datasets are often small and biased, meaning that real-world performance of predictive models can be substantially lower than expected from internal testing. This work proposes using generative image editing to simulate dataset shifts and diagnose failure modes of biomedical vision models; this can be used in advance of deployment to assess readiness, potentially reducing cost and patient harm. Existing editing methods can produce undesirable changes, with spurious correlations learned due to the co-occurrence of disease and treatment interventions, limiting practical applicability. To address this, we train a text-to-image diffusion model on multiple chest X-ray datasets and introduce a new editing method RadEdit that uses multiple masks, if present, to constrain changes and ensure consistency in the edited images. We consider three types of dataset shifts: acquisition shift, manifestation shift, and population shift, and demonstrate that our approach can diagnose failures and quantify model robustness without additional data collection, complementing more qualitative tools for explainable AI.

Following recent advancements in computer-aided detection and diagnosis systems for colonoscopy, the automated reporting of colonoscopy procedures is set to further revolutionize clinical practice. A crucial yet underexplored aspect in the development of these systems is the creation of computer vision models capable of autonomously segmenting full-procedure colonoscopy videos into anatomical sections and procedural phases. In this work, we aim to create the first open-access dataset for this task and propose a state-of-the-art approach, benchmarked against competitive models. We annotated the publicly available REAL-Colon dataset, consisting of 2.7 million frames from 60 complete colonoscopy videos, with frame-level labels for anatomical locations and colonoscopy phases across nine categories. We then present ColonTCN, a learning-based architecture that employs custom temporal convolutional blocks designed to efficiently capture long temporal dependencies for the temporal segmentation of colonoscopy videos. We also propose a dual k-fold cross-validation evaluation protocol for this benchmark, which includes model assessment on unseen, multi-center data.ColonTCN achieves state-of-the-art performance in classification accuracy while maintaining a low parameter count when evaluated using the two proposed k-fold cross-validation settings, outperforming competitive models. We report ablation studies to provide insights into the challenges of this task and highlight the benefits of the custom temporal convolutional blocks, which enhance learning and improve model efficiency. We believe that the proposed open-access benchmark and the ColonTCN approach represent a significant advancement in the temporal segmentation of colonoscopy procedures, fostering further open-access research to address this clinical need.

Developing self-supervised learning (SSL) models that can learn universal and transferable representations of H&E gigapixel whole-slide images (WSIs) is becoming increasingly valuable in computational pathology. These models hold the potential to advance critical tasks such as few-shot classification, slide retrieval, and patient stratification. Existing approaches for slide representation learning extend the principles of SSL from small images (e.g., 224 x 224 patches) to entire slides, usually by aligning two different augmentations (or views) of the slide. Yet the resulting representation remains constrained by the limited clinical and biological diversity of the views. Instead, we postulate that slides stained with multiple markers, such as immunohistochemistry, can be used as different views to form a rich task-agnostic training signal. To this end, we introduce Madeleine, a multimodal pretraining strategy for slide representation learning. Madeleine is trained with a dual global-local cross-stain alignment objective on large cohorts of breast cancer samples (N=4,211 WSIs across five stains) and kidney transplant samples (N=12,070 WSIs across four stains). We demonstrate the quality of slide representations learned by Madeleine on various downstream evaluations, ranging from morphological and molecular classification to prognostic prediction, comprising 21 tasks using 7,299 WSIs from multiple medical centers. Code is available at https://github.com/mahmoodlab/MADELEINE.

The remarkable success of deep learning in recent years has prompted applications in medical image classification and diagnosis tasks. While classification models have demonstrated robustness in classifying simpler datasets like MNIST or natural images such as ImageNet, this resilience is not consistently observed in complex medical image datasets where data is more scarce and lacks diversity. Moreover, previous findings on natural image datasets have indicated a potential trade-off between data likelihood and classification accuracy. In this study, we explore the use of score-based generative models as classifiers for medical images, specifically mammographic images. Our findings suggest that our proposed generative classifier model not only achieves superior classification results on CBIS-DDSM, INbreast and Vin-Dr Mammo datasets, but also introduces a novel approach to image classification in a broader context. Our code is publicly available at https://github.com/sushmitasarker/sgc_for_medical_image_classification

A crucial step within secondary analysis of electronic health records (EHRs) is to identify the patient cohort under investigation. While EHRs contain medical billing codes that aim to represent the conditions and treatments patients may have, much of the information is only present in the patient notes. Therefore, it is critical to develop robust algorithms to infer patients' conditions and treatments from their written notes. In this paper, we introduce a dataset for patient phenotyping, a task that is defined as the identification of whether a patient has a given medical condition (also referred to as clinical indication or phenotype) based on their patient note. Nursing Progress Notes and Discharge Summaries from the Intensive Care Unit of a large tertiary care hospital were manually annotated for the presence of several high-context phenotypes relevant to treatment and risk of re-hospitalization. This dataset contains 1102 Discharge Summaries and 1000 Nursing Progress Notes. Each Discharge Summary and Progress Note has been annotated by at least two expert human annotators (one clinical researcher and one resident physician). Annotated phenotypes include treatment non-adherence, chronic pain, advanced/metastatic cancer, as well as 10 other phenotypes. This dataset can be utilized for academic and industrial research in medicine and computer science, particularly within the field of medical natural language processing.

Segmentation of the coronary artery is an important task for the quantitative analysis of coronary computed tomography angiography (CCTA) images and is being stimulated by the field of deep learning. However, the complex structures with tiny and narrow branches of the coronary artery bring it a great challenge. Coupled with the medical image limitations of low resolution and poor contrast, fragmentations of segmented vessels frequently occur in the prediction. Therefore, a geometry-based cascaded segmentation method is proposed for the coronary artery, which has the following innovations: 1) Integrating geometric deformation networks, we design a cascaded network for segmenting the coronary artery and vectorizing results. The generated meshes of the coronary artery are continuous and accurate for twisted and sophisticated coronary artery structures, without fragmentations. 2) Different from mesh annotations generated by the traditional marching cube method from voxel-based labels, a finer vectorized mesh of the coronary artery is reconstructed with the regularized morphology. The novel mesh annotation benefits the geometry-based segmentation network, avoiding bifurcation adhesion and point cloud dispersion in intricate branches. 3) A dataset named CCA-200 is collected, consisting of 200 CCTA images with coronary artery disease. The ground truths of 200 cases are coronary internal diameter annotations by professional radiologists. Extensive experiments verify our method on our collected dataset CCA-200 and public ASOCA dataset, with a Dice of 0.778 on CCA-200 and 0.895 on ASOCA, showing superior results. Especially, our geometry-based model generates an accurate, intact and smooth coronary artery, devoid of any fragmentations of segmented vessels.

Misinformation is a complex societal issue, and mitigating solutions are difficult to create due to data deficiencies. To address this problem, we have curated the largest collection of (mis)information datasets in the literature, totaling 75. From these, we evaluated the quality of all of the 36 datasets that consist of statements or claims. We assess these datasets to identify those with solid foundations for empirical work and those with flaws that could result in misleading and non-generalizable results, such as insufficient label quality, spurious correlations, or political bias. We further provide state-of-the-art baselines on all these datasets, but show that regardless of label quality, categorical labels may no longer give an accurate evaluation of detection model performance. We discuss alternatives to mitigate this problem. Overall, this guide aims to provide a roadmap for obtaining higher quality data and conducting more effective evaluations, ultimately improving research in misinformation detection. All datasets and other artifacts are available at https://misinfo-datasets.complexdatalab.com/.

Improving the quality of search results can significantly enhance users experience and engagement with search engines. In spite of several recent advancements in the fields of machine learning and data mining, correctly classifying items for a particular user search query has been a long-standing challenge, which still has a large room for improvement. This paper introduces the "Shopping Queries Dataset", a large dataset of difficult Amazon search queries and results, publicly released with the aim of fostering research in improving the quality of search results. The dataset contains around 130 thousand unique queries and 2.6 million manually labeled (query,product) relevance judgements. The dataset is multilingual with queries in English, Japanese, and Spanish. The Shopping Queries Dataset is being used in one of the KDDCup'22 challenges. In this paper, we describe the dataset and present three evaluation tasks along with baseline results: (i) ranking the results list, (ii) classifying product results into relevance categories, and (iii) identifying substitute products for a given query. We anticipate that this data will become the gold standard for future research in the topic of product search.

The cross-domain text-to-SQL task aims to build a system that can parse user questions into SQL on complete unseen databases, and the single-domain text-to-SQL task evaluates the performance on identical databases. Both of these setups confront unavoidable difficulties in real-world applications. To this end, we introduce the cross-schema text-to-SQL task, where the databases of evaluation data are different from that in the training data but come from the same domain. Furthermore, we present CSS, a large-scale CrosS-Schema Chinese text-to-SQL dataset, to carry on corresponding studies. CSS originally consisted of 4,340 question/SQL pairs across 2 databases. In order to generalize models to different medical systems, we extend CSS and create 19 new databases along with 29,280 corresponding dataset examples. Moreover, CSS is also a large corpus for single-domain Chinese text-to-SQL studies. We present the data collection approach and a series of analyses of the data statistics. To show the potential and usefulness of CSS, benchmarking baselines have been conducted and reported. Our dataset is publicly available at https://huggingface.co/datasets/zhanghanchong/css.

Table Detection has become a fundamental task for visually rich document understanding with the surging number of electronic documents. However, popular public datasets widely used in related studies have inherent limitations, including noisy and inconsistent samples, limited training samples, and limited data sources. These limitations make these datasets unreliable to evaluate the model performance and cannot reflect the actual capacity of models. Therefore, this study revisits some open datasets with high-quality annotations, identifies and cleans the noise, and aligns the annotation definitions of these datasets to merge a larger dataset, termed Open-Tables. Moreover, to enrich the data sources, we propose a new ICT-TD dataset using the PDF files of Information and Communication Technologies (ICT) commodities, a different domain containing unique samples that hardly appear in open datasets. To ensure the label quality of the dataset, we annotated the dataset manually following the guidance of a domain expert. The proposed dataset is challenging and can be a sample of actual cases in the business context. We built strong baselines using various state-of-the-art object detection models. Our experimental results show that the domain differences among existing open datasets are minor despite having different data sources. Our proposed Open-Tables and ICT-TD can provide a more reliable evaluation for models because of their high quality and consistent annotations. Besides, they are more suitable for cross-domain settings. Our experimental results show that in the cross-domain setting, benchmark models trained with cleaned Open-Tables dataset can achieve 0.6\%-2.6\% higher weighted average F1 than the corresponding ones trained with the noisy version of Open-Tables, demonstrating the reliability of the proposed datasets. The datasets are public available.

Instance-level image classification tasks have traditionally relied on single-instance labels to train models, e.g., few-shot learning and transfer learning. However, set-level coarse-grained labels that capture relationships among instances can provide richer information in real-world scenarios. In this paper, we present a novel approach to enhance instance-level image classification by leveraging set-level labels. We provide a theoretical analysis of the proposed method, including recognition conditions for fast excess risk rate, shedding light on the theoretical foundations of our approach. We conducted experiments on two distinct categories of datasets: natural image datasets and histopathology image datasets. Our experimental results demonstrate the effectiveness of our approach, showcasing improved classification performance compared to traditional single-instance label-based methods. Notably, our algorithm achieves 13% improvement in classification accuracy compared to the strongest baseline on the histopathology image classification benchmarks. Importantly, our experimental findings align with the theoretical analysis, reinforcing the robustness and reliability of our proposed method. This work bridges the gap between instance-level and set-level image classification, offering a promising avenue for advancing the capabilities of image classification models with set-level coarse-grained labels.

Breast cancer is a common cancer for women. Early detection of breast cancer can considerably increase the survival rate of women. This paper mainly focuses on transfer learning process to detect breast cancer. Modified VGG (MVGG), residual network, mobile network is proposed and implemented in this paper. DDSM dataset is used in this paper. Experimental results show that our proposed hybrid transfers learning model (Fusion of MVGG16 and ImageNet) provides an accuracy of 88.3% where the number of epoch is 15. On the other hand, only modified VGG 16 architecture (MVGG 16) provides an accuracy 80.8% and MobileNet provides an accuracy of 77.2%. So, it is clearly stated that the proposed hybrid pre-trained network outperforms well compared to single architecture. This architecture can be considered as an effective tool for the radiologists in order to reduce the false negative and false positive rate. Therefore, the efficiency of mammography analysis will be improved.

The body of research on classification of solar panel arrays from aerial imagery is increasing, yet there are still not many public benchmark datasets. This paper introduces two novel benchmark datasets for classifying and localizing solar panel arrays in Denmark: A human annotated dataset for classification and segmentation, as well as a classification dataset acquired using self-reported data from the Danish national building registry. We explore the performance of prior works on the new benchmark dataset, and present results after fine-tuning models using a similar approach as recent works. Furthermore, we train models of newer architectures and provide benchmark baselines to our datasets in several scenarios. We believe the release of these datasets may improve future research in both local and global geospatial domains for identifying and mapping of solar panel arrays from aerial imagery. The data is accessible at https://osf.io/aj539/.

In domains ranging from computer vision to natural language processing, machine learning models have been shown to exhibit stark disparities, often performing worse for members of traditionally underserved groups. One factor contributing to these performance gaps is a lack of representation in the data the models are trained on. It is often unclear, however, how to operationalize representativeness in specific applications. Here we formalize the problem of creating equitable training datasets, and propose a statistical framework for addressing this problem. We consider a setting where a model builder must decide how to allocate a fixed data collection budget to gather training data from different subgroups. We then frame dataset creation as a constrained optimization problem, in which one maximizes a function of group-specific performance metrics based on (estimated) group-specific learning rates and costs per sample. This flexible approach incorporates preferences of model-builders and other stakeholders, as well as the statistical properties of the learning task. When data collection decisions are made sequentially, we show that under certain conditions this optimization problem can be efficiently solved even without prior knowledge of the learning rates. To illustrate our approach, we conduct a simulation study of polygenic risk scores on synthetic genomic data -- an application domain that often suffers from non-representative data collection. We find that our adaptive sampling strategy outperforms several common data collection heuristics, including equal and proportional sampling, demonstrating the value of strategic dataset design for building equitable models.

In this paper, we present a novel approach for segmenting pediatric brain tumors using a deep learning architecture, inspired by expert radiologists' segmentation strategies. Our model delineates four distinct tumor labels and is benchmarked on a held-out PED BraTS 2024 test set (i.e., pediatric brain tumor datasets introduced by BraTS). Furthermore, we evaluate our model's performance against the state-of-the-art (SOTA) model using a new external dataset of 30 patients from CBTN (Children's Brain Tumor Network), labeled in accordance with the PED BraTS 2024 guidelines and 2023 BraTS Adult Glioma dataset. We compare segmentation outcomes with the winning algorithm from the PED BraTS 2023 challenge as the SOTA model. Our proposed algorithm achieved an average Dice score of 0.642 and an HD95 of 73.0 mm on the CBTN test data, outperforming the SOTA model, which achieved a Dice score of 0.626 and an HD95 of 84.0 mm. Moreover, our model exhibits strong generalizability, attaining a 0.877 Dice score in whole tumor segmentation on the BraTS 2023 Adult Glioma dataset, surpassing existing SOTA. Our results indicate that the proposed model is a step towards providing more accurate segmentation for pediatric brain tumors, which is essential for evaluating therapy response and monitoring patient progress. Our source code is available at https://github.com/NUBagciLab/Pediatric-Brain-Tumor-Segmentation-Model.

Automatic medical report generation (MRG) is of great research value as it has the potential to relieve radiologists from the heavy burden of report writing. Despite recent advancements, accurate MRG remains challenging due to the need for precise clinical understanding and the identification of clinical findings. Moreover, the imbalanced distribution of diseases makes the challenge even more pronounced, as rare diseases are underrepresented in training data, making their diagnostic performance unreliable. To address these challenges, we propose diagnosis-driven prompts for medical report generation (PromptMRG), a novel framework that aims to improve the diagnostic accuracy of MRG with the guidance of diagnosis-aware prompts. Specifically, PromptMRG is based on encoder-decoder architecture with an extra disease classification branch. When generating reports, the diagnostic results from the classification branch are converted into token prompts to explicitly guide the generation process. To further improve the diagnostic accuracy, we design cross-modal feature enhancement, which retrieves similar reports from the database to assist the diagnosis of a query image by leveraging the knowledge from a pre-trained CLIP. Moreover, the disease imbalanced issue is addressed by applying an adaptive logit-adjusted loss to the classification branch based on the individual learning status of each disease, which overcomes the barrier of text decoder's inability to manipulate disease distributions. Experiments on two MRG benchmarks show the effectiveness of the proposed method, where it obtains state-of-the-art clinical efficacy performance on both datasets.

The widespread use of chest X-rays (CXRs), coupled with a shortage of radiologists, has driven growing interest in automated CXR analysis and AI-assisted reporting. While existing vision-language models (VLMs) show promise in specific tasks such as report generation or abnormality detection, they often lack support for interactive diagnostic capabilities. In this work we present RadVLM, a compact, multitask conversational foundation model designed for CXR interpretation. To this end, we curate a large-scale instruction dataset comprising over 1 million image-instruction pairs containing both single-turn tasks -- such as report generation, abnormality classification, and visual grounding -- and multi-turn, multi-task conversational interactions. After fine-tuning RadVLM on this instruction dataset, we evaluate it across different tasks along with re-implemented baseline VLMs. Our results show that RadVLM achieves state-of-the-art performance in conversational capabilities and visual grounding while remaining competitive in other radiology tasks. Ablation studies further highlight the benefit of joint training across multiple tasks, particularly for scenarios with limited annotated data. Together, these findings highlight the potential of RadVLM as a clinically relevant AI assistant, providing structured CXR interpretation and conversational capabilities to support more effective and accessible diagnostic workflows.

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.

Benchmarks that closely reflect downstream application scenarios are essential for the streamlined adoption of new research in tabular machine learning (ML). In this work, we examine existing tabular benchmarks and find two common characteristics of industry-grade tabular data that are underrepresented in the datasets available to the academic community. First, tabular data often changes over time in real-world deployment scenarios. This impacts model performance and requires time-based train and test splits for correct model evaluation. Yet, existing academic tabular datasets often lack timestamp metadata to enable such evaluation. Second, a considerable portion of datasets in production settings stem from extensive data acquisition and feature engineering pipelines. For each specific dataset, this can have a different impact on the absolute and relative number of predictive, uninformative, and correlated features, which in turn can affect model selection. To fill the aforementioned gaps in academic benchmarks, we introduce TabReD -- a collection of eight industry-grade tabular datasets covering a wide range of domains from finance to food delivery services. We assess a large number of tabular ML models in the feature-rich, temporally-evolving data setting facilitated by TabReD. We demonstrate that evaluation on time-based data splits leads to different methods ranking, compared to evaluation on random splits more common in academic benchmarks. Furthermore, on the TabReD datasets, MLP-like architectures and GBDT show the best results, while more sophisticated DL models are yet to prove their effectiveness.

This study investigates the feasibility of automating clinical coding in Russian, a language with limited biomedical resources. We present a new dataset for ICD coding, which includes diagnosis fields from electronic health records (EHRs) annotated with over 10,000 entities and more than 1,500 unique ICD codes. This dataset serves as a benchmark for several state-of-the-art models, including BERT, LLaMA with LoRA, and RAG, with additional experiments examining transfer learning across domains (from PubMed abstracts to medical diagnosis) and terminologies (from UMLS concepts to ICD codes). We then apply the best-performing model to label an in-house EHR dataset containing patient histories from 2017 to 2021. Our experiments, conducted on a carefully curated test set, demonstrate that training with the automated predicted codes leads to a significant improvement in accuracy compared to manually annotated data from physicians. We believe our findings offer valuable insights into the potential for automating clinical coding in resource-limited languages like Russian, which could enhance clinical efficiency and data accuracy in these contexts.

Most existing large-scale academic search engines are built to retrieve text-based information. However, there are no large-scale retrieval services for scientific figures and tables. One challenge for such services is understanding scientific figures' semantics, such as their types and purposes. A key obstacle is the need for datasets containing annotated scientific figures and tables, which can then be used for classification, question-answering, and auto-captioning. Here, we develop a pipeline that extracts figures and tables from the scientific literature and a deep-learning-based framework that classifies scientific figures using visual features. Using this pipeline, we built the first large-scale automatically annotated corpus, ACL-Fig, consisting of 112,052 scientific figures extracted from ~56K research papers in the ACL Anthology. The ACL-Fig-Pilot dataset contains 1,671 manually labeled scientific figures belonging to 19 categories. The dataset is accessible at https://huggingface.co/datasets/citeseerx/ACL-fig under a CC BY-NC license.

Multimodal models trained on large natural image-text pair datasets have exhibited astounding abilities in generating high-quality images. Medical imaging data is fundamentally different to natural images, and the language used to succinctly capture relevant details in medical data uses a different, narrow but semantically rich, domain-specific vocabulary. Not surprisingly, multi-modal models trained on natural image-text pairs do not tend to generalize well to the medical domain. Developing generative imaging models faithfully representing medical concepts while providing compositional diversity could mitigate the existing paucity of high-quality, annotated medical imaging datasets. In this work, we develop a strategy to overcome the large natural-medical distributional shift by adapting a pre-trained latent diffusion model on a corpus of publicly available chest x-rays (CXR) and their corresponding radiology (text) reports. We investigate the model's ability to generate high-fidelity, diverse synthetic CXR conditioned on text prompts. We assess the model outputs quantitatively using image quality metrics, and evaluate image quality and text-image alignment by human domain experts. We present evidence that the resulting model (RoentGen) is able to create visually convincing, diverse synthetic CXR images, and that the output can be controlled to a new extent by using free-form text prompts including radiology-specific language. Fine-tuning this model on a fixed training set and using it as a data augmentation method, we measure a 5% improvement of a classifier trained jointly on synthetic and real images, and a 3% improvement when trained on a larger but purely synthetic training set. Finally, we observe that this fine-tuning distills in-domain knowledge in the text-encoder and can improve its representation capabilities of certain diseases like pneumothorax by 25%.

In recent years, the machine learning research community has benefited tremendously from the availability of openly accessible benchmark datasets. Clinical data are usually not openly available due to their highly confidential nature. This has hampered the development of reproducible and generalisable machine learning applications in health care. Here we introduce the Health Gym - a growing collection of highly realistic synthetic medical datasets that can be freely accessed to prototype, evaluate, and compare machine learning algorithms, with a specific focus on reinforcement learning. The three synthetic datasets described in this paper present patient cohorts with acute hypotension and sepsis in the intensive care unit, and people with human immunodeficiency virus (HIV) receiving antiretroviral therapy in ambulatory care. The datasets were created using a novel generative adversarial network (GAN). The distributions of variables, and correlations between variables and trends over time in the synthetic datasets mirror those in the real datasets. Furthermore, the risk of sensitive information disclosure associated with the public distribution of the synthetic datasets is estimated to be very low.

Medical images and radiology reports are crucial for diagnosing medical conditions, highlighting the importance of quantitative analysis for clinical decision-making. However, the diversity and cross-source heterogeneity of these data challenge the generalizability of current data-mining methods. Multimodal large language models (MLLMs) have recently transformed many domains, significantly affecting the medical field. Notably, Gemini-Vision-series (Gemini) and GPT-4-series (GPT-4) models have epitomized a paradigm shift in Artificial General Intelligence (AGI) for computer vision, showcasing their potential in the biomedical domain. In this study, we evaluated the performance of the Gemini, GPT-4, and 4 popular large models for an exhaustive evaluation across 14 medical imaging datasets, including 5 medical imaging categories (dermatology, radiology, dentistry, ophthalmology, and endoscopy), and 3 radiology report datasets. The investigated tasks encompass disease classification, lesion segmentation, anatomical localization, disease diagnosis, report generation, and lesion detection. Our experimental results demonstrated that Gemini-series models excelled in report generation and lesion detection but faces challenges in disease classification and anatomical localization. Conversely, GPT-series models exhibited proficiency in lesion segmentation and anatomical localization but encountered difficulties in disease diagnosis and lesion detection. Additionally, both the Gemini series and GPT series contain models that have demonstrated commendable generation efficiency. While both models hold promise in reducing physician workload, alleviating pressure on limited healthcare resources, and fostering collaboration between clinical practitioners and artificial intelligence technologies, substantial enhancements and comprehensive validations remain imperative before clinical deployment.

Background: General-purpose large language models that utilize both text and images have not been evaluated on a diverse array of challenging medical cases. Methods: Using 934 cases from the NEJM Image Challenge published between 2005 and 2023, we evaluated the accuracy of the recently released Generative Pre-trained Transformer 4 with Vision model (GPT-4V) compared to human respondents overall and stratified by question difficulty, image type, and skin tone. We further conducted a physician evaluation of GPT-4V on 69 NEJM clinicopathological conferences (CPCs). Analyses were conducted for models utilizing text alone, images alone, and both text and images. Results: GPT-4V achieved an overall accuracy of 61% (95% CI, 58 to 64%) compared to 49% (95% CI, 49 to 50%) for humans. GPT-4V outperformed humans at all levels of difficulty and disagreement, skin tones, and image types; the exception was radiographic images, where performance was equivalent between GPT-4V and human respondents. Longer, more informative captions were associated with improved performance for GPT-4V but similar performance for human respondents. GPT-4V included the correct diagnosis in its differential for 80% (95% CI, 68 to 88%) of CPCs when using text alone, compared to 58% (95% CI, 45 to 70%) of CPCs when using both images and text. Conclusions: GPT-4V outperformed human respondents on challenging medical cases and was able to synthesize information from both images and text, but performance deteriorated when images were added to highly informative text. Overall, our results suggest that multimodal AI models may be useful in medical diagnostic reasoning but that their accuracy may depend heavily on context.

Tumor documentation in Germany is largely done manually, requiring reading patient records and entering data into structured databases. Large language models (LLMs) could potentially enhance this process by improving efficiency and reliability. This evaluation tests eleven different open source LLMs with sizes ranging from 1-70 billion model parameters on three basic tasks of the tumor documentation process: identifying tumor diagnoses, assigning ICD-10 codes, and extracting the date of first diagnosis. For evaluating the LLMs on these tasks, a dataset of annotated text snippets based on anonymized doctors' notes from urology was prepared. Different prompting strategies were used to investigate the effect of the number of examples in few-shot prompting and to explore the capabilities of the LLMs in general. The models Llama 3.1 8B, Mistral 7B, and Mistral NeMo 12 B performed comparably well in the tasks. Models with less extensive training data or having fewer than 7 billion parameters showed notably lower performance, while larger models did not display performance gains. Examples from a different medical domain than urology could also improve the outcome in few-shot prompting, which demonstrates the ability of LLMs to handle tasks needed for tumor documentation. Open source LLMs show a strong potential for automating tumor documentation. Models from 7-12 billion parameters could offer an optimal balance between performance and resource efficiency. With tailored fine-tuning and well-designed prompting, these models might become important tools for clinical documentation in the future. The code for the evaluation is available from https://github.com/stefan-m-lenz/UroLlmEval. We also release the dataset as a new valuable resource that addresses the shortage of authentic and easily accessible benchmarks in German-language medical NLP.

Empirically validating new 3D-printing related algorithms and implementations requires testing data representative of inputs encountered in the wild. An ideal benchmarking dataset should not only draw from the same distribution of shapes people print in terms of class (e.g., toys, mechanisms, jewelry), representation type (e.g., triangle soup meshes) and complexity (e.g., number of facets), but should also capture problems and artifacts endemic to 3D printing models (e.g., self-intersections, non-manifoldness). We observe that the contextual and geometric characteristics of 3D printing models differ significantly from those used for computer graphics applications, not to mention standard models (e.g., Stanford bunny, Armadillo, Fertility). We present a new dataset of 10,000 models collected from an online 3D printing model-sharing database. Via analysis of both geometric (e.g., triangle aspect ratios, manifoldness) and contextual (e.g., licenses, tags, classes) characteristics, we demonstrate that this dataset represents a more concise summary of real-world models used for 3D printing compared to existing datasets. To facilitate future research endeavors, we also present an online query interface to select subsets of the dataset according to project-specific characteristics. The complete dataset and per-model statistical data are freely available to the public.

The field of computational pathology has been transformed with recent advances in foundation models that encode histopathology region-of-interests (ROIs) into versatile and transferable feature representations via self-supervised learning (SSL). However, translating these advancements to address complex clinical challenges at the patient and slide level remains constrained by limited clinical data in disease-specific cohorts, especially for rare clinical conditions. We propose TITAN, a multimodal whole slide foundation model pretrained using 335,645 WSIs via visual self-supervised learning and vision-language alignment with corresponding pathology reports and 423,122 synthetic captions generated from a multimodal generative AI copilot for pathology. Without any finetuning or requiring clinical labels, TITAN can extract general-purpose slide representations and generate pathology reports that generalize to resource-limited clinical scenarios such as rare disease retrieval and cancer prognosis. We evaluate TITAN on diverse clinical tasks and find that TITAN outperforms both ROI and slide foundation models across machine learning settings such as linear probing, few-shot and zero-shot classification, rare cancer retrieval and cross-modal retrieval, and pathology report generation.

Exploiting the recent advancements in artificial intelligence, showcased by ChatGPT and DALL-E, in real-world applications necessitates vast, domain-specific, and publicly accessible datasets. Unfortunately, the scarcity of such datasets poses a significant challenge for researchers aiming to apply these breakthroughs in engineering design. Synthetic datasets emerge as a viable alternative. However, practitioners are often uncertain about generating high-quality datasets that accurately represent real-world data and are suitable for the intended downstream applications. This study aims to fill this knowledge gap by proposing comprehensive guidelines for generating, annotating, and validating synthetic datasets. The trade-offs and methods associated with each of these aspects are elaborated upon. Further, the practical implications of these guidelines are illustrated through the creation of a turbo-compressors dataset. The study underscores the importance of thoughtful sampling methods to ensure the appropriate size, diversity, utility, and realism of a dataset. It also highlights that design diversity does not equate to performance diversity or realism. By employing test sets that represent uniform, real, or task-specific samples, the influence of sample size and sampling strategy is scrutinized. Overall, this paper offers valuable insights for researchers intending to create and publish synthetic datasets for engineering design, thereby paving the way for more effective applications of AI advancements in the field. The code and data for the dataset and methods are made publicly accessible at https://github.com/cyrilpic/radcomp .

While conversational generative AI has shown considerable potential in enhancing decision-making for agricultural professionals, its exploration has predominantly been anchored in text-based interactions. The evolution of multimodal conversational AI, leveraging vast amounts of image-text data from diverse sources, marks a significant stride forward. However, the application of such advanced vision-language models in the agricultural domain, particularly for crop disease diagnosis, remains underexplored. In this work, we present the crop disease domain multimodal (CDDM) dataset, a pioneering resource designed to advance the field of agricultural research through the application of multimodal learning techniques. The dataset comprises 137,000 images of various crop diseases, accompanied by 1 million question-answer pairs that span a broad spectrum of agricultural knowledge, from disease identification to management practices. By integrating visual and textual data, CDDM facilitates the development of sophisticated question-answering systems capable of providing precise, useful advice to farmers and agricultural professionals. We demonstrate the utility of the dataset by finetuning state-of-the-art multimodal models, showcasing significant improvements in crop disease diagnosis. Specifically, we employed a novel finetuning strategy that utilizes low-rank adaptation (LoRA) to finetune the visual encoder, adapter and language model simultaneously. Our contributions include not only the dataset but also a finetuning strategy and a benchmark to stimulate further research in agricultural technology, aiming to bridge the gap between advanced AI techniques and practical agricultural applications. The dataset is available at https: //github.com/UnicomAI/UnicomBenchmark/tree/main/CDDMBench.

In the past few years, convolutional neural networks (CNNs) have achieved impressive results in computer vision tasks, which however mainly focus on photos with natural scene content. Besides, non-sensor derived images such as illustrations, data visualizations, figures, etc. are typically used to convey complex information or to explore large datasets. However, this kind of images has received little attention in computer vision. CNNs and similar techniques use large volumes of training data. Currently, many document analysis systems are trained in part on scene images due to the lack of large datasets of educational image data. In this paper, we address this issue and present SlideImages, a dataset for the task of classifying educational illustrations. SlideImages contains training data collected from various sources, e.g., Wikimedia Commons and the AI2D dataset, and test data collected from educational slides. We have reserved all the actual educational images as a test dataset in order to ensure that the approaches using this dataset generalize well to new educational images, and potentially other domains. Furthermore, we present a baseline system using a standard deep neural architecture and discuss dealing with the challenge of limited training data.

How do we most effectively treat a disease or condition? Ideally, we could consult a database of evidence gleaned from clinical trials to answer such questions. Unfortunately, no such database exists; clinical trial results are instead disseminated primarily via lengthy natural language articles. Perusing all such articles would be prohibitively time-consuming for healthcare practitioners; they instead tend to depend on manually compiled systematic reviews of medical literature to inform care. NLP may speed this process up, and eventually facilitate immediate consult of published evidence. The Evidence Inference dataset was recently released to facilitate research toward this end. This task entails inferring the comparative performance of two treatments, with respect to a given outcome, from a particular article (describing a clinical trial) and identifying supporting evidence. For instance: Does this article report that chemotherapy performed better than surgery for five-year survival rates of operable cancers? In this paper, we collect additional annotations to expand the Evidence Inference dataset by 25\%, provide stronger baseline models, systematically inspect the errors that these make, and probe dataset quality. We also release an abstract only (as opposed to full-texts) version of the task for rapid model prototyping. The updated corpus, documentation, and code for new baselines and evaluations are available at http://evidence-inference.ebm-nlp.com/.

Purpose: To evaluate the performance of an automated deep learning method in detecting ascites and subsequently quantifying its volume in patients with liver cirrhosis and ovarian cancer. Materials and Methods: This retrospective study included contrast-enhanced and non-contrast abdominal-pelvic CT scans of patients with cirrhotic ascites and patients with ovarian cancer from two institutions, National Institutes of Health (NIH) and University of Wisconsin (UofW). The model, trained on The Cancer Genome Atlas Ovarian Cancer dataset (mean age, 60 years +/- 11 [s.d.]; 143 female), was tested on two internal (NIH-LC and NIH-OV) and one external dataset (UofW-LC). Its performance was measured by the Dice coefficient, standard deviations, and 95% confidence intervals, focusing on ascites volume in the peritoneal cavity. Results: On NIH-LC (25 patients; mean age, 59 years +/- 14 [s.d.]; 14 male) and NIH-OV (166 patients; mean age, 65 years +/- 9 [s.d.]; all female), the model achieved Dice scores of 0.855 +/- 0.061 (CI: 0.831-0.878) and 0.826 +/- 0.153 (CI: 0.764-0.887), with median volume estimation errors of 19.6% (IQR: 13.2-29.0) and 5.3% (IQR: 2.4-9.7) respectively. On UofW-LC (124 patients; mean age, 46 years +/- 12 [s.d.]; 73 female), the model had a Dice score of 0.830 +/- 0.107 (CI: 0.798-0.863) and median volume estimation error of 9.7% (IQR: 4.5-15.1). The model showed strong agreement with expert assessments, with r^2 values of 0.79, 0.98, and 0.97 across the test sets. Conclusion: The proposed deep learning method performed well in segmenting and quantifying the volume of ascites in concordance with expert radiologist assessments.

Classical self-supervised networks suffer from convergence problems and reduced segmentation accuracy due to forceful termination. Qubits or bi-level quantum bits often describe quantum neural network models. In this article, a novel self-supervised shallow learning network model exploiting the sophisticated three-level qutrit-inspired quantum information system referred to as Quantum Fully Self-Supervised Neural Network (QFS-Net) is presented for automated segmentation of brain MR images. The QFS-Net model comprises a trinity of a layered structure of qutrits inter-connected through parametric Hadamard gates using an 8-connected second-order neighborhood-based topology. The non-linear transformation of the qutrit states allows the underlying quantum neural network model to encode the quantum states, thereby enabling a faster self-organized counter-propagation of these states between the layers without supervision. The suggested QFS-Net model is tailored and extensively validated on Cancer Imaging Archive (TCIA) data set collected from Nature repository and also compared with state of the art supervised (U-Net and URes-Net architectures) and the self-supervised QIS-Net model. Results shed promising segmented outcome in detecting tumors in terms of dice similarity and accuracy with minimum human intervention and computational resources.