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A visual-language model (VLM) pre-trained on natural images and text pairs poses a significant barrier when applied to medical contexts due to domain shift. Yet, adapting or fine-tuning these VLMs for medical use presents considerable hurdles, including domain misalignment, limited access to extensive datasets, and high-class imbalances. Hence, there is a pressing need for strategies to effectively adapt these VLMs to the medical domain, as such adaptations would prove immensely valuable in healthcare applications. In this study, we propose a framework designed to adeptly tailor VLMs to the medical domain, employing selective sampling and hard-negative mining techniques for enhanced performance in retrieval tasks. We validate the efficacy of our proposed approach by implementing it across two distinct VLMs: the in-domain VLM (MedCLIP) and out-of-domain VLMs (ALBEF). We assess the performance of these models both in their original off-the-shelf state and after undergoing our proposed training strategies, using two extensive datasets containing mammograms and their corresponding reports. Our evaluation spans zero-shot, few-shot, and supervised scenarios. Through our approach, we observe a notable enhancement in Recall@K performance for the image-text retrieval task.

The integration of Large Language Models (LLMs) into the healthcare domain has the potential to significantly enhance patient care and support through the development of empathetic, patient-facing chatbots. This study investigates an intriguing question Can ChatGPT respond with a greater degree of empathy than those typically offered by physicians? To answer this question, we collect a de-identified dataset of patient messages and physician responses from Mayo Clinic and generate alternative replies using ChatGPT. Our analyses incorporate novel empathy ranking evaluation (EMRank) involving both automated metrics and human assessments to gauge the empathy level of responses. Our findings indicate that LLM-powered chatbots have the potential to surpass human physicians in delivering empathetic communication, suggesting a promising avenue for enhancing patient care and reducing professional burnout. The study not only highlights the importance of empathy in patient interactions but also proposes a set of effective automatic empathy ranking metrics, paving the way for the broader adoption of LLMs in healthcare.

Automated classification of cancer pathology reports can extract information from unstructured reports and categorize each report into structured diagnosis and severity categories. Thus, such system can reduce the burden for populating tumor registries, help registration for clinical trial as well as developing large dataset for deep learning model development using true pathologic ground truth. However, the content of breast pathology reports can be difficult for categorize due to the high linguistic variability in content and wide variety of potential diagnoses >50. Existing NLP models are primarily focused on developing classifier for primary breast cancer types (e.g. IDC, DCIS, ILC) and tumor characteristics, and ignore the rare diagnosis of cancer subtypes. We then developed a hierarchical hybrid transformer-based pipeline (59 labels) - Hierarchical Classification System for Breast Cancer Specimen Report (HCSBC), which utilizes the potential of the transformer context-preserving NLP technique and compared our model to several state of the art ML and DL models. We trained the model on the EUH data and evaluated our model's performance on two external datasets - MGH and Mayo Clinic. We publicly release the code and a live application under Huggingface spaces repository

Although deep learning models for abnormality classification can perform well in screening mammography, the demographic, imaging, and clinical characteristics associated with increased risk of model failure remain unclear. This retrospective study uses the Emory BrEast Imaging Dataset(EMBED) containing mammograms from 115931 patients imaged at Emory Healthcare between 2013-2020, with BI-RADS assessment, region of interest coordinates for abnormalities, imaging features, pathologic outcomes, and patient demographics. Multiple deep learning models were trained to distinguish between abnormal tissue patches and randomly selected normal tissue patches from screening mammograms. We assessed model performance by subgroups defined by age, race, pathologic outcome, tissue density, and imaging characteristics and investigated their associations with false negatives (FN) and false positives (FP). We also performed multivariate logistic regression to control for confounding between subgroups. The top-performing model, ResNet152V2, achieved accuracy of 92.6%(95%CI=92.0-93.2%), and AUC 0.975(95%CI=0.972-0.978). Before controlling for confounding, nearly all subgroups showed statistically significant differences in model performance. However, after controlling for confounding, we found lower FN risk associates with Other race(RR=0.828;p=.050), biopsy-proven benign lesions(RR=0.927;p=.011), and mass(RR=0.921;p=.010) or asymmetry(RR=0.854;p=.040); higher FN risk associates with architectural distortion (RR=1.037;p<.001). Higher FP risk associates to BI-RADS density C(RR=1.891;p<.001) and D(RR=2.486;p<.001). Our results demonstrate subgroup analysis is important in mammogram classifier performance evaluation, and controlling for confounding between subgroups elucidates the true associations between variables and model failure. These results can help guide developing future breast cancer detection models., Comment: 29 pages, 6 tables, 7 figures, 2 supplemental tables

Migraine is a high-prevalence and disabling neurological disorder. However, information migraine management in real-world settings could be limited to traditional health information sources. In this paper, we (i) verify that there is substantial migraine-related chatter available on social media (Twitter and Reddit), self-reported by migraine sufferers; (ii) develop a platform-independent text classification system for automatically detecting self-reported migraine-related posts, and (iii) conduct analyses of the self-reported posts to assess the utility of social media for studying this problem. We manually annotated 5750 Twitter posts and 302 Reddit posts. Our system achieved an F1 score of 0.90 on Twitter and 0.93 on Reddit. Analysis of information posted by our 'migraine cohort' revealed the presence of a plethora of relevant information about migraine therapies and patient sentiments associated with them. Our study forms the foundation for conducting an in-depth analysis of migraine-related information using social media data., Comment: Accepted by AMIA 2023 Informatics Summit

In this work, we study a natural nonparametric estimator of the transition probability matrices of a finite controlled Markov chain. We consider an offline setting with a fixed dataset, collected using a so-called logging policy. We develop sample complexity bounds for the estimator and establish conditions for minimaxity. Our statistical bounds depend on the logging policy through its mixing properties. We show that achieving a particular statistical risk bound involves a subtle and interesting trade-off between the strength of the mixing properties and the number of samples. We demonstrate the validity of our results under various examples, such as ergodic Markov chains, weakly ergodic inhomogeneous Markov chains, and controlled Markov chains with non-stationary Markov, episodic, and greedy controls. Lastly, we use these sample complexity bounds to establish concomitant ones for offline evaluation of stationary Markov control policies., Comment: 71 pages, 23 main

We study the meta-learning for support (i.e. the set of non-zero entries) recovery in high-dimensional Principal Component Analysis. We reduce the sufficient sample complexity in a novel task with the information that is learned from auxiliary tasks. We assume each task to be a different random Principal Component (PC) matrix with a possibly different support and that the support union of the PC matrices is small. We then pool the data from all the tasks to execute an improper estimation of a single PC matrix by maximising the $l_1$-regularised predictive covariance to establish that with high probability the true support union can be recovered provided a sufficient number of tasks $m$ and a sufficient number of samples $ O\left(\frac{\log(p)}{m}\right)$ for each task, for $p$-dimensional vectors. Then, for a novel task, we prove that the maximisation of the $l_1$-regularised predictive covariance with the additional constraint that the support is a subset of the estimated support union could reduce the sufficient sample complexity of successful support recovery to $O(\log |J|)$, where $J$ is the support union recovered from the auxiliary tasks. Typically, $|J|$ would be much less than $p$ for sparse matrices. Finally, we demonstrate the validity of our experiments through numerical simulations., Comment: 29 pages, 7 figures

Language modality within the vision language pretraining framework is innately discretized, endowing each word in the language vocabulary a semantic meaning. In contrast, visual modality is inherently continuous and high-dimensional, which potentially prohibits the alignment as well as fusion between vision and language modalities. We therefore propose to "discretize" the visual representation by joint learning a codebook that imbues each visual token a semantic. We then utilize these discretized visual semantics as self-supervised ground-truths for building our Masked Image Modeling objective, a counterpart of Masked Language Modeling which proves successful for language models. To optimize the codebook, we extend the formulation of VQ-VAE which gives a theoretic guarantee. Experiments validate the effectiveness of our approach across common vision-language benchmarks., Comment: 7 pages, 4 figures, ICPR2022. arXiv admin note: text overlap with arXiv:2203.00048

30-day hospital readmission is a long standing medical problem that affects patients' morbidity and mortality and costs billions of dollars annually. Recently, machine learning models have been created to predict risk of inpatient readmission for patients with specific diseases, however no model exists to predict this risk across all patients. We developed a bi-directional Long Short Term Memory (LSTM) Network that is able to use readily available insurance data (inpatient visits, outpatient visits, and drug prescriptions) to predict 30 day re-admission for any admitted patient, regardless of reason. The top-performing model achieved an ROC AUC of 0.763 (0.011) when using historical, inpatient, and post-discharge data. The LSTM model significantly outperformed a baseline random forest classifier, indicating that understanding the sequence of events is important for model prediction. Incorporation of 30-days of historical data also significantly improved model performance compared to inpatient data alone, indicating that a patients clinical history prior to admission, including outpatient visits and pharmacy data is a strong contributor to readmission. Our results demonstrate that a machine learning model is able to predict risk of inpatient readmission with reasonable accuracy for all patients using structured insurance billing data. Because billing data or equivalent surrogates can be extracted from sites, such a model could be deployed to identify patients at risk for readmission before they are discharged, or to assign more robust follow up (closer follow up, home health, mailed medications) to at-risk patients after discharge., Comment: 7 pages, 3 figures, 3 tables

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., Comment: submitted to "American Medical Informatics Association (AMIA)" 2022 Annual Symposium

Measures to predict 30-day readmission are considered an important quality factor for hospitals as accurate predictions can reduce the overall cost of care by identifying high risk patients before they are discharged. While recent deep learning-based studies have shown promising empirical results on readmission prediction, several limitations exist that may hinder widespread clinical utility, such as (a) only patients with certain conditions are considered, (b) existing approaches do not leverage data temporality, (c) individual admissions are assumed independent of each other, which is unrealistic, (d) prior studies are usually limited to single source of data and single center data. To address these limitations, we propose a multimodal, modality-agnostic spatiotemporal graph neural network (MM-STGNN) for prediction of 30-day all-cause hospital readmission that fuses multimodal in-patient longitudinal data. By training and evaluating our methods using longitudinal chest radiographs and electronic health records from two independent centers, we demonstrate that MM-STGNN achieves AUROC of 0.79 on both primary and external datasets. Furthermore, MM-STGNN significantly outperforms the current clinical reference standard, LACE+ score (AUROC=0.61), on the primary dataset. For subset populations of patients with heart and vascular disease, our model also outperforms baselines on predicting 30-day readmission (e.g., 3.7 point improvement in AUROC in patients with heart disease). Lastly, qualitative model interpretability analysis indicates that while patients' primary diagnoses were not explicitly used to train the model, node features crucial for model prediction directly reflect patients' primary diagnoses. Importantly, our MM-STGNN is agnostic to node feature modalities and could be utilized to integrate multimodal data for triaging patients in various downstream resource allocation tasks.

Improving the retrieval relevance on noisy datasets is an emerging need for the curation of a large-scale clean dataset in the medical domain. While existing methods can be applied for class-wise retrieval (aka. inter-class), they cannot distinguish the granularity of likeness within the same class (aka. intra-class). The problem is exacerbated on medical external datasets, where noisy samples of the same class are treated equally during training. Our goal is to identify both intra/inter-class similarities for fine-grained retrieval. To achieve this, we propose an Outlier-Sensitive Content-based rAdiologhy Retrieval System (OSCARS), consisting of two steps. First, we train an outlier detector on a clean internal dataset in an unsupervised manner. Then we use the trained detector to generate the anomaly scores on the external dataset, whose distribution will be used to bin intra-class variations. Second, we propose a quadruplet (a, p, nintra, ninter) sampling strategy, where intra-class negatives nintra are sampled from bins of the same class other than the bin anchor a belongs to, while niner are randomly sampled from inter-classes. We suggest a weighted metric learning objective to balance the intra and inter-class feature learning. We experimented on two representative public radiography datasets. Experiments show the effectiveness of our approach. The training and evaluation code can be found in https://github.com/XiaoyuanGuo/oscars., Comment: 12 pages, 6 figures, 2 tables

Developing and validating artificial intelligence models in medical imaging requires datasets that are large, granular, and diverse. To date, the majority of publicly available breast imaging datasets lack in one or more of these areas. Models trained on these data may therefore underperform on patient populations or pathologies that have not previously been encountered. The EMory BrEast imaging Dataset (EMBED) addresses these gaps by providing 3650,000 2D and DBT screening and diagnostic mammograms for 116,000 women divided equally between White and African American patients. The dataset also contains 40,000 annotated lesions linked to structured imaging descriptors and 61 ground truth pathologic outcomes grouped into six severity classes. Our goal is to share this dataset with research partners to aid in development and validation of breast AI models that will serve all patients fairly and help decrease bias in medical AI.

To curate a high-quality dataset, identifying data variance between the internal and external sources is a fundamental and crucial step. However, methods to detect shift or variance in data have not been significantly researched. Challenges to this are the lack of effective approaches to learn dense representation of a dataset and difficulties of sharing private data across medical institutions. To overcome the problems, we propose a unified pipeline called MedShift to detect the top-level shift samples and thus facilitate the medical curation. Given an internal dataset A as the base source, we first train anomaly detectors for each class of dataset A to learn internal distributions in an unsupervised way. Second, without exchanging data across sources, we run the trained anomaly detectors on an external dataset B for each class. The data samples with high anomaly scores are identified as shift data. To quantify the shiftness of the external dataset, we cluster B's data into groups class-wise based on the obtained scores. We then train a multi-class classifier on A and measure the shiftness with the classifier's performance variance on B by gradually dropping the group with the largest anomaly score for each class. Additionally, we adapt a dataset quality metric to help inspect the distribution differences for multiple medical sources. We verify the efficacy of MedShift with musculoskeletal radiographs (MURA) and chest X-rays datasets from more than one external source. Experiments show our proposed shift data detection pipeline can be beneficial for medical centers to curate high-quality datasets more efficiently. An interface introduction video to visualize our results is available at https://youtu.be/V3BF0P1sxQE., Comment: 35 pages, 28 figures, 2 tables

Despite the routine use of electronic health record (EHR) data by radiologists to contextualize clinical history and inform image interpretation, the majority of deep learning architectures for medical imaging are unimodal, i.e., they only learn features from pixel-level information. Recent research revealing how race can be recovered from pixel data alone highlights the potential for serious biases in models which fail to account for demographics and other key patient attributes. Yet the lack of imaging datasets which capture clinical context, inclusive of demographics and longitudinal medical history, has left multimodal medical imaging underexplored. To better assess these challenges, we present RadFusion, a multimodal, benchmark dataset of 1794 patients with corresponding EHR data and high-resolution computed tomography (CT) scans labeled for pulmonary embolism. We evaluate several representative multimodal fusion models and benchmark their fairness properties across protected subgroups, e.g., gender, race/ethnicity, age. Our results suggest that integrating imaging and EHR data can improve classification performance and robustness without introducing large disparities in the true positive rate between population groups., Comment: RadFusion dataset: https://stanfordaimi.azurewebsites.net/datasets/3a7548a4-8f65-4ab7-85fa-3d68c9efc1bd

The use of artificial intelligence (AI) in healthcare has become a very active research area in the last few years. While significant progress has been made in image classification tasks, only a few AI methods are actually being deployed in hospitals. A major hurdle in actively using clinical AI models currently is the trustworthiness of these models. More often than not, these complex models are black boxes in which promising results are generated. However, when scrutinized, these models begin to reveal implicit biases during the decision making, such as detecting race and having bias towards ethnic groups and subpopulations. In our ongoing study, we develop a two-step adversarial debiasing approach with partial learning that can reduce the racial disparity while preserving the performance of the targeted task. The methodology has been evaluated on two independent medical image case-studies - chest X-ray and mammograms, and showed promises in bias reduction while preserving the targeted performance.

Detecting out-of-distribution (OOD) samples in medical imaging plays an important role for downstream medical diagnosis. However, existing OOD detectors are demonstrated on natural images composed of inter-classes and have difficulty generalizing to medical images. The key issue is the granularity of OOD data in the medical domain, where intra-class OOD samples are predominant. We focus on the generalizability of OOD detection for medical images and propose a self-supervised Cascade Variational autoencoder-based Anomaly Detector (CVAD). We use a variational autoencoders' cascade architecture, which combines latent representation at multiple scales, before being fed to a discriminator to distinguish the OOD data from the in-distribution (ID) data. Finally, both the reconstruction error and the OOD probability predicted by the binary discriminator are used to determine the anomalies. We compare the performance with the state-of-the-art deep learning models to demonstrate our model's efficacy on various open-access medical imaging datasets for both intra- and inter-class OOD. Further extensive results on datasets including common natural datasets show our model's effectiveness and generalizability. The code is available at https://github.com/XiaoyuanGuo/CVAD., Comment: 6 pages, 4 figures, 4 tables

Traditional anomaly detection methods focus on detecting inter-class variations while medical image novelty identification is inherently an intra-class detection problem. For example, a machine learning model trained with normal chest X-ray and common lung abnormalities, is expected to discover and flag idiopathic pulmonary fibrosis which a rare lung disease and unseen by the model during training. The nuances from intra-class variations and lack of relevant training data in medical image analysis pose great challenges for existing anomaly detection methods. To tackle the challenges, we propose a hybrid model - Transformation-based Embedding learning for Novelty Detection (TEND) which without any out-of-distribution training data, performs novelty identification by combining both autoencoder-based and classifier-based method. With a pre-trained autoencoder as image feature extractor, TEND learns to discriminate the feature embeddings of in-distribution data from the transformed counterparts as fake out-of-distribution inputs. To enhance the separation, a distance objective is optimized to enforce a margin between the two classes. Extensive experimental results on both natural image datasets and medical image datasets are presented and our method out-performs state-of-the-art approaches., Comment: 35 pages, 8 figures

Background: In medical imaging, prior studies have demonstrated disparate AI performance by race, yet there is no known correlation for race on medical imaging that would be obvious to the human expert interpreting the images. Methods: Using private and public datasets we evaluate: A) performance quantification of deep learning models to detect race from medical images, including the ability of these models to generalize to external environments and across multiple imaging modalities, B) assessment of possible confounding anatomic and phenotype population features, such as disease distribution and body habitus as predictors of race, and C) investigation into the underlying mechanism by which AI models can recognize race. Findings: Standard deep learning models can be trained to predict race from medical images with high performance across multiple imaging modalities. Our findings hold under external validation conditions, as well as when models are optimized to perform clinically motivated tasks. We demonstrate this detection is not due to trivial proxies or imaging-related surrogate covariates for race, such as underlying disease distribution. Finally, we show that performance persists over all anatomical regions and frequency spectrum of the images suggesting that mitigation efforts will be challenging and demand further study. Interpretation: We emphasize that model ability to predict self-reported race is itself not the issue of importance. However, our findings that AI can trivially predict self-reported race -- even from corrupted, cropped, and noised medical images -- in a setting where clinical experts cannot, creates an enormous risk for all model deployments in medical imaging: if an AI model secretly used its knowledge of self-reported race to misclassify all Black patients, radiologists would not be able to tell using the same data the model has access to.

Datasets displaying temporal dependencies abound in science and engineering applications, with Markov models representing a simplified and popular view of the temporal dependence structure. In this paper, we consider Bayesian settings that place prior distributions over the parameters of the transition kernel of a Markov model, and seeks to characterize the resulting, typically intractable, posterior distributions. We present a PAC-Bayesian analysis of variational Bayes (VB) approximations to tempered Bayesian posterior distributions, bounding the model risk of the VB approximations. Tempered posteriors are known to be robust to model misspecification, and their variational approximations do not suffer the usual problems of over confident approximations. Our results tie the risk bounds to the mixing and ergodic properties of the Markov data generating model. We illustrate the PAC-Bayes bounds through a number of example Markov models, and also consider the situation where the Markov model is misspecified., Comment: 14 pages main, 24 pages appendix and citations

Deep Convolutional Neural Networks (DCNNs) have attracted extensive attention and been applied in many areas, including medical image analysis and clinical diagnosis. One major challenge is to conceive a DCNN model with remarkable performance on both internal and external data. We demonstrate that DCNNs may not generalize to new data, but increasing the quality and heterogeneity of the training data helps to improve the generalizibility factor. We use InceptionResNetV2 and DenseNet121 architectures to predict the risk of 5 common chest pathologies. The experiments were conducted on three publicly available databases: CheXpert, ChestX-ray14, and MIMIC Chest Xray JPG. The results show the internal performance of each of the 5 pathologies outperformed external performance on both of the models. Moreover, our strategy of exposing the models to a mix of different datasets during the training phase helps to improve model performance on the external dataset.

Purpose: Since the recent COVID-19 outbreak, there has been an avalanche of research papers applying deep learning based image processing to chest radiographs for detection of the disease. To test the performance of the two top models for CXR COVID-19 diagnosis on external datasets to assess model generalizability. Methods: In this paper, we present our argument regarding the efficiency and applicability of existing deep learning models for COVID-19 diagnosis. We provide results from two popular models - COVID-Net and CoroNet evaluated on three publicly available datasets and an additional institutional dataset collected from EMORY Hospital between January and May 2020, containing patients tested for COVID-19 infection using RT-PCR. Results: There is a large false positive rate (FPR) for COVID-Net on both ChexPert (55.3%) and MIMIC-CXR (23.4%) dataset. On the EMORY Dataset, COVID-Net has 61.4% sensitivity, 0.54 F1-score and 0.49 precision value. The FPR of the CoroNet model is significantly lower across all the datasets as compared to COVID-Net - EMORY(9.1%), ChexPert (1.3%), ChestX-ray14 (0.02%), MIMIC-CXR (0.06%). Conclusion: The models reported good to excellent performance on their internal datasets, however we observed from our testing that their performance dramatically worsened on external data. This is likely from several causes including overfitting models due to lack of appropriate control patients and ground truth labels. The fourth institutional dataset was labeled using RT-PCR, which could be positive without radiographic findings and vice versa. Therefore, a fusion model of both clinical and radiographic data may have better performance and generalization.

Executing machine learning (ML) pipelines in real-time on radiology images is hard due to the limited computing resources in clinical environments and the lack of efficient data transfer capabilities to run them on research clusters. We propose Niffler, an integrated framework that enables the execution of ML pipelines at research clusters by efficiently querying and retrieving radiology images from the Picture Archiving and Communication Systems (PACS) of the hospitals. Niffler uses the Digital Imaging and Communications in Medicine (DICOM) protocol to fetch and store imaging data and provides metadata extraction capabilities and Application programming interfaces (APIs) to apply filters on the images. Niffler further enables the sharing of the outcomes from the ML pipelines in a de-identified manner. Niffler has been running stable for more than 19 months and has supported several research projects at the department. In this paper, we present its architecture and three of its use cases: an inferior vena cava (IVC) filter detection from the images in real-time, identification of scanner utilization, and scanner clock calibration. Evaluations on the Niffler prototype highlight its feasibility and efficiency in facilitating the ML pipelines on the images and metadata in real-time and retrospectively., Comment: Preprint

We propose a hybrid sequential deep learning model to predict the risk of AMD progression in non-exudative AMD eyes at multiple timepoints, starting from short-term progression (3-months) up to long-term progression (21-months). Proposed model combines radiomics and deep learning to handle challenges related to imperfect ratio of OCT scan dimension and training cohort size. We considered a retrospective clinical trial dataset that includes 671 fellow eyes with 13,954 dry AMD observations for training and validating the machine learning models on a 10-fold cross validation setting. The proposed RNN model achieved high accuracy (0.96 AUCROC) for the prediction of both short term and long-term AMD progression, and outperformed the traditional random forest model trained. High accuracy achieved by the RNN establishes the ability to identify AMD patients at risk of progressing to advanced AMD at an early stage which could have a high clinical impact as it allows for optimal clinical follow-up, with more frequent screening and potential earlier treatment for those patients at high risk.