Daily Papers

In this paper we present a hybrid method for the automatic detection of dermatological pathologies in medical reports. We use a large language model combined with medical ontologies to predict, given a first appointment or follow-up medical report, the pathology a person may suffer from. The results show that teaching the model to learn the type, severity and location on the body of a dermatological pathology, as well as in which order it has to learn these three features, significantly increases its accuracy. The article presents the demonstration of state-of-the-art results for classification of medical texts with a precision of 0.84, micro and macro F1-score of 0.82 and 0.75, and makes both the method and the data set used available to the community.

In recent years, Deep Learning (DL) models are becoming important due to their demonstrated success at overcoming complex learning problems. DL models have been applied effectively for different Natural Language Processing (NLP) tasks such as part-of-Speech (PoS) tagging and Machine Translation (MT). Disease Named Entity Recognition (Disease-NER) is a crucial task which aims at extracting disease Named Entities (NEs) from text. In this paper, a DL model for Disease-NER using dictionary information is proposed and evaluated on National Center for Biotechnology Information (NCBI) disease corpus and BC5CDR dataset. Word embeddings trained over general domain texts as well as biomedical texts have been used to represent input to the proposed model. This study also compares two different Segment Representation (SR) schemes, namely IOB2 and IOBES for Disease-NER. The results illustrate that using dictionary information, pre-trained word embeddings, character embeddings and CRF with global score improves the performance of Disease-NER system.

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.

Heart disease, also known as cardiovascular disease, is a prevalent and critical medical condition characterized by the impairment of the heart and blood vessels, leading to various complications such as coronary artery disease, heart failure, and myocardial infarction. The timely and accurate detection of heart disease is of paramount importance in clinical practice. Early identification of individuals at risk enables proactive interventions, preventive measures, and personalized treatment strategies to mitigate the progression of the disease and reduce adverse outcomes. In recent years, the field of heart disease detection has witnessed notable advancements due to the integration of sophisticated technologies and computational approaches. These include machine learning algorithms, data mining techniques, and predictive modeling frameworks that leverage vast amounts of clinical and physiological data to improve diagnostic accuracy and risk stratification. In this work, we propose to detect heart disease from ECG images using cutting-edge technologies, namely vision transformer models. These models are Google-Vit, Microsoft-Beit, and Swin-Tiny. To the best of our knowledge, this is the initial endeavor concentrating on the detection of heart diseases through image-based ECG data by employing cuttingedge technologies namely, transformer models. To demonstrate the contribution of the proposed framework, the performance of vision transformer models are compared with state-of-the-art studies. Experiment results show that the proposed framework exhibits remarkable classification results.

Automatic phenotype concept recognition from unstructured text remains a challenging task in biomedical text mining research. Previous works that address the task typically use dictionary-based matching methods, which can achieve high precision but suffer from lower recall. Recently, machine learning-based methods have been proposed to identify biomedical concepts, which can recognize more unseen concept synonyms by automatic feature learning. However, most methods require large corpora of manually annotated data for model training, which is difficult to obtain due to the high cost of human annotation. In this paper, we propose PhenoTagger, a hybrid method that combines both dictionary and machine learning-based methods to recognize Human Phenotype Ontology (HPO) concepts in unstructured biomedical text. We first use all concepts and synonyms in HPO to construct a dictionary, which is then used to automatically build a distantly supervised training dataset for machine learning. Next, a cutting-edge deep learning model is trained to classify each candidate phrase (n-gram from input sentence) into a corresponding concept label. Finally, the dictionary and machine learning-based prediction results are combined for improved performance. Our method is validated with two HPO corpora, and the results show that PhenoTagger compares favorably to previous methods. In addition, to demonstrate the generalizability of our method, we retrained PhenoTagger using the disease ontology MEDIC for disease concept recognition to investigate the effect of training on different ontologies. Experimental results on the NCBI disease corpus show that PhenoTagger without requiring manually annotated training data achieves competitive performance as compared with state-of-the-art supervised methods.

Automatically classifying electronic health records (EHRs) into diagnostic codes has been challenging to the NLP community. State-of-the-art methods treated this problem as a multilabel classification problem and proposed various architectures to model this problem. However, these systems did not leverage the superb performance of pretrained language models, which achieved superb performance on natural language understanding tasks. Prior work has shown that pretrained language models underperformed on this task with the regular finetuning scheme. Therefore, this paper aims at analyzing the causes of the underperformance and developing a framework for automatic ICD coding with pretrained language models. We spotted three main issues through the experiments: 1) large label space, 2) long input sequences, and 3) domain mismatch between pretraining and fine-tuning. We propose PLMICD, a framework that tackles the challenges with various strategies. The experimental results show that our proposed framework can overcome the challenges and achieves state-of-the-art performance in terms of multiple metrics on the benchmark MIMIC data. The source code is available at https://github.com/MiuLab/PLM-ICD

Automatic coding of International Classification of Diseases (ICD) is a multi-label text categorization task that involves extracting disease or procedure codes from clinical notes. Despite the application of state-of-the-art natural language processing (NLP) techniques, there are still challenges including limited availability of data due to privacy constraints and the high variability of clinical notes caused by different writing habits of medical professionals and various pathological features of patients. In this work, we investigate the semi-structured nature of clinical notes and propose an automatic algorithm to segment them into sections. To address the variability issues in existing ICD coding models with limited data, we introduce a contrastive pre-training approach on sections using a soft multi-label similarity metric based on tree edit distance. Additionally, we design a masked section training strategy to enable ICD coding models to locate sections related to ICD codes. Extensive experimental results demonstrate that our proposed training strategies effectively enhance the performance of existing ICD coding methods.

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.

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.

Disease risk prediction has attracted increasing attention in the field of modern healthcare, especially with the latest advances in artificial intelligence (AI). Electronic health records (EHRs), which contain heterogeneous patient information, are widely used in disease risk prediction tasks. One challenge of applying AI models for risk prediction lies in generating interpretable evidence to support the prediction results while retaining the prediction ability. In order to address this problem, we propose the method of jointly embedding words and labels whereby attention modules learn the weights of words from medical notes according to their relevance to the names of risk prediction labels. This approach boosts interpretability by employing an attention mechanism and including the names of prediction tasks in the model. However, its application is only limited to the handling of textual inputs such as medical notes. In this paper, we propose a label dependent attention model LDAM to 1) improve the interpretability by exploiting Clinical-BERT (a biomedical language model pre-trained on a large clinical corpus) to encode biomedically meaningful features and labels jointly; 2) extend the idea of joint embedding to the processing of time-series data, and develop a multi-modal learning framework for integrating heterogeneous information from medical notes and time-series health status indicators. To demonstrate our method, we apply LDAM to the MIMIC-III dataset to predict different disease risks. We evaluate our method both quantitatively and qualitatively. Specifically, the predictive power of LDAM will be shown, and case studies will be carried out to illustrate its interpretability.

Automatic disease diagnosis has become increasingly valuable in clinical practice. The advent of large language models (LLMs) has catalyzed a paradigm shift in artificial intelligence, with growing evidence supporting the efficacy of LLMs in diagnostic tasks. Despite the increasing attention in this field, a holistic view is still lacking. Many critical aspects remain unclear, such as the diseases and clinical data to which LLMs have been applied, the LLM techniques employed, and the evaluation methods used. In this article, we perform a comprehensive review of LLM-based methods for disease diagnosis. Our review examines the existing literature across various dimensions, including disease types and associated clinical specialties, clinical data, LLM techniques, and evaluation methods. Additionally, we offer recommendations for applying and evaluating LLMs for diagnostic tasks. Furthermore, we assess the limitations of current research and discuss future directions. To our knowledge, this is the first comprehensive review for LLM-based disease diagnosis.

A user-generated text on social media enables health workers to keep track of information, identify possible outbreaks, forecast disease trends, monitor emergency cases, and ascertain disease awareness and response to official health correspondence. This exchange of health information on social media has been regarded as an attempt to enhance public health surveillance (PHS). Despite its potential, the technology is still in its early stages and is not ready for widespread application. Advancements in pretrained language models (PLMs) have facilitated the development of several domain-specific PLMs and a variety of downstream applications. However, there are no PLMs for social media tasks involving PHS. We present and release PHS-BERT, a transformer-based PLM, to identify tasks related to public health surveillance on social media. We compared and benchmarked the performance of PHS-BERT on 25 datasets from different social medial platforms related to 7 different PHS tasks. Compared with existing PLMs that are mainly evaluated on limited tasks, PHS-BERT achieved state-of-the-art performance on all 25 tested datasets, showing that our PLM is robust and generalizable in the common PHS tasks. By making PHS-BERT available, we aim to facilitate the community to reduce the computational cost and introduce new baselines for future works across various PHS-related tasks.

Background: Natural Language Processing (NLP) is widely used to extract clinical insights from Electronic Health Records (EHRs). However, the lack of annotated data, automated tools, and other challenges hinder the full utilisation of NLP for EHRs. Various Machine Learning (ML), Deep Learning (DL) and NLP techniques are studied and compared to understand the limitations and opportunities in this space comprehensively. Methodology: After screening 261 articles from 11 databases, we included 127 papers for full-text review covering seven categories of articles: 1) medical note classification, 2) clinical entity recognition, 3) text summarisation, 4) deep learning (DL) and transfer learning architecture, 5) information extraction, 6) Medical language translation and 7) other NLP applications. This study follows the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Result and Discussion: EHR was the most commonly used data type among the selected articles, and the datasets were primarily unstructured. Various ML and DL methods were used, with prediction or classification being the most common application of ML or DL. The most common use cases were: the International Classification of Diseases, Ninth Revision (ICD-9) classification, clinical note analysis, and named entity recognition (NER) for clinical descriptions and research on psychiatric disorders. Conclusion: We find that the adopted ML models were not adequately assessed. In addition, the data imbalance problem is quite important, yet we must find techniques to address this underlining problem. Future studies should address key limitations in studies, primarily identifying Lupus Nephritis, Suicide Attempts, perinatal self-harmed and ICD-9 classification.

Automatic International Classification of Diseases (ICD) coding aims to assign multiple ICD codes to a medical note with average length of 3,000+ tokens. This task is challenging due to a high-dimensional space of multi-label assignment (tens of thousands of ICD codes) and the long-tail challenge: only a few codes (common diseases) are frequently assigned while most codes (rare diseases) are infrequently assigned. This study addresses the long-tail challenge by adapting a prompt-based fine-tuning technique with label semantics, which has been shown to be effective under few-shot setting. To further enhance the performance in medical domain, we propose a knowledge-enhanced longformer by injecting three domain-specific knowledge: hierarchy, synonym, and abbreviation with additional pretraining using contrastive learning. Experiments on MIMIC-III-full, a benchmark dataset of code assignment, show that our proposed method outperforms previous state-of-the-art method in 14.5% in marco F1 (from 10.3 to 11.8, P<0.001). To further test our model on few-shot setting, we created a new rare diseases coding dataset, MIMIC-III-rare50, on which our model improves marco F1 from 17.1 to 30.4 and micro F1 from 17.2 to 32.6 compared to previous method.

Chest X-rays play a pivotal role in diagnosing respiratory diseases such as pneumonia, tuberculosis, and COVID-19, which are prevalent and present unique diagnostic challenges due to overlapping visual features and variability in image quality. Severe class imbalance and the complexity of medical images hinder automated analysis. This study leverages deep learning techniques, including transfer learning on pre-trained models (AlexNet, ResNet, and InceptionNet), to enhance disease detection and classification. By fine-tuning these models and incorporating focal loss to address class imbalance, significant performance improvements were achieved. Grad-CAM visualizations further enhance model interpretability, providing insights into clinically relevant regions influencing predictions. The InceptionV3 model, for instance, achieved a 28% improvement in AUC and a 15% increase in F1-Score. These findings highlight the potential of deep learning to improve diagnostic workflows and support clinical decision-making.

Generalist Large Language Models (LLMs), such as GPT-4, have shown considerable promise in various domains, including medical diagnosis. Rare diseases, affecting approximately 300 million people worldwide, often have unsatisfactory clinical diagnosis rates primarily due to a lack of experienced physicians and the complexity of differentiating among many rare diseases. In this context, recent news such as "ChatGPT correctly diagnosed a 4-year-old's rare disease after 17 doctors failed" underscore LLMs' potential, yet underexplored, role in clinically diagnosing rare diseases. To bridge this research gap, we introduce RareBench, a pioneering benchmark designed to systematically evaluate the capabilities of LLMs on 4 critical dimensions within the realm of rare diseases. Meanwhile, we have compiled the largest open-source dataset on rare disease patients, establishing a benchmark for future studies in this domain. To facilitate differential diagnosis of rare diseases, we develop a dynamic few-shot prompt methodology, leveraging a comprehensive rare disease knowledge graph synthesized from multiple knowledge bases, significantly enhancing LLMs' diagnostic performance. Moreover, we present an exhaustive comparative study of GPT-4's diagnostic capabilities against those of specialist physicians. Our experimental findings underscore the promising potential of integrating LLMs into the clinical diagnostic process for rare diseases. This paves the way for exciting possibilities in future advancements in this field.

Mental health is a significant and growing public health concern. As language usage can be leveraged to obtain crucial insights into mental health conditions, there is a need for large-scale, labeled, mental health-related datasets of users who have been diagnosed with one or more of such conditions. In this paper, we investigate the creation of high-precision patterns to identify self-reported diagnoses of nine different mental health conditions, and obtain high-quality labeled data without the need for manual labelling. We introduce the SMHD (Self-reported Mental Health Diagnoses) dataset and make it available. SMHD is a novel large dataset of social media posts from users with one or multiple mental health conditions along with matched control users. We examine distinctions in users' language, as measured by linguistic and psychological variables. We further explore text classification methods to identify individuals with mental conditions through their language.

Background:Speech patterns have emerged as potential diagnostic markers for conditions with varying etiologies. Machine learning (ML) presents an opportunity to harness these patterns for accurate disease diagnosis. Objective: This review synthesized findings from studies exploring ML's capability in leveraging speech for the diagnosis of neurological, laryngeal and mental disorders. Methods: A systematic examination of 564 articles was conducted with 91 articles included in the study, which encompassed a wide spectrum of conditions, ranging from voice pathologies to mental and neurological disorders. Methods for speech classifications were assessed based on the relevant studies and scored between 0-10 based on the reported diagnostic accuracy of their ML models. Results: High diagnostic accuracies were consistently observed for laryngeal disorders, dysarthria, and changes related to speech in Parkinsons disease. These findings indicate the robust potential of speech as a diagnostic tool. Disorders like depression, schizophrenia, mild cognitive impairment and Alzheimers dementia also demonstrated high accuracies, albeit with some variability across studies. Meanwhile, disorders like OCD and autism highlighted the need for more extensive research to ascertain the relationship between speech patterns and the respective conditions. Conclusion: ML models utilizing speech patterns demonstrate promising potential in diagnosing a range of mental, laryngeal, and neurological disorders. However, the efficacy varies across conditions, and further research is needed. The integration of these models into clinical practice could potentially revolutionize the evaluation and diagnosis of a number of different medical conditions.

When developing deep neural networks for segmenting intraoperative ultrasound images, several practical issues are encountered frequently, such as the presence of ultrasound frames that do not contain regions of interest and the high variance in ground-truth labels. In this study, we evaluate the utility of a pre-screening classification network prior to the segmentation network. Experimental results demonstrate that such a classifier, minimising frame classification errors, was able to directly impact the number of false positive and false negative frames. Importantly, the segmentation accuracy on the classifier-selected frames, that would be segmented, remains comparable to or better than those from standalone segmentation networks. Interestingly, the efficacy of the pre-screening classifier was affected by the sampling methods for training labels from multiple observers, a seemingly independent problem. We show experimentally that a previously proposed approach, combining random sampling and consensus labels, may need to be adapted to perform well in our application. Furthermore, this work aims to share practical experience in developing a machine learning application that assists highly variable interventional imaging for prostate cancer patients, to present robust and reproducible open-source implementations, and to report a set of comprehensive results and analysis comparing these practical, yet important, options in a real-world clinical application.

Identifying disease phenotypes from electronic health records (EHRs) is critical for numerous secondary uses. Manually encoding physician knowledge into rules is particularly challenging for rare diseases due to inadequate EHR coding, necessitating review of clinical notes. Large language models (LLMs) offer promise in text understanding but may not efficiently handle real-world clinical documentation. We propose a zero-shot LLM-based method enriched by retrieval-augmented generation and MapReduce, which pre-identifies disease-related text snippets to be used in parallel as queries for the LLM to establish diagnosis. We show that this method as applied to pulmonary hypertension (PH), a rare disease characterized by elevated arterial pressures in the lungs, significantly outperforms physician logic rules (F_1 score of 0.62 vs. 0.75). This method has the potential to enhance rare disease cohort identification, expanding the scope of robust clinical research and care gap identification.

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.

International Classification of Disease (ICD) coding procedure which refers to tagging medical notes with diagnosis codes has been shown to be effective and crucial to the billing system in medical sector. Currently, ICD codes are assigned to a clinical note manually which is likely to cause many errors. Moreover, training skilled coders also requires time and human resources. Therefore, automating the ICD code determination process is an important task. With the advancement of artificial intelligence theory and computational hardware, machine learning approach has emerged as a suitable solution to automate this process. In this project, we apply a transformer-based architecture to capture the interdependence among the tokens of a document and then use a code-wise attention mechanism to learn code-specific representations of the entire document. Finally, they are fed to separate dense layers for corresponding code prediction. Furthermore, to handle the imbalance in the code frequency of clinical datasets, we employ a label distribution aware margin (LDAM) loss function. The experimental results on the MIMIC-III dataset show that our proposed model outperforms other baselines by a significant margin. In particular, our best setting achieves a micro-AUC score of 0.923 compared to 0.868 of bidirectional recurrent neural networks. We also show that by using the code-wise attention mechanism, the model can provide more insights about its prediction, and thus it can support clinicians to make reliable decisions. Our code is available online (https://github.com/biplob1ly/TransICD)

Pretrained language models have been used in various natural language processing applications. In the mental health domain, domain-specific language models are pretrained and released, which facilitates the early detection of mental health conditions. Social posts, e.g., on Reddit, are usually long documents. However, there are no domain-specific pretrained models for long-sequence modeling in the mental health domain. This paper conducts domain-specific continued pretraining to capture the long context for mental health. Specifically, we train and release MentalXLNet and MentalLongformer based on XLNet and Longformer. We evaluate the mental health classification performance and the long-range ability of these two domain-specific pretrained models. Our models are released in HuggingFace.

Recent advances in natural language processing (NLP) can be largely attributed to the advent of pre-trained language models such as BERT and RoBERTa. While these models demonstrate remarkable performance on general datasets, they can struggle in specialized domains such as medicine, where unique domain-specific terminologies, domain-specific abbreviations, and varying document structures are common. This paper explores strategies for adapting these models to domain-specific requirements, primarily through continuous pre-training on domain-specific data. We pre-trained several German medical language models on 2.4B tokens derived from translated public English medical data and 3B tokens of German clinical data. The resulting models were evaluated on various German downstream tasks, including named entity recognition (NER), multi-label classification, and extractive question answering. Our results suggest that models augmented by clinical and translation-based pre-training typically outperform general domain models in medical contexts. We conclude that continuous pre-training has demonstrated the ability to match or even exceed the performance of clinical models trained from scratch. Furthermore, pre-training on clinical data or leveraging translated texts have proven to be reliable methods for domain adaptation in medical NLP tasks.

Alzheimer's disease (AD) is a degenerative brain disease impairing a person's ability to perform day to day activities. The clinical manifestations of Alzheimer's disease are characterized by heterogeneity in age, disease span, progression rate, impairment of memory and cognitive abilities. Due to these variabilities, personalized care and treatment planning, as well as patient counseling about their individual progression is limited. Recent developments in machine learning to detect hidden patterns in complex, multi-dimensional datasets provides significant opportunities to address this critical need. In this work, we use unsupervised and supervised machine learning approaches for subtype identification and prediction. We apply machine learning methods to the extensive clinical observations available at the Alzheimer's Disease Neuroimaging Initiative (ADNI) data set to identify patient subtypes and to predict disease progression. Our analysis depicts the progression space for the Alzheimer's disease into low, moderate and high disease progression zones. The proposed work will enable early detection and characterization of distinct disease subtypes based on clinical heterogeneity. We anticipate that our models will enable patient counseling, clinical trial design, and ultimately individualized clinical care.

Efficient Human Epithelial-2 (HEp-2) cell image classification can facilitate the diagnosis of many autoimmune diseases. This paper presents an automatic framework for this classification task, by utilizing the deep convolutional neural networks (CNNs) which have recently attracted intensive attention in visual recognition. This paper elaborates the important components of this framework, discusses multiple key factors that impact the efficiency of training a deep CNN, and systematically compares this framework with the well-established image classification models in the literature. Experiments on benchmark datasets show that i) the proposed framework can effectively outperform existing models by properly applying data augmentation; ii) our CNN-based framework demonstrates excellent adaptability across different datasets, which is highly desirable for classification under varying laboratory settings. Our system is ranked high in the cell image classification competition hosted by ICPR 2014.

Skin disease is one of the most common types of human diseases, which may happen to everyone regardless of age, gender or race. Due to the high visual diversity, human diagnosis highly relies on personal experience; and there is a serious shortage of experienced dermatologists in many countries. To alleviate this problem, computer-aided diagnosis with state-of-the-art (SOTA) machine learning techniques would be a promising solution. In this paper, we aim at understanding the performance of convolutional neural network (CNN) based approaches. We first build two versions of skin disease datasets from Internet images: (a) Skin-10, which contains 10 common classes of skin disease with a total of 10,218 images; (b) Skin-100, which is a larger dataset that consists of 19,807 images of 100 skin disease classes. Based on these datasets, we benchmark several SOTA CNN models and show that the accuracy of skin-100 is much lower than the accuracy of skin-10. We then implement an ensemble method based on several CNN models and achieve the best accuracy of 79.01\% for Skin-10 and 53.54\% for Skin-100. We also present an object detection based approach by introducing bounding boxes into the Skin-10 dataset. Our results show that object detection can help improve the accuracy of some skin disease classes.

Biomedical text mining is becoming increasingly important as the number of biomedical documents rapidly grows. With the progress in natural language processing (NLP), extracting valuable information from biomedical literature has gained popularity among researchers, and deep learning has boosted the development of effective biomedical text mining models. However, directly applying the advancements in NLP to biomedical text mining often yields unsatisfactory results due to a word distribution shift from general domain corpora to biomedical corpora. In this article, we investigate how the recently introduced pre-trained language model BERT can be adapted for biomedical corpora. We introduce BioBERT (Bidirectional Encoder Representations from Transformers for Biomedical Text Mining), which is a domain-specific language representation model pre-trained on large-scale biomedical corpora. With almost the same architecture across tasks, BioBERT largely outperforms BERT and previous state-of-the-art models in a variety of biomedical text mining tasks when pre-trained on biomedical corpora. While BERT obtains performance comparable to that of previous state-of-the-art models, BioBERT significantly outperforms them on the following three representative biomedical text mining tasks: biomedical named entity recognition (0.62% F1 score improvement), biomedical relation extraction (2.80% F1 score improvement) and biomedical question answering (12.24% MRR improvement). Our analysis results show that pre-training BERT on biomedical corpora helps it to understand complex biomedical texts. We make the pre-trained weights of BioBERT freely available at https://github.com/naver/biobert-pretrained, and the source code for fine-tuning BioBERT available at https://github.com/dmis-lab/biobert.

Learning to represent free text is a core task in many clinical machine learning (ML) applications, as clinical text contains observations and plans not otherwise available for inference. State-of-the-art methods use large language models developed with immense computational resources and training data; however, applying these models is challenging because of the highly varying syntax and vocabulary in clinical free text. Structured information such as International Classification of Disease (ICD) codes often succinctly abstracts the most important facts of a clinical encounter and yields good performance, but is often not as available as clinical text in real-world scenarios. We propose a multi-view learning framework that jointly learns from codes and text to combine the availability and forward-looking nature of text and better performance of ICD codes. The learned text embeddings can be used as inputs to predictive algorithms independent of the ICD codes during inference. Our approach uses a Graph Neural Network (GNN) to process ICD codes, and Bi-LSTM to process text. We apply Deep Canonical Correlation Analysis (DCCA) to enforce the two views to learn a similar representation of each patient. In experiments using planned surgical procedure text, our model outperforms BERT models fine-tuned to clinical data, and in experiments using diverse text in MIMIC-III, our model is competitive to a fine-tuned BERT at a tiny fraction of its computational effort.

The medical domain is vast and diverse, with many existing embedding models focused on general healthcare applications. However, these models often struggle to capture a deep understanding of diseases due to their broad generalization across the entire medical field. To address this gap, I present DisEmbed, a disease-focused embedding model. DisEmbed is trained on a synthetic dataset specifically curated to include disease descriptions, symptoms, and disease-related Q\&A pairs, making it uniquely suited for disease-related tasks. For evaluation, I benchmarked DisEmbed against existing medical models using disease-specific datasets and the triplet evaluation method. My results demonstrate that DisEmbed outperforms other models, particularly in identifying disease-related contexts and distinguishing between similar diseases. This makes DisEmbed highly valuable for disease-specific use cases, including retrieval-augmented generation (RAG) tasks, where its performance is particularly robust.

Linking clinical narratives to standardized vocabularies and coding systems is a key component of unlocking the information in medical text for analysis. However, many domains of medical concepts lack well-developed terminologies that can support effective coding of medical text. We present a framework for developing natural language processing (NLP) technologies for automated coding of under-studied types of medical information, and demonstrate its applicability via a case study on physical mobility function. Mobility is a component of many health measures, from post-acute care and surgical outcomes to chronic frailty and disability, and is coded in the International Classification of Functioning, Disability, and Health (ICF). However, mobility and other types of functional activity remain under-studied in medical informatics, and neither the ICF nor commonly-used medical terminologies capture functional status terminology in practice. We investigated two data-driven paradigms, classification and candidate selection, to link narrative observations of mobility to standardized ICF codes, using a dataset of clinical narratives from physical therapy encounters. Recent advances in language modeling and word embedding were used as features for established machine learning models and a novel deep learning approach, achieving a macro F-1 score of 84% on linking mobility activity reports to ICF codes. Both classification and candidate selection approaches present distinct strengths for automated coding in under-studied domains, and we highlight that the combination of (i) a small annotated data set; (ii) expert definitions of codes of interest; and (iii) a representative text corpus is sufficient to produce high-performing automated coding systems. This study has implications for the ongoing growth of NLP tools for a variety of specialized applications in clinical care and research.

Self-supervised pre-training of deep learning models with contrastive learning is a widely used technique in image analysis. Current findings indicate a strong potential for contrastive pre-training on medical images. However, further research is necessary to incorporate the particular characteristics of these images. We hypothesize that the similarity of medical images hinders the success of contrastive learning in the medical imaging domain. To this end, we investigate different strategies based on deep embedding, information theory, and hashing in order to identify and reduce redundancy in medical pre-training datasets. The effect of these different reduction strategies on contrastive learning is evaluated on two pre-training datasets and several downstream classification tasks. In all of our experiments, dataset reduction leads to a considerable performance gain in downstream tasks, e.g., an AUC score improvement from 0.78 to 0.83 for the COVID CT Classification Grand Challenge, 0.97 to 0.98 for the OrganSMNIST Classification Challenge and 0.73 to 0.83 for a brain hemorrhage classification task. Furthermore, pre-training is up to nine times faster due to the dataset reduction. In conclusion, the proposed approach highlights the importance of dataset quality and provides a transferable approach to improve contrastive pre-training for classification downstream tasks on medical images.

Employing a machine learning approach we predict, up to 24 hours prior, a diagnosis of severe sepsis. Strongly predictive models are possible that use only text reports from the Electronic Health Record (EHR), and omit structured numerical data. Unstructured text alone gives slightly better performance than structured data alone, and the combination further improves performance. We also discuss advantages of using unstructured EHR text for modeling, as compared to structured EHR data.

Alzheimer's Disease (AD) is a progressive neurodegenerative disorder that primarily affects the aging population by impairing cognitive and motor functions. Early detection of AD through accessible methodologies like magnetic resonance imaging (MRI) is vital for developing effective interventions to halt or slow the disease's progression. This study aims to perform a comprehensive analysis of machine learning techniques for selecting MRI-based biomarkers and classifying individuals into healthy controls (HC) and unstable controls (uHC) who later show mild cognitive impairment within five years. The research utilizes MRI data from the Alzheimer's Disease Neuroinformatics Initiative (ADNI) and the Open Access Series of Imaging Studies 3 (OASIS-3), focusing on both HC and uHC participants. The study addresses the challenges of imbalanced data by testing classification methods on balanced and unbalanced datasets, and harmonizes data using polynomial regression to mitigate nuisance variables like age, gender, and intracranial volume. Results indicate that Gaussian Naive Bayes and RusBoost classifiers shows an optimal performance, achieving accuracies of up to 76.46% and 72.48% respectively on the ADNI dataset. For the OASIS-3 dataset, Kernel Naive Bayes and RusBoost yield accuracies ranging from 64.66% to 75.71%, improving further in age-matched datasets. Brain regions like the entorhinal cortex, hippocampus, lateral ventricle, and lateral orbitofrontal cortex are identified as significantly impacted during early cognitive decline. Despite limitations such as small sample sizes, the study's harmonization approach enhances the robustness of biomarker selection, suggesting the potential of this semi-automatic machine learning pipeline for early AD detection using MRI.

Obesity, the leading cause of many non-communicable diseases, occurs mainly for eating more than our body requirements and lack of proper activity. So, being healthy requires heathy diet plans, especially for patients with comorbidities. But it is difficult to figure out the exact quantity of each nutrient because nutrients requirement varies based on physical and disease conditions. In our study we proposed a novel machine learning based system to predict the amount of nutrients one individual requires for being healthy. We applied different machine learning algorithms: linear regression, support vector machine (SVM), decision tree, random forest, XGBoost, LightGBM on fluid and 3 other major micronutrients: carbohydrate, protein, fat consumption prediction. We achieved high accuracy with low root mean square error (RMSE) by using linear regression in fluid prediction, random forest in carbohydrate prediction and LightGBM in protein and fat prediction. We believe our diet recommender system, OBESEYE, is the only of its kind which recommends diet with the consideration of comorbidities and physical conditions and promote encouragement to get rid of obesity.

The complex nature of big biological systems pushed some scientists to classify its understanding under the inconceivable missions. Different leveled challenges complicated this task, one of is the prediction of a protein's function. In recent years, significant progress has been made in this field through the development of various machine learning approaches. However, most existing methods formulate the task as a multi-classification problem, i.e assigning predefined labels to proteins. In this work, we propose a novel approach, Prot2Text, which predicts a protein function's in a free text style, moving beyond the conventional binary or categorical classifications. By combining Graph Neural Networks(GNNs) and Large Language Models(LLMs), in an encoder-decoder framework, our model effectively integrates diverse data types including proteins' sequences, structures, and textual annotations. This multimodal approach allows for a holistic representation of proteins' functions, enabling the generation of detailed and accurate descriptions. To evaluate our model, we extracted a multimodal protein dataset from SwissProt, and demonstrate empirically the effectiveness of Prot2Text. These results highlight the transformative impact of multimodal models, specifically the fusion of GNNs and LLMs, empowering researchers with powerful tools for more accurate prediction of proteins' functions. The code, the models and a demo will be publicly released.

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.

Skin diseases affect over a third of the global population, yet their impact is often underestimated. Automating skin disease classification to assist doctors with their prognosis might be difficult. Nevertheless, due to efficient feature extraction pipelines, deep learning techniques have shown much promise for various tasks, including dermatological disease identification. This study uses a skin disease dataset with 31 classes and compares it with all versions of Vision Transformers, Swin Transformers and DivoV2. The analysis is also extended to compare with benchmark convolution-based architecture presented in the literature. Transfer learning with ImageNet1k weights on the skin disease dataset contributes to a high test accuracy of 96.48\% and an F1-Score of 0.9727 using DinoV2, which is almost a 10\% improvement over this data's current benchmark results. The performance of DinoV2 was also compared for the HAM10000 and Dermnet datasets to test the model's robustness, and the trained model overcomes the benchmark results by a slight margin in test accuracy and in F1-Score on the 23 and 7 class datasets. The results are substantiated using explainable AI frameworks like GradCAM and SHAP, which provide precise image locations to map the disease, assisting dermatologists in early detection, prompt prognosis, and treatment.

In recent years, pre-trained language models (PLMs) achieve the best performance on a wide range of natural language processing (NLP) tasks. While the first models were trained on general domain data, specialized ones have emerged to more effectively treat specific domains. In this paper, we propose an original study of PLMs in the medical domain on French language. We compare, for the first time, the performance of PLMs trained on both public data from the web and private data from healthcare establishments. We also evaluate different learning strategies on a set of biomedical tasks. In particular, we show that we can take advantage of already existing biomedical PLMs in a foreign language by further pre-train it on our targeted data. Finally, we release the first specialized PLMs for the biomedical field in French, called DrBERT, as well as the largest corpus of medical data under free license on which these models are trained.

Clinical diagnosis prediction models, when provided with a patient's medical history, aim to detect potential diseases early, facilitating timely intervention and improving prognostic outcomes. However, the inherent scarcity of patient data and large disease candidate space often pose challenges in developing satisfactory models for this intricate task. The exploration of leveraging Large Language Models (LLMs) for encapsulating clinical decision processes has been limited. We introduce MERA, a clinical diagnosis prediction model that bridges pertaining natural language knowledge with medical practice. We apply hierarchical contrastive learning on a disease candidate ranking list to alleviate the large decision space issue. With concept memorization through fine-tuning, we bridge the natural language clinical knowledge with medical codes. Experimental results on MIMIC-III and IV datasets show that MERA achieves the state-of-the-art diagnosis prediction performance and dramatically elevates the diagnosis prediction capabilities of generative LMs.

This paper presents medBERTde, a pre-trained German BERT model specifically designed for the German medical domain. The model has been trained on a large corpus of 4.7 Million German medical documents and has been shown to achieve new state-of-the-art performance on eight different medical benchmarks covering a wide range of disciplines and medical document types. In addition to evaluating the overall performance of the model, this paper also conducts a more in-depth analysis of its capabilities. We investigate the impact of data deduplication on the model's performance, as well as the potential benefits of using more efficient tokenization methods. Our results indicate that domain-specific models such as medBERTde are particularly useful for longer texts, and that deduplication of training data does not necessarily lead to improved performance. Furthermore, we found that efficient tokenization plays only a minor role in improving model performance, and attribute most of the improved performance to the large amount of training data. To encourage further research, the pre-trained model weights and new benchmarks based on radiological data are made publicly available for use by the scientific community.

Speech patterns have been identified as potential diagnostic markers for neuropsychiatric conditions. However, most studies only compare a single clinical group to healthy controls, whereas clinical practice often requires differentiating between multiple potential diagnoses (multiclass settings). To address this, we assembled a dataset of repeated recordings from 420 participants (67 with major depressive disorder, 106 with schizophrenia and 46 with autism, as well as matched controls), and tested the performance of a range of conventional machine learning models and advanced Transformer models on both binary and multiclass classification, based on voice and text features. While binary models performed comparably to previous research (F1 scores between 0.54-0.75 for autism spectrum disorder, ASD; 0.67-0.92 for major depressive disorder, MDD; and 0.71-0.83 for schizophrenia); when differentiating between multiple diagnostic groups performance decreased markedly (F1 scores between 0.35-0.44 for ASD, 0.57-0.75 for MDD, 0.15-0.66 for schizophrenia, and 0.38-0.52 macro F1). Combining voice and text-based models yielded increased performance, suggesting that they capture complementary diagnostic information. Our results indicate that models trained on binary classification may learn to rely on markers of generic differences between clinical and non-clinical populations, or markers of clinical features that overlap across conditions, rather than identifying markers specific to individual conditions. We provide recommendations for future research in the field, suggesting increased focus on developing larger transdiagnostic datasets that include more fine-grained clinical features, and that can support the development of models that better capture the complexity of neuropsychiatric conditions and naturalistic diagnostic assessment.

During times of increasing antibiotic resistance and the spread of infectious diseases like COVID-19, it is important to classify genes related to antibiotic resistance. As natural language processing has advanced with transformer-based language models, many language models that learn characteristics of nucleotide sequences have also emerged. These models show good performance in classifying various features of nucleotide sequences. When classifying nucleotide sequences, not only the sequence itself, but also various background knowledge is utilized. In this study, we use not only a nucleotide sequence-based language model but also a text language model based on PubMed articles to reflect more biological background knowledge in the model. We propose a method to fine-tune the nucleotide sequence language model and the text language model based on various databases of antibiotic resistance genes. We also propose an LLM-based augmentation technique to supplement the data and an ensemble method to effectively combine the two models. We also propose a benchmark for evaluating the model. Our method achieved better performance than the nucleotide sequence language model in the drug resistance class prediction.

Millions of users share their experiences on social media sites, such as Twitter, which in turn generate valuable data for public health monitoring, digital epidemiology, and other analyses of population health at global scale. The first, critical, task for these applications is classifying whether a personal health event was mentioned, which we call the (PHM) problem. This task is challenging for many reasons, including typically short length of social media posts, inventive spelling and lexicons, and figurative language, including hyperbole using diseases like "heart attack" or "cancer" for emphasis, and not as a health self-report. This problem is even more challenging for rarely reported, or frequent but ambiguously expressed conditions, such as "stroke". To address this problem, we propose a general, robust method for detecting PHMs in social media, which we call WESPAD, that combines lexical, syntactic, word embedding-based, and context-based features. WESPAD is able to generalize from few examples by automatically distorting the word embedding space to most effectively detect the true health mentions. Unlike previously proposed state-of-the-art supervised and deep-learning techniques, WESPAD requires relatively little training data, which makes it possible to adapt, with minimal effort, to each new disease and condition. We evaluate WESPAD on both an established publicly available Flu detection benchmark, and on a new dataset that we have constructed with mentions of multiple health conditions. Our experiments show that WESPAD outperforms the baselines and state-of-the-art methods, especially in cases when the number and proportion of true health mentions in the training data is small.

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.

Language-supervised pre-training has proven to be a valuable method for extracting semantically meaningful features from images, serving as a foundational element in multimodal systems within the computer vision and medical imaging domains. However, resulting features are limited by the information contained within the text. This is particularly problematic in medical imaging, where radiologists' written findings focus on specific observations; a challenge compounded by the scarcity of paired imaging-text data due to concerns over leakage of personal health information. In this work, we fundamentally challenge the prevailing reliance on language supervision for learning general purpose biomedical imaging encoders. We introduce RAD-DINO, a biomedical image encoder pre-trained solely on unimodal biomedical imaging data that obtains similar or greater performance than state-of-the-art biomedical language supervised models on a diverse range of benchmarks. Specifically, the quality of learned representations is evaluated on standard imaging tasks (classification and semantic segmentation), and a vision-language alignment task (text report generation from images). To further demonstrate the drawback of language supervision, we show that features from RAD-DINO correlate with other medical records (e.g., sex or age) better than language-supervised models, which are generally not mentioned in radiology reports. Finally, we conduct a series of ablations determining the factors in RAD-DINO's performance; notably, we observe that RAD-DINO's downstream performance scales well with the quantity and diversity of training data, demonstrating that image-only supervision is a scalable approach for training a foundational biomedical image encoder.

In this paper, we consider enhancing medical visual-language pre-training (VLP) with domain-specific knowledge, by exploiting the paired image-text reports from the radiological daily practice. In particular, we make the following contributions: First, unlike existing works that directly process the raw reports, we adopt a novel triplet extraction module to extract the medical-related information, avoiding unnecessary complexity from language grammar and enhancing the supervision signals; Second, we propose a novel triplet encoding module with entity translation by querying a knowledge base, to exploit the rich domain knowledge in medical field, and implicitly build relationships between medical entities in the language embedding space; Third, we propose to use a Transformer-based fusion model for spatially aligning the entity description with visual signals at the image patch level, enabling the ability for medical diagnosis; Fourth, we conduct thorough experiments to validate the effectiveness of our architecture, and benchmark on numerous public benchmarks, e.g., ChestX-ray14, RSNA Pneumonia, SIIM-ACR Pneumothorax, COVIDx CXR-2, COVID Rural, and EdemaSeverity. In both zero-shot and fine-tuning settings, our model has demonstrated strong performance compared with the former methods on disease classification and grounding.

Mental health is a critical issue in modern society, and mental disorders could sometimes turn to suicidal ideation without adequate treatment. Early detection of mental disorders and suicidal ideation from social content provides a potential way for effective social intervention. Recent advances in pretrained contextualized language representations have promoted the development of several domain-specific pretrained models and facilitated several downstream applications. However, there are no existing pretrained language models for mental healthcare. This paper trains and release two pretrained masked language models, i.e., MentalBERT and MentalRoBERTa, to benefit machine learning for the mental healthcare research community. Besides, we evaluate our trained domain-specific models and several variants of pretrained language models on several mental disorder detection benchmarks and demonstrate that language representations pretrained in the target domain improve the performance of mental health detection tasks.

The World Health Organization added Disease X to their shortlist of blueprint priority diseases to represent a hypothetical, unknown pathogen that could cause a future epidemic. During different virus outbreaks of the past, such as COVID-19, Influenza, Lyme Disease, and Zika virus, researchers from various disciplines utilized Google Trends to mine multimodal components of web behavior to study, investigate, and analyze the global awareness, preparedness, and response associated with these respective virus outbreaks. As the world prepares for Disease X, a dataset on web behavior related to Disease X would be crucial to contribute towards the timely advancement of research in this field. Furthermore, none of the prior works in this field have focused on the development of a dataset to compile relevant web behavior data, which would help to prepare for Disease X. To address these research challenges, this work presents a dataset of web behavior related to Disease X, which emerged from different geographic regions of the world, between February 2018 and August 2023. Specifically, this dataset presents the search interests related to Disease X from 94 geographic regions. The dataset was developed by collecting data using Google Trends. The relevant search interests for all these regions for each month in this time range are available in this dataset. This paper also discusses the compliance of this dataset with the FAIR principles of scientific data management. Finally, an analysis of this dataset is presented to uphold the applicability, relevance, and usefulness of this dataset for the investigation of different research questions in the interrelated fields of Big Data, Data Mining, Healthcare, Epidemiology, and Data Analysis with a specific focus on Disease X.

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.

Pretraining large neural language models, such as BERT, has led to impressive gains on many natural language processing (NLP) tasks. However, most pretraining efforts focus on general domain corpora, such as newswire and Web. A prevailing assumption is that even domain-specific pretraining can benefit by starting from general-domain language models. In this paper, we challenge this assumption by showing that for domains with abundant unlabeled text, such as biomedicine, pretraining language models from scratch results in substantial gains over continual pretraining of general-domain language models. To facilitate this investigation, we compile a comprehensive biomedical NLP benchmark from publicly-available datasets. Our experiments show that domain-specific pretraining serves as a solid foundation for a wide range of biomedical NLP tasks, leading to new state-of-the-art results across the board. Further, in conducting a thorough evaluation of modeling choices, both for pretraining and task-specific fine-tuning, we discover that some common practices are unnecessary with BERT models, such as using complex tagging schemes in named entity recognition (NER). To help accelerate research in biomedical NLP, we have released our state-of-the-art pretrained and task-specific models for the community, and created a leaderboard featuring our BLURB benchmark (short for Biomedical Language Understanding & Reasoning Benchmark) at https://aka.ms/BLURB.

Large language models (LLMs) have demonstrated impressive capabilities in disease diagnosis. However, their effectiveness in identifying rarer diseases, which are inherently more challenging to diagnose, remains an open question. Rare disease performance is critical with the increasing use of LLMs in healthcare settings. This is especially true if a primary care physician needs to make a rarer prognosis from only a patient conversation so that they can take the appropriate next step. To that end, several clinical decision support systems are designed to support providers in rare disease identification. Yet their utility is limited due to their lack of knowledge of common disorders and difficulty of use. In this paper, we propose RareScale to combine the knowledge LLMs with expert systems. We use jointly use an expert system and LLM to simulate rare disease chats. This data is used to train a rare disease candidate predictor model. Candidates from this smaller model are then used as additional inputs to black-box LLM to make the final differential diagnosis. Thus, RareScale allows for a balance between rare and common diagnoses. We present results on over 575 rare diseases, beginning with Abdominal Actinomycosis and ending with Wilson's Disease. Our approach significantly improves the baseline performance of black-box LLMs by over 17% in Top-5 accuracy. We also find that our candidate generation performance is high (e.g. 88.8% on gpt-4o generated chats).

The timely identification of socio-economic sectors vulnerable to a disease outbreak presents an important challenge to the civic authorities and healthcare workers interested in outbreak mitigation measures. This problem was traditionally solved by studying the aberrances in small-scale healthcare data. In this paper, we leverage data driven models to determine the relationship between the trends of World Development Indicators and occurrence of disease outbreaks using worldwide historical data from 2000-2019, and treat it as a classic supervised classification problem. CART based feature selection was employed in an unorthodox fashion to determine the covariates getting affected by the disease outbreak, thus giving the most vulnerable sectors. The result involves a comprehensive analysis of different classification algorithms and is indicative of the relationship between the disease outbreak occurrence and the magnitudes of various development indicators.

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.

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.

Generalist vision language models (VLMs) have made significant strides in computer vision, but they fall short in specialized fields like healthcare, where expert knowledge is essential. In traditional computer vision tasks, creative or approximate answers may be acceptable, but in healthcare, precision is paramount.Current large multimodal models like Gemini and GPT-4o are insufficient for medical tasks due to their reliance on memorized internet knowledge rather than the nuanced expertise required in healthcare. VLMs are usually trained in three stages: vision pre-training, vision-language pre-training, and instruction fine-tuning (IFT). IFT has been typically applied using a mixture of generic and healthcare data. In contrast, we propose that for medical VLMs, a fourth stage of specialized IFT is necessary, which focuses on medical data and includes information from domain expert models. Domain expert models developed for medical use are crucial because they are specifically trained for certain clinical tasks, e.g. to detect tumors and classify abnormalities through segmentation and classification, which learn fine-grained features of medical data-features that are often too intricate for a VLM to capture effectively especially in radiology. This paper introduces a new framework, VILA-M3, for medical VLMs that utilizes domain knowledge via expert models. Through our experiments, we show an improved state-of-the-art (SOTA) performance with an average improvement of ~9% over the prior SOTA model Med-Gemini and ~6% over models trained on the specific tasks. Our approach emphasizes the importance of domain expertise in creating precise, reliable VLMs for medical applications.

The pandemic resulted in vast repositories of unstructured data, including radiology reports, due to increased medical examinations. Previous research on automated diagnosis of COVID-19 primarily focuses on X-ray images, despite their lower precision compared to computed tomography (CT) scans. In this work, we leverage unstructured data from a hospital and harness the fine-grained details offered by CT scans to perform zero-shot multi-label classification based on contrastive visual language learning. In collaboration with human experts, we investigate the effectiveness of multiple zero-shot models that aid radiologists in detecting pulmonary embolisms and identifying intricate lung details like ground glass opacities and consolidations. Our empirical analysis provides an overview of the possible solutions to target such fine-grained tasks, so far overlooked in the medical multimodal pretraining literature. Our investigation promises future advancements in the medical image analysis community by addressing some challenges associated with unstructured data and fine-grained multi-label classification.

Automatically summarizing patients' main problems from daily progress notes using natural language processing methods helps to battle against information and cognitive overload in hospital settings and potentially assists providers with computerized diagnostic decision support. Problem list summarization requires a model to understand, abstract, and generate clinical documentation. In this work, we propose a new NLP task that aims to generate a list of problems in a patient's daily care plan using input from the provider's progress notes during hospitalization. We investigate the performance of T5 and BART, two state-of-the-art seq2seq transformer architectures, in solving this problem. We provide a corpus built on top of progress notes from publicly available electronic health record progress notes in the Medical Information Mart for Intensive Care (MIMIC)-III. T5 and BART are trained on general domain text, and we experiment with a data augmentation method and a domain adaptation pre-training method to increase exposure to medical vocabulary and knowledge. Evaluation methods include ROUGE, BERTScore, cosine similarity on sentence embedding, and F-score on medical concepts. Results show that T5 with domain adaptive pre-training achieves significant performance gains compared to a rule-based system and general domain pre-trained language models, indicating a promising direction for tackling the problem summarization task.

Pathology plays a critical role in diagnosing a wide range of diseases, yet existing approaches often rely heavily on task-specific models trained on extensive, well-labeled datasets. These methods face sustainability challenges due to the diversity of pathologies and the labor-intensive nature of data collection. To address these limitations, we highlight the need for universal multimodal embeddings that can support multiple downstream tasks. Previous approaches often involve fine-tuning CLIP-based models, which handle images and text separately, limiting their ability to capture complex multimodal relationships. Additionally, these models are evaluated across diverse datasets without a unified benchmark for assessing multimodal embeddings in pathology. To address these challenges, we propose MLLM4PUE, a novel framework that leverages Multimodal Large Language Models (MLLMs) to generate Pathology Universal Embeddings. The MLLM4PUE framework not only facilitates robust integration of images and text but also enhances understanding and fusion capabilities across various tasks. We further introduce the Pathology Multimodal Embedding Benchmark (PMEB), a comprehensive benchmark designed to assess the quality of pathology multimodal embeddings. PMEB comprises 15 original tasks drawn from 14 datasets, organized into three meta-tasks: retrieval, classification, and composed retrieval. Experimental results demonstrate the superiority of MLLM4PUE, illustrating MLLM-based models can effectively support a wide range of downstream tasks and unify the research direction for foundation models in pathology.

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

Vision-language pre-training for chest X-rays has made significant strides, primarily by utilizing paired radiographs and radiology reports. However, existing approaches often face challenges in encoding medical knowledge effectively. While radiology reports provide insights into the current disease manifestation, medical definitions (as used by contemporary methods) tend to be overly abstract, creating a gap in knowledge. To address this, we propose DeViDe, a novel transformer-based method that leverages radiographic descriptions from the open web. These descriptions outline general visual characteristics of diseases in radiographs, and when combined with abstract definitions and radiology reports, provide a holistic snapshot of knowledge. DeViDe incorporates three key features for knowledge-augmented vision language alignment: First, a large-language model-based augmentation is employed to homogenise medical knowledge from diverse sources. Second, this knowledge is aligned with image information at various levels of granularity. Third, a novel projection layer is proposed to handle the complexity of aligning each image with multiple descriptions arising in a multi-label setting. In zero-shot settings, DeViDe performs comparably to fully supervised models on external datasets and achieves state-of-the-art results on three large-scale datasets. Additionally, fine-tuning DeViDe on four downstream tasks and six segmentation tasks showcases its superior performance across data from diverse distributions.

Tissue phenotyping is a fundamental task in learning objective characterizations of histopathologic biomarkers within the tumor-immune microenvironment in cancer pathology. However, whole-slide imaging (WSI) is a complex computer vision in which: 1) WSIs have enormous image resolutions with precludes large-scale pixel-level efforts in data curation, and 2) diversity of morphological phenotypes results in inter- and intra-observer variability in tissue labeling. To address these limitations, current efforts have proposed using pretrained image encoders (transfer learning from ImageNet, self-supervised pretraining) in extracting morphological features from pathology, but have not been extensively validated. In this work, we conduct a search for good representations in pathology by training a variety of self-supervised models with validation on a variety of weakly-supervised and patch-level tasks. Our key finding is in discovering that Vision Transformers using DINO-based knowledge distillation are able to learn data-efficient and interpretable features in histology images wherein the different attention heads learn distinct morphological phenotypes. We make evaluation code and pretrained weights publicly-available at: https://github.com/Richarizardd/Self-Supervised-ViT-Path.

Using language models (LMs) pre-trained in a self-supervised setting on large corpora and then fine-tuning for a downstream task has helped to deal with the problem of limited label data for supervised learning tasks such as Named Entity Recognition (NER). Recent research in biomedical language processing has offered a number of biomedical LMs pre-trained using different methods and techniques that advance results on many BioNLP tasks, including NER. However, there is still a lack of a comprehensive comparison of pre-training approaches that would work more optimally in the biomedical domain. This paper aims to investigate different pre-training methods, such as pre-training the biomedical LM from scratch and pre-training it in a continued fashion. We compare existing methods with our proposed pre-training method of initializing weights for new tokens by distilling existing weights from the BERT model inside the context where the tokens were found. The method helps to speed up the pre-training stage and improve performance on NER. In addition, we compare how masking rate, corruption strategy, and masking strategies impact the performance of the biomedical LM. Finally, using the insights from our experiments, we introduce a new biomedical LM (BIOptimus), which is pre-trained using Curriculum Learning (CL) and contextualized weight distillation method. Our model sets new states of the art on several biomedical Named Entity Recognition (NER) tasks. We release our code and all pre-trained models

Computational pathology can lead to saving human lives, but models are annotation hungry and pathology images are notoriously expensive to annotate. Self-supervised learning has shown to be an effective method for utilizing unlabeled data, and its application to pathology could greatly benefit its downstream tasks. Yet, there are no principled studies that compare SSL methods and discuss how to adapt them for pathology. To address this need, we execute the largest-scale study of SSL pre-training on pathology image data, to date. Our study is conducted using 4 representative SSL methods on diverse downstream tasks. We establish that large-scale domain-aligned pre-training in pathology consistently out-performs ImageNet pre-training in standard SSL settings such as linear and fine-tuning evaluations, as well as in low-label regimes. Moreover, we propose a set of domain-specific techniques that we experimentally show leads to a performance boost. Lastly, for the first time, we apply SSL to the challenging task of nuclei instance segmentation and show large and consistent performance improvements under diverse settings.

Breast cancer is a prevalent form of cancer among women, with over 1.5 million women being diagnosed each year. Unfortunately, the survival rates for breast cancer patients in certain third-world countries, like South Africa, are alarmingly low, with only 40% of diagnosed patients surviving beyond five years. The inadequate availability of resources, including qualified pathologists, delayed diagnoses, and ineffective therapy planning, contribute to this low survival rate. To address this pressing issue, medical specialists and researchers have turned to domain-specific AI approaches, specifically deep learning models, to develop end-to-end solutions that can be integrated into computer-aided diagnosis (CAD) systems. By improving the workflow of pathologists, these AI models have the potential to enhance the detection and diagnosis of breast cancer. This research focuses on evaluating the performance of various cutting-edge convolutional neural network (CNN) architectures in comparison to a relatively new model called the Vision Trans-former (ViT). The objective is to determine the superiority of these models in terms of their accuracy and effectiveness. The experimental results reveal that the ViT models outperform the other selected state-of-the-art CNN architectures, achieving an impressive accuracy rate of 95.15%. This study signifies a significant advancement in the field, as it explores the utilization of data augmentation and other relevant preprocessing techniques in conjunction with deep learning models for the detection and diagnosis of breast cancer using datasets of Breast Cancer Histopathological Image Classification.

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.

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.

The rapid and accurate detection of COVID-19 cases is critical for timely treatment and preventing the spread of the disease. In this study, a two-stage feature extraction framework using eight state-of-the-art pre-trained deep Convolutional Neural Networks (CNNs) and an autoencoder is proposed to determine the health conditions of patients (COVID-19, Normal, Viral Pneumonia) based on chest X-rays. The X-ray scans are divided into four equally sized sections and analyzed by deep pre-trained CNNs. Subsequently, an autoencoder with three hidden layers is trained to extract reproductive features from the concatenated ouput of CNNs. To evaluate the performance of the proposed framework, three different classifiers, which are single-layer perceptron (SLP), multi-layer perceptron (MLP), and support vector machine (SVM) are used. Furthermore, the deep CNN architectures are used to create benchmark models and trained on the same dataset for comparision. The proposed framework outperforms other frameworks wih pre-trained feature extractors in binary classification and shows competitive results in three-class classification. The proposed methodology is task-independent and suitable for addressing various problems. The results show that the discriminative features are a subset of the reproductive features, suggesting that extracting task-independent features is superior to the extraction only task-based features. The flexibility and task-independence of the reproductive features make the conceptive information approach more favorable. The proposed methodology is novel and shows promising results for analyzing medical image data.

Depression is a global burden and one of the most challenging mental health conditions to control. Experts can detect its severity early using the Beck Depression Inventory (BDI) questionnaire, administer appropriate medication to patients, and impede its progression. Due to the fear of potential stigmatization, many patients turn to social media platforms like Reddit for advice and assistance at various stages of their journey. This research extracts text from Reddit to facilitate the diagnostic process. It employs a proposed labeling approach to categorize the text and subsequently fine-tunes the Longformer model. The model's performance is compared against baseline models, including Naive Bayes, Random Forest, Support Vector Machines, and Gradient Boosting. Our findings reveal that the Longformer model outperforms the baseline models in both English (48%) and Luganda (45%) languages on a custom-made dataset.

Pre-trained language models (PLMs), such as BERT and GPT, have revolutionized the field of NLP, not only in the general domain but also in the biomedical domain. Most prior efforts in building biomedical PLMs have resorted simply to domain adaptation and focused mainly on English. In this work we introduce eHealth, a Chinese biomedical PLM built from scratch with a new pre-training framework. This new framework pre-trains eHealth as a discriminator through both token- and sequence-level discrimination. The former is to detect input tokens corrupted by a generator and recover their original identities from plausible candidates, while the latter is to further distinguish corruptions of a same original sequence from those of others. As such, eHealth can learn language semantics at both token and sequence levels. Extensive experiments on 11 Chinese biomedical language understanding tasks of various forms verify the effectiveness and superiority of our approach. We release the pre-trained model at https://github.com/PaddlePaddle/Research/tree/master/KG/eHealth and will also release the code later.

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.

Farmers face several challenges when growing crops like uncertain irrigation, poor soil quality, etc. Especially in India, a major fraction of farmers do not have the knowledge to select appropriate crops and fertilizers. Moreover, crop failure due to disease causes a significant loss to the farmers, as well as the consumers. While there have been recent developments in the automated detection of these diseases using Machine Learning techniques, the utilization of Deep Learning has not been fully explored. Additionally, such models are not easy to use because of the high-quality data used in their training, lack of computational power, and poor generalizability of the models. To this end, we create an open-source easy-to-use web application to address some of these issues which may help improve crop production. In particular, we support crop recommendation, fertilizer recommendation, plant disease prediction, and an interactive news-feed. In addition, we also use interpretability techniques in an attempt to explain the prediction made by our disease detection model.

Skin cancer is one of the most threatening diseases worldwide. However, diagnosing skin cancer correctly is challenging. Recently, deep learning algorithms have emerged to achieve excellent performance on various tasks. Particularly, they have been applied to the skin disease diagnosis tasks. In this paper, we present a review on deep learning methods and their applications in skin disease diagnosis. We first present a brief introduction to skin diseases and image acquisition methods in dermatology, and list several publicly available skin datasets for training and testing algorithms. Then, we introduce the conception of deep learning and review popular deep learning architectures. Thereafter, popular deep learning frameworks facilitating the implementation of deep learning algorithms and performance evaluation metrics are presented. As an important part of this article, we then review the literature involving deep learning methods for skin disease diagnosis from several aspects according to the specific tasks. Additionally, we discuss the challenges faced in the area and suggest possible future research directions. The major purpose of this article is to provide a conceptual and systematically review of the recent works on skin disease diagnosis with deep learning. Given the popularity of deep learning, there remains great challenges in the area, as well as opportunities that we can explore in the future.

Models that can predict the occurrence of events ahead of time with low false-alarm rates are critical to the acceptance of decision support systems in the medical community. This challenging task is typically treated as a simple binary classification, ignoring temporal dependencies between samples, whereas we propose to exploit this structure. We first introduce a common theoretical framework unifying dynamic survival analysis and early event prediction. Following an analysis of objectives from both fields, we propose Temporal Label Smoothing (TLS), a simpler, yet best-performing method that preserves prediction monotonicity over time. By focusing the objective on areas with a stronger predictive signal, TLS improves performance over all baselines on two large-scale benchmark tasks. Gains are particularly notable along clinically relevant measures, such as event recall at low false-alarm rates. TLS reduces the number of missed events by up to a factor of two over previously used approaches in early event prediction.

Radiology reports are one of the main forms of communication between radiologists and other clinicians and contain important information for patient care. In order to use this information for research and automated patient care programs, it is necessary to convert the raw text into structured data suitable for analysis. State-of-the-art natural language processing (NLP) domain-specific contextual word embeddings have been shown to achieve impressive accuracy for these tasks in medicine, but have yet to be utilized for section structure segmentation. In this work, we pre-trained a contextual embedding BERT model using breast radiology reports and developed a classifier that incorporated the embedding with auxiliary global textual features in order to perform section segmentation. This model achieved a 98% accuracy at segregating free text reports sentence by sentence into sections of information outlined in the Breast Imaging Reporting and Data System (BI-RADS) lexicon, a significant improvement over the Classic BERT model without auxiliary information. We then evaluated whether using section segmentation improved the downstream extraction of clinically relevant information such as modality/procedure, previous cancer, menopausal status, the purpose of the exam, breast density, and breast MRI background parenchymal enhancement. Using the BERT model pre-trained on breast radiology reports combined with section segmentation resulted in an overall accuracy of 95.9% in the field extraction tasks. This is a 17% improvement compared to an overall accuracy of 78.9% for field extraction with models using Classic BERT embeddings and not using section segmentation. Our work shows the strength of using BERT in radiology report analysis and the advantages of section segmentation in identifying key features of patient factors recorded in breast radiology reports.

Detecting dental diseases through panoramic X-rays images is a standard procedure for dentists. Normally, a dentist need to identify diseases and find the infected teeth. While numerous machine learning models adopting this two-step procedure have been developed, there has not been an end-to-end model that can identify teeth and their associated diseases at the same time. To fill the gap, we develop YOLOrtho, a unified framework for teeth enumeration and dental disease detection. We develop our model on Dentex Challenge 2023 data, which consists of three distinct types of annotated data. The first part is labeled with quadrant, and the second part is labeled with quadrant and enumeration and the third part is labeled with quadrant, enumeration and disease. To further improve detection, we make use of Tufts Dental public dataset. To fully utilize the data and learn both teeth detection and disease identification simultaneously, we formulate diseases as attributes attached to their corresponding teeth. Due to the nature of position relation in teeth enumeration, We replace convolution layer with CoordConv in our model to provide more position information for the model. We also adjust the model architecture and insert one more upsampling layer in FPN in favor of large object detection. Finally, we propose a post-process strategy for teeth layout that corrects teeth enumeration based on linear sum assignment. Results from experiments show that our model exceeds large Diffusion-based model.

Objective: We investigate whether deep learning techniques for natural language processing (NLP) can be used efficiently for patient phenotyping. Patient phenotyping is a classification task for determining whether a patient has a medical condition, and is a crucial part of secondary analysis of healthcare data. We assess the performance of deep learning algorithms and compare them with classical NLP approaches. Materials and Methods: We compare convolutional neural networks (CNNs), n-gram models, and approaches based on cTAKES that extract pre-defined medical concepts from clinical notes and use them to predict patient phenotypes. The performance is tested on 10 different phenotyping tasks using 1,610 discharge summaries extracted from the MIMIC-III database. Results: CNNs outperform other phenotyping algorithms in all 10 tasks. The average F1-score of our model is 76 (PPV of 83, and sensitivity of 71) with our model having an F1-score up to 37 points higher than alternative approaches. We additionally assess the interpretability of our model by presenting a method that extracts the most salient phrases for a particular prediction. Conclusion: We show that NLP methods based on deep learning improve the performance of patient phenotyping. Our CNN-based algorithm automatically learns the phrases associated with each patient phenotype. As such, it reduces the annotation complexity for clinical domain experts, who are normally required to develop task-specific annotation rules and identify relevant phrases. Our method performs well in terms of both performance and interpretability, which indicates that deep learning is an effective approach to patient phenotyping based on clinicians' notes.

Accurate diagnostic coding of medical notes is crucial for enhancing patient care, medical research, and error-free billing in healthcare organizations. Manual coding is a time-consuming task for providers, and diagnostic codes often exhibit low sensitivity and specificity, whereas the free text in medical notes can be a more precise description of a patients status. Thus, accurate automated diagnostic coding of medical notes has become critical for a learning healthcare system. Recent developments in long-document transformer architectures have enabled attention-based deep-learning models to adjudicate medical notes. In addition, contrastive loss functions have been used to jointly pre-train large language and image models with noisy labels. To further improve the automated adjudication of medical notes, we developed an approach based on i) models for ICD-10 diagnostic code sequences using a large real-world data set, ii) large language models for medical notes, and iii) contrastive pre-training to build an integrated model of both ICD-10 diagnostic codes and corresponding medical text. We demonstrate that a contrastive approach for pre-training improves performance over prior state-of-the-art models for the MIMIC-III-50, MIMIC-III-rare50, and MIMIC-III-full diagnostic coding tasks.

The Russian Drug Reaction Corpus (RuDReC) is a new partially annotated corpus of consumer reviews in Russian about pharmaceutical products for the detection of health-related named entities and the effectiveness of pharmaceutical products. The corpus itself consists of two parts, the raw one and the labelled one. The raw part includes 1.4 million health-related user-generated texts collected from various Internet sources, including social media. The labelled part contains 500 consumer reviews about drug therapy with drug- and disease-related information. Labels for sentences include health-related issues or their absence. The sentences with one are additionally labelled at the expression level for identification of fine-grained subtypes such as drug classes and drug forms, drug indications, and drug reactions. Further, we present a baseline model for named entity recognition (NER) and multi-label sentence classification tasks on this corpus. The macro F1 score of 74.85% in the NER task was achieved by our RuDR-BERT model. For the sentence classification task, our model achieves the macro F1 score of 68.82% gaining 7.47% over the score of BERT model trained on Russian data. We make the RuDReC corpus and pretrained weights of domain-specific BERT models freely available at https://github.com/cimm-kzn/RuDReC

We introduce a new visual-interactive tool: Explainable Labeling Assistant (XLabel) that takes an explainable machine learning approach to data labeling. The main component of XLabel is the Explainable Boosting Machine (EBM), a predictive model that can calculate the contribution of each input feature towards the final prediction. As a case study, we use XLabel to predict the labels of four non-communicable diseases (NCDs): diabetes, hypertension, chronic kidney disease, and dyslipidemia. We demonstrate that EBM is an excellent choice of predictive model by comparing it against a rule-based and four other machine learning models. By performing 5-fold cross-validation on 427 medical records, EBM's prediction accuracy, precision, and F1-score are greater than 0.95 in all four NCDs. It performed as well as two black-box models and outperformed the other models in these metrics. In an additional experiment, when 40% of the records were intentionally mislabeled, EBM could recall the correct labels of more than 90% of these records.

In the light of the COVID-19 pandemic, deep learning methods have been widely investigated in detecting COVID-19 from chest X-rays. However, a more pragmatic approach to applying AI methods to a medical diagnosis is designing a framework that facilitates human-machine interaction and expert decision making. Studies have shown that categorization can play an essential rule in accelerating real-world decision making. Inspired by descriptive document clustering, we propose a domain-independent explanatory clustering framework to group contextually related instances and support radiologists' decision making. While most descriptive clustering approaches employ domain-specific characteristics to form meaningful clusters, we focus on model-level explanation as a more general-purpose element of every learning process to achieve cluster homogeneity. We employ DeepSHAP to generate homogeneous clusters in terms of disease severity and describe the clusters using favorable and unfavorable saliency maps, which visualize the class discriminating regions of an image. These human-interpretable maps complement radiologist knowledge to investigate the whole cluster at once. Besides, as part of this study, we evaluate a model based on VGG-19, which can identify COVID and pneumonia cases with a positive predictive value of 95% and 97%, respectively, comparable to the recent explainable approaches for COVID diagnosis.

In Natural Language Processing (NLP), Machine Reading Comprehension (MRC) is the task of answering a question based on a given context. To handle questions in the medical domain, modern language models such as BioBERT, SciBERT and even ChatGPT are trained on vast amounts of in-domain medical corpora. However, in-domain pre-training is expensive in terms of time and resources. In this paper, we propose a resource-efficient approach for injecting domain knowledge into a model without relying on such domain-specific pre-training. Knowledge graphs are powerful resources for accessing medical information. Building on existing work, we introduce a method using Multi-Layer Perceptrons (MLPs) for aligning and integrating embeddings extracted from medical knowledge graphs with the embedding spaces of pre-trained language models (LMs). The aligned embeddings are fused with open-domain LMs BERT and RoBERTa that are fine-tuned for two MRC tasks, span detection (COVID-QA) and multiple-choice questions (PubMedQA). We compare our method to prior techniques that rely on a vocabulary overlap for embedding alignment and show how our method circumvents this requirement to deliver better performance. On both datasets, our method allows BERT/RoBERTa to either perform on par (occasionally exceeding) with stronger domain-specific models or show improvements in general over prior techniques. With the proposed approach, we signal an alternative method to in-domain pre-training to achieve domain proficiency.

Medical applications challenge today's text categorization techniques by demanding both high accuracy and ease-of-interpretation. Although deep learning has provided a leap ahead in accuracy, this leap comes at the sacrifice of interpretability. To address this accuracy-interpretability challenge, we here introduce, for the first time, a text categorization approach that leverages the recently introduced Tsetlin Machine. In all brevity, we represent the terms of a text as propositional variables. From these, we capture categories using simple propositional formulae, such as: if "rash" and "reaction" and "penicillin" then Allergy. The Tsetlin Machine learns these formulae from a labelled text, utilizing conjunctive clauses to represent the particular facets of each category. Indeed, even the absence of terms (negated features) can be used for categorization purposes. Our empirical comparison with Na\"ive Bayes, decision trees, linear support vector machines (SVMs), random forest, long short-term memory (LSTM) neural networks, and other techniques, is quite conclusive. The Tsetlin Machine either performs on par with or outperforms all of the evaluated methods on both the 20 Newsgroups and IMDb datasets, as well as on a non-public clinical dataset. On average, the Tsetlin Machine delivers the best recall and precision scores across the datasets. Finally, our GPU implementation of the Tsetlin Machine executes 5 to 15 times faster than the CPU implementation, depending on the dataset. We thus believe that our novel approach can have a significant impact on a wide range of text analysis applications, forming a promising starting point for deeper natural language understanding with the Tsetlin Machine.

Limited labeled data makes it hard to train models from scratch in medical domain, and an important paradigm is pre-training and then fine-tuning. Large pre-trained models contain rich representations, which can be adapted to downstream medical tasks. However, existing methods either tune all the parameters or the task-specific layers of the pre-trained models, ignoring the input variations of medical images, and thus they are not efficient or effective. In this work, we aim to study parameter-efficient fine-tuning (PEFT) for medical image analysis, and propose a dynamic visual prompt tuning method, named DVPT. It can extract knowledge beneficial to downstream tasks from large models with a few trainable parameters. Firstly, the frozen features are transformed by an lightweight bottleneck layer to learn the domain-specific distribution of downstream medical tasks, and then a few learnable visual prompts are used as dynamic queries and then conduct cross-attention with the transformed features, attempting to acquire sample-specific knowledge that are suitable for each sample. Finally, the features are projected to original feature dimension and aggregated with the frozen features. This DVPT module can be shared between different Transformer layers, further reducing the trainable parameters. To validate DVPT, we conduct extensive experiments with different pre-trained models on medical classification and segmentation tasks. We find such PEFT method can not only efficiently adapt the pre-trained models to the medical domain, but also brings data efficiency with partial labeled data. For example, with 0.5\% extra trainable parameters, our method not only outperforms state-of-the-art PEFT methods, even surpasses the full fine-tuning by more than 2.20\% Kappa score on medical classification task. It can saves up to 60\% labeled data and 99\% storage cost of ViT-B/16.

Clinical machine learning research and AI driven clinical decision support models rely on clinically accurate labels. Manually extracting these labels with the help of clinical specialists is often time-consuming and expensive. This study tests the feasibility of automatic span- and document-level diagnosis extraction from unstructured Dutch echocardiogram reports. We included 115,692 unstructured echocardiogram reports from the UMCU a large university hospital in the Netherlands. A randomly selected subset was manually annotated for the occurrence and severity of eleven commonly described cardiac characteristics. We developed and tested several automatic labelling techniques at both span and document levels, using weighted and macro F1-score, precision, and recall for performance evaluation. We compared the performance of span labelling against document labelling methods, which included both direct document classifiers and indirect document classifiers that rely on span classification results. The SpanCategorizer and MedRoBERTa.nl models outperformed all other span and document classifiers, respectively. The weighted F1-score varied between characteristics, ranging from 0.60 to 0.93 in SpanCategorizer and 0.96 to 0.98 in MedRoBERTa.nl. Direct document classification was superior to indirect document classification using span classifiers. SetFit achieved competitive document classification performance using only 10\% of the training data. Utilizing a reduced label set yielded near-perfect document classification results. We recommend using our published SpanCategorizer and MedRoBERTa.nl models for span- and document-level diagnosis extraction from Dutch echocardiography reports. For settings with limited training data, SetFit may be a promising alternative for document classification.

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.

Tuberculosis (TB) is a chronic lung disease that occurs due to bacterial infection and is one of the top 10 leading causes of death. Accurate and early detection of TB is very important, otherwise, it could be life-threatening. In this work, we have detected TB reliably from the chest X-ray images using image pre-processing, data augmentation, image segmentation, and deep-learning classification techniques. Several public databases were used to create a database of 700 TB infected and 3500 normal chest X-ray images for this study. Nine different deep CNNs (ResNet18, ResNet50, ResNet101, ChexNet, InceptionV3, Vgg19, DenseNet201, SqueezeNet, and MobileNet), which were used for transfer learning from their pre-trained initial weights and trained, validated and tested for classifying TB and non-TB normal cases. Three different experiments were carried out in this work: segmentation of X-ray images using two different U-net models, classification using X-ray images, and segmented lung images. The accuracy, precision, sensitivity, F1-score, specificity in the detection of tuberculosis using X-ray images were 97.07 %, 97.34 %, 97.07 %, 97.14 % and 97.36 % respectively. However, segmented lungs for the classification outperformed than whole X-ray image-based classification and accuracy, precision, sensitivity, F1-score, specificity were 99.9 %, 99.91 %, 99.9 %, 99.9 %, and 99.52 % respectively. The paper also used a visualization technique to confirm that CNN learns dominantly from the segmented lung regions results in higher detection accuracy. The proposed method with state-of-the-art performance can be useful in the computer-aided faster diagnosis of tuberculosis.

Skin cancer is a widespread, global, and potentially deadly disease, which over the last three decades has afflicted more lives in the USA than all other forms of cancer combined. There have been a lot of promising recent works utilizing deep network architectures, such as FCNs, U-Nets, and ResNets, for developing automated skin lesion segmentation. This paper investigates various pre- and post-processing techniques for improving the performance of U-Nets as measured by the Jaccard Index. The dataset provided as part of the "2017 ISBI Challenges on Skin Lesion Analysis Towards Melanoma Detection" was used for this evaluation and the performance of the finalist competitors was the standard for comparison. The pre-processing techniques employed in the proposed system included contrast enhancement, artifact removal, and vignette correction. More advanced image transformations, such as local binary patterns and wavelet decomposition, were also employed to augment the raw grayscale images used as network input features. While the performance of the proposed system fell short of the winners of the challenge, it was determined that using wavelet decomposition as an early transformation step improved the overall performance of the system over pre- and post-processing steps alone.

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.

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.

Pathology, the microscopic examination of diseased tissue, is critical for diagnosing various medical conditions, particularly cancers. Traditional methods are labor-intensive and prone to human error. Digital pathology, which converts glass slides into high-resolution digital images for analysis by computer algorithms, revolutionizes the field by enhancing diagnostic accuracy, consistency, and efficiency through automated image analysis and large-scale data processing. Foundational transformer pretraining is crucial for developing robust, generalizable models as it enables learning from vast amounts of unannotated data. This paper introduces the Hibou family of foundational vision transformers for pathology, leveraging the DINOv2 framework to pretrain two model variants, Hibou-B and Hibou-L, on a proprietary dataset of over 1 million whole slide images (WSIs) representing diverse tissue types and staining techniques. Our pretrained models demonstrate superior performance on both patch-level and slide-level benchmarks, surpassing existing state-of-the-art methods. Notably, Hibou-L achieves the highest average accuracy across multiple benchmark datasets. To support further research and application in the field, we have open-sourced the Hibou-B model, which can be accessed at https://github.com/HistAI/hibou

The rapid advancement of large-scale vision-language models has showcased remarkable capabilities across various tasks. However, the lack of extensive and high-quality image-text data in medicine has greatly hindered the development of large-scale medical vision-language models. In this work, we present a diagnosis-guided bootstrapping strategy that exploits both image and label information to construct vision-language datasets. Based on the constructed dataset, we developed MedDr, a generalist foundation model for healthcare capable of handling diverse medical data modalities, including radiology, pathology, dermatology, retinography, and endoscopy. Moreover, during inference, we propose a simple but effective retrieval-augmented medical diagnosis strategy, which enhances the model's generalization ability. Extensive experiments on visual question answering, medical report generation, and medical image diagnosis demonstrate the superiority of our method.

In recent years, there is strong emphasis on mining medical data using machine learning techniques. A common problem is to obtain a noiseless set of textual documents, with a relevant content for the research question, and developing a Question Answering (QA) model for a specific medical field. The purpose of this paper is to present a new methodology for building a medical dataset and obtain a QA model for analysis of symptoms and impact on daily life for a specific disease domain. The ``Mental Health'' forum was used, a forum dedicated to people suffering from schizophrenia and different mental disorders. Relevant posts of active users, who regularly participate, were extrapolated providing a new method of obtaining low-bias content and without privacy issues. Furthermore, it is shown how to pre-process the dataset to convert it into a QA dataset. The Bidirectional Encoder Representations from Transformers (BERT), DistilBERT, RoBERTa, and BioBERT models were fine-tuned and evaluated via F1-Score, Exact Match, Precision and Recall. Accurate empirical experiments demonstrated the effectiveness of the proposed method for obtaining an accurate dataset for QA model implementation. By fine-tuning the BioBERT QA model, we achieved an F1 score of 0.885, showing a considerable improvement and outperforming the state-of-the-art model for mental disorders domain.

Objective: To transform heterogeneous clinical data from electronic health records into clinically meaningful constructed features using data driven method that rely, in part, on temporal relations among data. Materials and Methods: The clinically meaningful representations of medical concepts and patients are the key for health analytic applications. Most of existing approaches directly construct features mapped to raw data (e.g., ICD or CPT codes), or utilize some ontology mapping such as SNOMED codes. However, none of the existing approaches leverage EHR data directly for learning such concept representation. We propose a new way to represent heterogeneous medical concepts (e.g., diagnoses, medications and procedures) based on co-occurrence patterns in longitudinal electronic health records. The intuition behind the method is to map medical concepts that are co-occuring closely in time to similar concept vectors so that their distance will be small. We also derive a simple method to construct patient vectors from the related medical concept vectors. Results: For qualitative evaluation, we study similar medical concepts across diagnosis, medication and procedure. In quantitative evaluation, our proposed representation significantly improves the predictive modeling performance for onset of heart failure (HF), where classification methods (e.g. logistic regression, neural network, support vector machine and K-nearest neighbors) achieve up to 23% improvement in area under the ROC curve (AUC) using this proposed representation. Conclusion: We proposed an effective method for patient and medical concept representation learning. The resulting representation can map relevant concepts together and also improves predictive modeling performance.

In this work, we release COVID-Twitter-BERT (CT-BERT), a transformer-based model, pretrained on a large corpus of Twitter messages on the topic of COVID-19. Our model shows a 10-30% marginal improvement compared to its base model, BERT-Large, on five different classification datasets. The largest improvements are on the target domain. Pretrained transformer models, such as CT-BERT, are trained on a specific target domain and can be used for a wide variety of natural language processing tasks, including classification, question-answering and chatbots. CT-BERT is optimised to be used on COVID-19 content, in particular social media posts from Twitter.

Gastrointestinal (GI) diseases represent a significant global health concern, with Capsule Endoscopy (CE) offering a non-invasive method for diagnosis by capturing a large number of GI tract images. However, the sheer volume of video frames necessitates automated analysis to reduce the workload on doctors and increase the diagnostic accuracy. In this paper, we present CapsuleNet, a deep learning model developed for the Capsule Vision 2024 Challenge, aimed at classifying 10 distinct GI abnormalities. Using a highly imbalanced dataset, we implemented various data augmentation strategies, reducing the data imbalance to a manageable level. Our model leverages a pretrained EfficientNet-b7 backbone, tuned with additional layers for classification and optimized with PReLU activation functions. The model demonstrated superior performance on validation data, achieving a micro accuracy of 84.5% and outperforming the VGG16 baseline across most classes. Despite these advances, challenges remain in classifying certain abnormalities, such as Erythema. Our findings suggest that CNN-based models like CapsuleNet can provide an efficient solution for GI tract disease classification, particularly when inference time is a critical factor.

Advances in large language models (LLMs) provide new opportunities in healthcare for improved patient care, clinical decision-making, and enhancement of physician and administrator workflows. However, the potential of these models importantly depends on their ability to generalize effectively across clinical environments and populations, a challenge often underestimated in early development. To better understand reasons for these challenges and inform mitigation approaches, we evaluated ClinicLLM, an LLM trained on [HOSPITAL]'s clinical notes, analyzing its performance on 30-day all-cause readmission prediction focusing on variability across hospitals and patient characteristics. We found poorer generalization particularly in hospitals with fewer samples, among patients with government and unspecified insurance, the elderly, and those with high comorbidities. To understand reasons for lack of generalization, we investigated sample sizes for fine-tuning, note content (number of words per note), patient characteristics (comorbidity level, age, insurance type, borough), and health system aspects (hospital, all-cause 30-day readmission, and mortality rates). We used descriptive statistics and supervised classification to identify features. We found that, along with sample size, patient age, number of comorbidities, and the number of words in notes are all important factors related to generalization. Finally, we compared local fine-tuning (hospital specific), instance-based augmented fine-tuning and cluster-based fine-tuning for improving generalization. Among these, local fine-tuning proved most effective, increasing AUC by 0.25% to 11.74% (most helpful in settings with limited data). Overall, this study provides new insights for enhancing the deployment of large language models in the societally important domain of healthcare, and improving their performance for broader populations.

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.

Rare diseases present unique challenges in healthcare, often suffering from delayed diagnosis and fragmented information landscapes. The scarcity of reliable knowledge in these conditions poses a distinct challenge for Large Language Models (LLMs) in supporting clinical management and delivering precise patient information underscoring the need for focused training on these 'zebra' cases. We present Zebra-Llama, a specialized context-aware language model with high precision Retrieval Augmented Generation (RAG) capability, focusing on Ehlers-Danlos Syndrome (EDS) as our case study. EDS, affecting 1 in 5,000 individuals, exemplifies the complexities of rare diseases with its diverse symptoms, multiple subtypes, and evolving diagnostic criteria. By implementing a novel context-aware fine-tuning methodology trained on questions derived from medical literature, patient experiences, and clinical resources, along with expertly curated responses, Zebra-Llama demonstrates unprecedented capabilities in handling EDS-related queries. On a test set of real-world questions collected from EDS patients and clinicians, medical experts evaluated the responses generated by both models, revealing Zebra-Llama's substantial improvements over base model (Llama 3.1-8B-Instruct) in thoroughness (77.5% vs. 70.1%), accuracy (83.0% vs. 78.8%), clarity (74.7% vs. 72.0%) and citation reliability (70.6% vs. 52.3%). Released as an open-source resource, Zebra-Llama not only provides more accessible and reliable EDS information but also establishes a framework for developing specialized AI solutions for other rare conditions. This work represents a crucial step towards democratizing expert-level knowledge in rare disease management, potentially transforming how healthcare providers and patients navigate the complex landscape of rare diseases.

Pre-trained transformers are often fine-tuned to aid clinical decision-making using limited clinical notes. Model interpretability is crucial, especially in high-stakes domains like medicine, to establish trust and ensure safety, which requires human engagement. We introduce SUFO, a systematic framework that enhances interpretability of fine-tuned transformer feature spaces. SUFO utilizes a range of analytic and visualization techniques, including Supervised probing, Unsupervised similarity analysis, Feature dynamics, and Outlier analysis to address key questions about model trust and interpretability. We conduct a case study investigating the impact of pre-training data where we focus on real-world pathology classification tasks, and validate our findings on MedNLI. We evaluate five 110M-sized pre-trained transformer models, categorized into general-domain (BERT, TNLR), mixed-domain (BioBERT, Clinical BioBERT), and domain-specific (PubMedBERT) groups. Our SUFO analyses reveal that: (1) while PubMedBERT, the domain-specific model, contains valuable information for fine-tuning, it can overfit to minority classes when class imbalances exist. In contrast, mixed-domain models exhibit greater resistance to overfitting, suggesting potential improvements in domain-specific model robustness; (2) in-domain pre-training accelerates feature disambiguation during fine-tuning; and (3) feature spaces undergo significant sparsification during this process, enabling clinicians to identify common outlier modes among fine-tuned models as demonstrated in this paper. These findings showcase the utility of SUFO in enhancing trust and safety when using transformers in medicine, and we believe SUFO can aid practitioners in evaluating fine-tuned language models for other applications in medicine and in more critical domains.

Pre-training lays the foundation for recent successes in radiograph analysis supported by deep learning. It learns transferable image representations by conducting large-scale fully-supervised or self-supervised learning on a source domain. However, supervised pre-training requires a complex and labor intensive two-stage human-assisted annotation process while self-supervised learning cannot compete with the supervised paradigm. To tackle these issues, we propose a cross-supervised methodology named REviewing FreE-text Reports for Supervision (REFERS), which acquires free supervision signals from original radiology reports accompanying the radiographs. The proposed approach employs a vision transformer and is designed to learn joint representations from multiple views within every patient study. REFERS outperforms its transfer learning and self-supervised learning counterparts on 4 well-known X-ray datasets under extremely limited supervision. Moreover, REFERS even surpasses methods based on a source domain of radiographs with human-assisted structured labels. Thus REFERS has the potential to replace canonical pre-training methodologies.

Advances in deep learning and transfer learning have paved the way for various automation classification tasks in agriculture, including plant diseases, pests, weeds, and plant species detection. However, agriculture automation still faces various challenges, such as the limited size of datasets and the absence of plant-domain-specific pretrained models. Domain specific pretrained models have shown state of art performance in various computer vision tasks including face recognition and medical imaging diagnosis. In this paper, we propose AgriNet dataset, a collection of 160k agricultural images from more than 19 geographical locations, several images captioning devices, and more than 423 classes of plant species and diseases. We also introduce AgriNet models, a set of pretrained models on five ImageNet architectures: VGG16, VGG19, Inception-v3, InceptionResNet-v2, and Xception. AgriNet-VGG19 achieved the highest classification accuracy of 94 % and the highest F1-score of 92%. Additionally, all proposed models were found to accurately classify the 423 classes of plant species, diseases, pests, and weeds with a minimum accuracy of 87% for the Inception-v3 model.Finally, experiments to evaluate of superiority of AgriNet models compared to ImageNet models were conducted on two external datasets: pest and plant diseases dataset from Bangladesh and a plant diseases dataset from Kashmir.

Large language models (LLMs) have demonstrated remarkable success in NLP tasks. However, there is a paucity of studies that attempt to evaluate their performances on social media-based health-related natural language processing tasks, which have traditionally been difficult to achieve high scores in. We benchmarked one supervised classic machine learning model based on Support Vector Machines (SVMs), three supervised pretrained language models (PLMs) based on RoBERTa, BERTweet, and SocBERT, and two LLM based classifiers (GPT3.5 and GPT4), across 6 text classification tasks. We developed three approaches for leveraging LLMs for text classification: employing LLMs as zero-shot classifiers, us-ing LLMs as annotators to annotate training data for supervised classifiers, and utilizing LLMs with few-shot examples for augmentation of manually annotated data. Our comprehensive experiments demonstrate that employ-ing data augmentation using LLMs (GPT-4) with relatively small human-annotated data to train lightweight supervised classification models achieves superior results compared to training with human-annotated data alone. Supervised learners also outperform GPT-4 and GPT-3.5 in zero-shot settings. By leveraging this data augmentation strategy, we can harness the power of LLMs to develop smaller, more effective domain-specific NLP models. LLM-annotated data without human guidance for training light-weight supervised classification models is an ineffective strategy. However, LLM, as a zero-shot classifier, shows promise in excluding false negatives and potentially reducing the human effort required for data annotation. Future investigations are imperative to explore optimal training data sizes and the optimal amounts of augmented data.

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.

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.

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.

Medical systematic reviews typically require assessing all the documents retrieved by a search. The reason is two-fold: the task aims for ``total recall''; and documents retrieved using Boolean search are an unordered set, and thus it is unclear how an assessor could examine only a subset. Screening prioritisation is the process of ranking the (unordered) set of retrieved documents, allowing assessors to begin the downstream processes of the systematic review creation earlier, leading to earlier completion of the review, or even avoiding screening documents ranked least relevant. Screening prioritisation requires highly effective ranking methods. Pre-trained language models are state-of-the-art on many IR tasks but have yet to be applied to systematic review screening prioritisation. In this paper, we apply several pre-trained language models to the systematic review document ranking task, both directly and fine-tuned. An empirical analysis compares how effective neural methods compare to traditional methods for this task. We also investigate different types of document representations for neural methods and their impact on ranking performance. Our results show that BERT-based rankers outperform the current state-of-the-art screening prioritisation methods. However, BERT rankers and existing methods can actually be complementary, and thus, further improvements may be achieved if used in conjunction.

Since COVID strongly affects the respiratory system, lung CT-scans can be used for the analysis of a patients health. We introduce a neural network for the prediction of the severity of lung damage and the detection of a COVID-infection using three-dimensional CT-data. Therefore, we adapt the recent ConvNeXt model to process three-dimensional data. Furthermore, we design and analyze different pretraining methods specifically designed to improve the models ability to handle three-dimensional CT-data. We rank 2nd in the 1st COVID19 Severity Detection Challenge and 3rd in the 2nd COVID19 Detection Challenge.

A recently introduced classifier, called SS3, has shown to be well suited to deal with early risk detection (ERD) problems on text streams. It obtained state-of-the-art performance on early depression and anorexia detection on Reddit in the CLEF's eRisk open tasks. SS3 was created to deal with ERD problems naturally since: it supports incremental training and classification over text streams, and it can visually explain its rationale. However, SS3 processes the input using a bag-of-word model lacking the ability to recognize important word sequences. This aspect could negatively affect the classification performance and also reduces the descriptiveness of visual explanations. In the standard document classification field, it is very common to use word n-grams to try to overcome some of these limitations. Unfortunately, when working with text streams, using n-grams is not trivial since the system must learn and recognize which n-grams are important "on the fly". This paper introduces t-SS3, an extension of SS3 that allows it to recognize useful patterns over text streams dynamically. We evaluated our model in the eRisk 2017 and 2018 tasks on early depression and anorexia detection. Experimental results suggest that t-SS3 is able to improve both current results and the richness of visual explanations.

Pathology is the study of microscopic inspection of tissue, and a pathology diagnosis is often the medical gold standard to diagnose disease. Pathology images provide a unique challenge for computer-vision-based analysis: a single pathology Whole Slide Image (WSI) is gigapixel-sized and often contains hundreds of thousands to millions of objects of interest across multiple resolutions. In this work, we propose PathoLogy Universal TransfOrmer (PLUTO): a light-weight pathology FM that is pre-trained on a diverse dataset of 195 million image tiles collected from multiple sites and extracts meaningful representations across multiple WSI scales that enable a large variety of downstream pathology tasks. In particular, we design task-specific adaptation heads that utilize PLUTO's output embeddings for tasks which span pathology scales ranging from subcellular to slide-scale, including instance segmentation, tile classification, and slide-level prediction. We compare PLUTO's performance to other state-of-the-art methods on a diverse set of external and internal benchmarks covering multiple biologically relevant tasks, tissue types, resolutions, stains, and scanners. We find that PLUTO matches or outperforms existing task-specific baselines and pathology-specific foundation models, some of which use orders-of-magnitude larger datasets and model sizes when compared to PLUTO. Our findings present a path towards a universal embedding to power pathology image analysis, and motivate further exploration around pathology foundation models in terms of data diversity, architectural improvements, sample efficiency, and practical deployability in real-world applications.

Recent large language models (LLMs) in the general domain, such as ChatGPT, have shown remarkable success in following instructions and producing human-like responses. However, such language models have not been learned individually and carefully for the medical domain, resulting in poor diagnostic accuracy and inability to give correct recommendations for medical diagnosis, medications, etc. To address this issue, we collected more than 700 diseases and their corresponding symptoms, recommended medications, and required medical tests, and then generated 5K doctor-patient conversations. By fine-tuning models of doctor-patient conversations, these models emerge with great potential to understand patients' needs, provide informed advice, and offer valuable assistance in a variety of medical-related fields. The integration of these advanced language models into healthcare can revolutionize the way healthcare professionals and patients communicate, ultimately improving the overall quality of care and patient outcomes. In addition, we will open all source code, datasets and model weights to advance the further development of dialogue models in the medical field. In addition, the training data, code, and weights of this project are available at: https://github.com/Kent0n-Li/ChatDoctor.

The agriculture sector is essential for every country because it provides a basic income to a large number of people and food as well, which is a fundamental requirement to survive on this planet. We see as time passes, significant changes come in the present era, which begins with Green Revolution. Due to improper knowledge of plant diseases, farmers use fertilizers in excess, which ultimately degrade the quality of food. Earlier farmers use experts to determine the type of plant disease, which was expensive and time-consuming. In today time, Image processing is used to recognize and catalog plant diseases using the lesion region of plant leaf, and there are different modus-operandi for plant disease scent from leaf using Neural Networks (NN), Support Vector Machine (SVM), and others. In this paper, we improving the architecture of the Neural Networking by working on ten different types of training algorithms and the proper choice of neurons in the concealed layer. Our proposed approach gives 98.30% accuracy on general plant leaf disease and 100% accuracy on specific plant leaf disease based on Bayesian regularization, automation of cluster and without over-fitting on considered plant diseases over various other implemented methods.

Foodborne illness is a serious but preventable public health problem -- with delays in detecting the associated outbreaks resulting in productivity loss, expensive recalls, public safety hazards, and even loss of life. While social media is a promising source for identifying unreported foodborne illnesses, there is a dearth of labeled datasets for developing effective outbreak detection models. To accelerate the development of machine learning-based models for foodborne outbreak detection, we thus present TWEET-FID (TWEET-Foodborne Illness Detection), the first publicly available annotated dataset for multiple foodborne illness incident detection tasks. TWEET-FID collected from Twitter is annotated with three facets: tweet class, entity type, and slot type, with labels produced by experts as well as by crowdsource workers. We introduce several domain tasks leveraging these three facets: text relevance classification (TRC), entity mention detection (EMD), and slot filling (SF). We describe the end-to-end methodology for dataset design, creation, and labeling for supporting model development for these tasks. A comprehensive set of results for these tasks leveraging state-of-the-art single- and multi-task deep learning methods on the TWEET-FID dataset are provided. This dataset opens opportunities for future research in foodborne outbreak detection.

Medical research generates a large number of publications with the PubMed database already containing >35 million research articles. Integration of the knowledge scattered across this large body of literature could provide key insights into physiological mechanisms and disease processes leading to novel medical interventions. However, it is a great challenge for researchers to utilize this information in full since the scale and complexity of the data greatly surpasses human processing abilities. This becomes especially problematic in cases of extreme urgency like the COVID-19 pandemic. Automated text mining can help extract and connect information from the large body of medical research articles. The first step in text mining is typically the identification of specific classes of keywords (e.g., all protein or disease names), so called Named Entity Recognition (NER). Here we present an end-to-end pipeline for NER of typical entities found in medical research articles, including diseases, cells, chemicals, genes/proteins, and species. The pipeline can access and process large medical research article collections (PubMed, CORD-19) or raw text and incorporates a series of deep learning models fine-tuned on the HUNER corpora collection. In addition, the pipeline can perform dictionary-based NER related to COVID-19 and other medical topics. Users can also load their own NER models and dictionaries to include additional entities. The output consists of publication-ready ranked lists and graphs of detected entities and files containing the annotated texts. An associated script allows rapid inspection of the results for specific entities of interest. As model use cases, the pipeline was deployed on two collections of autophagy-related abstracts from PubMed and on the CORD19 dataset, a collection of 764 398 research article abstracts related to COVID-19.

Reading and interpreting chest X-ray images is one of the most radiologist's routines. However, it still can be challenging, even for the most experienced ones. Therefore, we proposed a multi-model deep learning-based automated chest X-ray report generator system designed to assist radiologists in their work. The basic idea of the proposed system is by utilizing multi binary-classification models for detecting multi abnormalities, with each model responsible for detecting one abnormality, in a single image. In this study, we limited the radiology abnormalities detection to only cardiomegaly, lung effusion, and consolidation. The system generates a radiology report by performing the following three steps: image pre-processing, utilizing deep learning models to detect abnormalities, and producing a report. The aim of the image pre-processing step is to standardize the input by scaling it to 128x128 pixels and slicing it into three segments, which covers the upper, lower, and middle parts of the lung. After pre-processing, each corresponding model classifies the image, resulting in a 0 (zero) for no abnormality detected and a 1 (one) for the presence of an abnormality. The prediction outputs of each model are then concatenated to form a 'result code'. The 'result code' is used to construct a report by selecting the appropriate pre-determined sentence for each detected abnormality in the report generation step. The proposed system is expected to reduce the workload of radiologists and increase the accuracy of chest X-ray diagnosis.

Social media is a great source of data for users reporting information and regarding their health and how various things have had an effect on them. This paper presents various approaches using Transformers and Large Language Models and their ensembles, their performance along with advantages and drawbacks for various tasks of SMM4H'24 - Classifying texts on impact of nature and outdoor spaces on the author's mental health (Task 3), Binary classification of tweets reporting their children's health disorders like Asthma, Autism, ADHD and Speech disorder (task 5), Binary classification of users self-reporting their age (task 6).

This paper presents several BERT-based models for Russian language biomedical text mining (RuBioBERT, RuBioRoBERTa). The models are pre-trained on a corpus of freely available texts in the Russian biomedical domain. With this pre-training, our models demonstrate state-of-the-art results on RuMedBench - Russian medical language understanding benchmark that covers a diverse set of tasks, including text classification, question answering, natural language inference, and named entity recognition.

Accurate diagnosis of Parkinson disease, especially in its early stages, can be a challenging task. The application of machine learning techniques helps improve the diagnostic accuracy of Parkinson disease detection but only few studies have presented work towards the prediction of disease progression. In this research work, Long Short Term Memory LSTM was trained using the diagnostic features on Parkinson patients speech signals, to predict the disease progression while a Multilayer Perceptron MLP was trained on the same diagnostic features to detect the disease. Diagnostic features selected using two well-known feature selection methods named Relief-F and Sequential Forward Selection and applied on LSTM and MLP have shown to accurately predict the disease progression as stage 2 and 3 and its existence respectively.

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.

Machine learning models are often trained to predict the outcome resulting from a human decision. For example, if a doctor decides to test a patient for disease, will the patient test positive? A challenge is that historical decision-making determines whether the outcome is observed: we only observe test outcomes for patients doctors historically tested. Untested patients, for whom outcomes are unobserved, may differ from tested patients along observed and unobserved dimensions. We propose a Bayesian model class which captures this setting. The purpose of the model is to accurately estimate risk for both tested and untested patients. Estimating this model is challenging due to the wide range of possibilities for untested patients. To address this, we propose two domain constraints which are plausible in health settings: a prevalence constraint, where the overall disease prevalence is known, and an expertise constraint, where the human decision-maker deviates from purely risk-based decision-making only along a constrained feature set. We show theoretically and on synthetic data that domain constraints improve parameter inference. We apply our model to a case study of cancer risk prediction, showing that the model's inferred risk predicts cancer diagnoses, its inferred testing policy captures known public health policies, and it can identify suboptimalities in test allocation. Though our case study is in healthcare, our analysis reveals a general class of domain constraints which can improve model estimation in many settings.

Large language models (LLMs) are increasingly essential in processing natural languages, yet their application is frequently compromised by biases and inaccuracies originating in their training data. In this study, we introduce Cross-Care, the first benchmark framework dedicated to assessing biases and real world knowledge in LLMs, specifically focusing on the representation of disease prevalence across diverse demographic groups. We systematically evaluate how demographic biases embedded in pre-training corpora like ThePile influence the outputs of LLMs. We expose and quantify discrepancies by juxtaposing these biases against actual disease prevalences in various U.S. demographic groups. Our results highlight substantial misalignment between LLM representation of disease prevalence and real disease prevalence rates across demographic subgroups, indicating a pronounced risk of bias propagation and a lack of real-world grounding for medical applications of LLMs. Furthermore, we observe that various alignment methods minimally resolve inconsistencies in the models' representation of disease prevalence across different languages. For further exploration and analysis, we make all data and a data visualization tool available at: www.crosscare.net.

Pre-trained language models have attracted increasing attention in the biomedical domain, inspired by their great success in the general natural language domain. Among the two main branches of pre-trained language models in the general language domain, i.e., BERT (and its variants) and GPT (and its variants), the first one has been extensively studied in the biomedical domain, such as BioBERT and PubMedBERT. While they have achieved great success on a variety of discriminative downstream biomedical tasks, the lack of generation ability constrains their application scope. In this paper, we propose BioGPT, a domain-specific generative Transformer language model pre-trained on large scale biomedical literature. We evaluate BioGPT on six biomedical NLP tasks and demonstrate that our model outperforms previous models on most tasks. Especially, we get 44.98%, 38.42% and 40.76% F1 score on BC5CDR, KD-DTI and DDI end-to-end relation extraction tasks respectively, and 78.2% accuracy on PubMedQA, creating a new record. Our larger model BioGPT-Large achieves 81.0% on PubMedQA. Our case study on text generation further demonstrates the advantage of BioGPT on biomedical literature to generate fluent descriptions for biomedical terms. Code is available at https://github.com/microsoft/BioGPT.

One of the biggest challenges that prohibit the use of many current NLP methods in clinical settings is the availability of public datasets. In this work, we present MeDAL, a large medical text dataset curated for abbreviation disambiguation, designed for natural language understanding pre-training in the medical domain. We pre-trained several models of common architectures on this dataset and empirically showed that such pre-training leads to improved performance and convergence speed when fine-tuning on downstream medical tasks.

Background: Social media platforms have become a viable source of medical information, with patients and healthcare professionals using them to share health-related information and track diseases. Similarly, YouTube, the largest video-sharing platform in the world contains vlogs where individuals talk about their illnesses. The aim of our study was to investigate the use of Natural Language Processing (NLP) to identify the spoken content of YouTube vlogs related to the diagnosis of Coronavirus disease of 2019 (COVID-19) for public health screening. Methods: COVID-19 videos on YouTube were searched using relevant keywords. A total of 1000 videos being spoken in English were downloaded out of which 791 were classified as vlogs, 192 were non-vlogs, and 17 were deleted by the channel. The videos were converted into a textual format using Microsoft Streams. The textual data was preprocessed using basic and advanced preprocessing methods. A lexicon of 200 words was created which contained words related to COVID-19. The data was analyzed using topic modeling, word clouds, and lexicon matching. Results: The word cloud results revealed discussions about COVID-19 symptoms like "fever", along with generic terms such as "mask" and "isolation". Lexical analysis demonstrated that in 96.46% of videos, patients discussed generic terms, and in 95.45% of videos, people talked about COVID-19 symptoms. LDA Topic Modeling results also generated topics that successfully captured key themes and content related to our investigation of COVID-19 diagnoses in YouTube vlogs. Conclusion: By leveraging NLP techniques on YouTube vlogs public health practitioners can enhance their ability to mitigate the effects of pandemics and effectively respond to public health challenges.

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

Electronic health record (EHR) systems are used extensively throughout the healthcare domain. However, data interchangeability between EHR systems is limited due to the use of different coding standards across systems. Existing methods of mapping coding standards based on manual human experts mapping, dictionary mapping, symbolic NLP and classification are unscalable and cannot accommodate large scale EHR datasets. In this work, we present Text2Node, a cross-domain mapping system capable of mapping medical phrases to concepts in a large taxonomy (such as SNOMED CT). The system is designed to generalize from a limited set of training samples and map phrases to elements of the taxonomy that are not covered by training data. As a result, our system is scalable, robust to wording variants between coding systems and can output highly relevant concepts when no exact concept exists in the target taxonomy. Text2Node operates in three main stages: first, the lexicon is mapped to word embeddings; second, the taxonomy is vectorized using node embeddings; and finally, the mapping function is trained to connect the two embedding spaces. We compared multiple algorithms and architectures for each stage of the training, including GloVe and FastText word embeddings, CNN and Bi-LSTM mapping functions, and node2vec for node embeddings. We confirmed the robustness and generalisation properties of Text2Node by mapping ICD-9-CM Diagnosis phrases to SNOMED CT and by zero-shot training at comparable accuracy. This system is a novel methodological contribution to the task of normalizing and linking phrases to a taxonomy, advancing data interchangeability in healthcare. When applied, the system can use electronic health records to generate an embedding that incorporates taxonomical medical knowledge to improve clinical predictive models.

We evaluated the effectiveness of using language models, that were pre-trained in one domain, as the basis for a classification model in another domain: Dutch book reviews. Pre-trained language models have opened up new possibilities for classification tasks with limited labelled data, because representation can be learned in an unsupervised fashion. In our experiments we have studied the effects of training set size (100-1600 items) on the prediction accuracy of a ULMFiT classifier, based on a language models that we pre-trained on the Dutch Wikipedia. We also compared ULMFiT to Support Vector Machines, which is traditionally considered suitable for small collections. We found that ULMFiT outperforms SVM for all training set sizes and that satisfactory results (~90%) can be achieved using training sets that can be manually annotated within a few hours. We deliver both our new benchmark collection of Dutch book reviews for sentiment classification as well as the pre-trained Dutch language model to the community.

We classify seven months' worth of Belgian COVID-related Tweets using multilingual BERT and relate them to their governments' COVID measures. We classify Tweets by their stated opinion on Belgian government curfew measures (too strict, ok, too loose). We examine the change in topics discussed and views expressed over time and in reference to dates of related events such as implementation of new measures or COVID-19 related announcements in the media.

Coronavirus disease (COVID-19) is a pandemic disease, which has already caused thousands of causalities and infected several millions of people worldwide. Any technological tool enabling rapid screening of the COVID-19 infection with high accuracy can be crucially helpful to healthcare professionals. The main clinical tool currently in use for the diagnosis of COVID-19 is the Reverse transcription polymerase chain reaction (RT-PCR), which is expensive, less-sensitive and requires specialized medical personnel. X-ray imaging is an easily accessible tool that can be an excellent alternative in the COVID-19 diagnosis. This research was taken to investigate the utility of artificial intelligence (AI) in the rapid and accurate detection of COVID-19 from chest X-ray images. The aim of this paper is to propose a robust technique for automatic detection of COVID-19 pneumonia from digital chest X-ray images applying pre-trained deep-learning algorithms while maximizing the detection accuracy. A public database was created by the authors combining several public databases and also by collecting images from recently published articles. The database contains a mixture of 423 COVID-19, 1485 viral pneumonia, and 1579 normal chest X-ray images. Transfer learning technique was used with the help of image augmentation to train and validate several pre-trained deep Convolutional Neural Networks (CNNs). The networks were trained to classify two different schemes: i) normal and COVID-19 pneumonia; ii) normal, viral and COVID-19 pneumonia with and without image augmentation. The classification accuracy, precision, sensitivity, and specificity for both the schemes were 99.7%, 99.7%, 99.7% and 99.55% and 97.9%, 97.95%, 97.9%, and 98.8%, respectively.

Mental health research through data-driven methods has been hindered by a lack of standard typology and scarcity of adequate data. In this study, we leverage the clinical articulation of depression to build a typology for social media texts for detecting the severity of depression. It emulates the standard clinical assessment procedure Diagnostic and Statistical Manual of Mental Disorders (DSM-5) and Patient Health Questionnaire (PHQ-9) to encompass subtle indications of depressive disorders from tweets. Along with the typology, we present a new dataset of 40191 tweets labeled by expert annotators. Each tweet is labeled as 'non-depressed' or 'depressed'. Moreover, three severity levels are considered for 'depressed' tweets: (1) mild, (2) moderate, and (3) severe. An associated confidence score is provided with each label to validate the quality of annotation. We examine the quality of the dataset via representing summary statistics while setting strong baseline results using attention-based models like BERT and DistilBERT. Finally, we extensively address the limitations of the study to provide directions for further research.

Text classification is an important task in Natural Language Processing (NLP), where the goal is to categorize text data into predefined classes. In this study, we analyse the dataset creation steps and evaluation techniques of multi-label news categorisation task as part of text classification. We first present a newly obtained dataset for Uzbek text classification, which was collected from 10 different news and press websites and covers 15 categories of news, press and law texts. We also present a comprehensive evaluation of different models, ranging from traditional bag-of-words models to deep learning architectures, on this newly created dataset. Our experiments show that the Recurrent Neural Network (RNN) and Convolutional Neural Network (CNN) based models outperform the rule-based models. The best performance is achieved by the BERTbek model, which is a transformer-based BERT model trained on the Uzbek corpus. Our findings provide a good baseline for further research in Uzbek text classification.

We observe a recent behaviour on social media, in which users intentionally remove consonantal dots from Arabic letters, in order to bypass content-classification algorithms. Content classification is typically done by fine-tuning pre-trained language models, which have been recently employed by many natural-language-processing applications. In this work we study the effect of applying pre-trained Arabic language models on "undotted" Arabic texts. We suggest several ways of supporting undotted texts with pre-trained models, without additional training, and measure their performance on two Arabic natural-language-processing downstream tasks. The results are encouraging; in one of the tasks our method shows nearly perfect performance.

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

Vision Transformer (ViT) has become one of the most popular neural architectures due to its great scalability, computational efficiency, and compelling performance in many vision tasks. However, ViT has shown inferior performance to Convolutional Neural Network (CNN) on medical tasks due to its data-hungry nature and the lack of annotated medical data. In this paper, we pre-train ViTs on 266,340 chest X-rays using Masked Autoencoders (MAE) which reconstruct missing pixels from a small part of each image. For comparison, CNNs are also pre-trained on the same 266,340 X-rays using advanced self-supervised methods (e.g., MoCo v2). The results show that our pre-trained ViT performs comparably (sometimes better) to the state-of-the-art CNN (DenseNet-121) for multi-label thorax disease classification. This performance is attributed to the strong recipes extracted from our empirical studies for pre-training and fine-tuning ViT. The pre-training recipe signifies that medical reconstruction requires a much smaller proportion of an image (10% vs. 25%) and a more moderate random resized crop range (0.5~1.0 vs. 0.2~1.0) compared with natural imaging. Furthermore, we remark that in-domain transfer learning is preferred whenever possible. The fine-tuning recipe discloses that layer-wise LR decay, RandAug magnitude, and DropPath rate are significant factors to consider. We hope that this study can direct future research on the application of Transformers to a larger variety of medical imaging tasks.

Despite the remarkable progress in the development of predictive models for healthcare, applying these algorithms on a large scale has been challenging. Algorithms trained on a particular task, based on specific data formats available in a set of medical records, tend to not generalize well to other tasks or databases in which the data fields may differ. To address this challenge, we propose General Healthcare Predictive Framework (GenHPF), which is applicable to any EHR with minimal preprocessing for multiple prediction tasks. GenHPF resolves heterogeneity in medical codes and schemas by converting EHRs into a hierarchical textual representation while incorporating as many features as possible. To evaluate the efficacy of GenHPF, we conduct multi-task learning experiments with single-source and multi-source settings, on three publicly available EHR datasets with different schemas for 12 clinically meaningful prediction tasks. Our framework significantly outperforms baseline models that utilize domain knowledge in multi-source learning, improving average AUROC by 1.2%P in pooled learning and 2.6%P in transfer learning while also showing comparable results when trained on a single EHR dataset. Furthermore, we demonstrate that self-supervised pretraining using multi-source datasets is effective when combined with GenHPF, resulting in a 0.6%P AUROC improvement compared to models without pretraining. By eliminating the need for preprocessing and feature engineering, we believe that this work offers a solid framework for multi-task and multi-source learning that can be leveraged to speed up the scaling and usage of predictive algorithms in healthcare.

As the field of artificial intelligence progresses, assistive technologies are becoming more widely used across all industries. The healthcare industry is no different, with numerous studies being done to develop assistive tools for healthcare professionals. Automatic diagnostic systems are one such beneficial tool that can assist with a variety of tasks, including collecting patient information, analyzing test results, and diagnosing patients. However, the idea of developing systems that can provide a differential diagnosis has been largely overlooked in most of these research studies. In this study, we propose a transformer-based approach for providing differential diagnoses based on a patient's age, sex, medical history, and symptoms. We use the DDXPlus dataset, which provides differential diagnosis information for patients based on 49 disease types. Firstly, we propose a method to process the tabular patient data from the dataset and engineer them into patient reports to make them suitable for our research. In addition, we introduce two data modification modules to diversify the training data and consequently improve the robustness of the models. We approach the task as a multi-label classification problem and conduct extensive experiments using four transformer models. All the models displayed promising results by achieving over 97% F1 score on the held-out test set. Moreover, we design additional behavioral tests to get a broader understanding of the models. In particular, for one of our test cases, we prepared a custom test set of 100 samples with the assistance of a doctor. The results on the custom set showed that our proposed data modification modules improved the model's generalization capabilities. We hope our findings will provide future researchers with valuable insights and inspire them to develop reliable systems for automatic differential diagnosis.

With the rise of the Internet, there is a growing need to build intelligent systems that are capable of efficiently dealing with early risk detection (ERD) problems on social media, such as early depression detection, early rumor detection or identification of sexual predators. These systems, nowadays mostly based on machine learning techniques, must be able to deal with data streams since users provide their data over time. In addition, these systems must be able to decide when the processed data is sufficient to actually classify users. Moreover, since ERD tasks involve risky decisions by which people's lives could be affected, such systems must also be able to justify their decisions. However, most standard and state-of-the-art supervised machine learning models are not well suited to deal with this scenario. This is due to the fact that they either act as black boxes or do not support incremental classification/learning. In this paper we introduce SS3, a novel supervised learning model for text classification that naturally supports these aspects. SS3 was designed to be used as a general framework to deal with ERD problems. We evaluated our model on the CLEF's eRisk2017 pilot task on early depression detection. Most of the 30 contributions submitted to this competition used state-of-the-art methods. Experimental results show that our classifier was able to outperform these models and standard classifiers, despite being less computationally expensive and having the ability to explain its rationale.

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

Nasal Cytology is a new and efficient clinical technique to diagnose rhinitis and allergies that is not much widespread due to the time-consuming nature of cell counting; that is why AI-aided counting could be a turning point for the diffusion of this technique. In this article we present the first dataset of rhino-cytological field images: the NCD (Nasal Cytology Dataset), aimed to train and deploy Object Detection models to support physicians and biologists during clinical practice. The real distribution of the cytotypes, populating the nasal mucosa has been replicated, sampling images from slides of clinical patients, and manually annotating each cell found on them. The correspondent object detection task presents non'trivial issues associated with the strong class imbalancement, involving the rarest cell types. This work contributes to some of open challenges by presenting a novel machine learning-based approach to aid the automated detection and classification of nasal mucosa cells: the DETR and YOLO models shown good performance in detecting cells and classifying them correctly, revealing great potential to accelerate the work of rhinology experts.

The COVID-19 pandemic strained healthcare resources and prompted discussion about how machine learning can alleviate physician burdens and contribute to diagnosis. Chest x-rays (CXRs) are used for diagnosis of COVID-19, but few studies predict the severity of a patient's condition from CXRs. In this study, we produce a large COVID severity dataset by merging three sources and investigate the efficacy of transfer learning using ImageNet- and CXR-pretrained models and vision transformers (ViTs) in both severity regression and classification tasks. A pretrained DenseNet161 model performed the best on the three class severity prediction problem, reaching 80% accuracy overall and 77.3%, 83.9%, and 70% on mild, moderate and severe cases, respectively. The ViT had the best regression results, with a mean absolute error of 0.5676 compared to radiologist-predicted severity scores. The project's source code is publicly available.

We address a challenging and practical task of labeling questions in speech in real time during telephone calls to emergency medical services in English, which embeds within a broader decision support system for emergency call-takers. We propose a novel multimodal approach to real-time sequence labeling in speech. Our model treats speech and its own textual representation as two separate modalities or views, as it jointly learns from streamed audio and its noisy transcription into text via automatic speech recognition. Our results show significant gains of jointly learning from the two modalities when compared to text or audio only, under adverse noise and limited volume of training data. The results generalize to medical symptoms detection where we observe a similar pattern of improvements with multimodal learning.

Due to privacy restrictions, there's a shortage of publicly available speech recognition datasets in the medical domain. In this work, we present VietMed - a Vietnamese speech recognition dataset in the medical domain comprising 16h of labeled medical speech, 1000h of unlabeled medical speech and 1200h of unlabeled general-domain speech. To our best knowledge, VietMed is by far the world's largest public medical speech recognition dataset in 7 aspects: total duration, number of speakers, diseases, recording conditions, speaker roles, unique medical terms and accents. VietMed is also by far the largest public Vietnamese speech dataset in terms of total duration. Additionally, we are the first to present a medical ASR dataset covering all ICD-10 disease groups and all accents within a country. Moreover, we release the first public large-scale pre-trained models for Vietnamese ASR, w2v2-Viet and XLSR-53-Viet, along with the first public large-scale fine-tuned models for medical ASR. Even without any medical data in unsupervised pre-training, our best pre-trained model XLSR-53-Viet generalizes very well to the medical domain by outperforming state-of-the-art XLSR-53, from 51.8% to 29.6% WER on test set (a relative reduction of more than 40%). All code, data and models are made publicly available here: https://github.com/leduckhai/MultiMed.

Autism spectrum disorder (ASD) is a prevalent psychiatric condition characterized by atypical cognitive, emotional, and social patterns. Timely and accurate diagnosis is crucial for effective interventions and improved outcomes in individuals with ASD. In this study, we propose a novel Multi-Atlas Enhanced Transformer framework, METAFormer, ASD classification. Our framework utilizes resting-state functional magnetic resonance imaging data from the ABIDE I dataset, comprising 406 ASD and 476 typical control (TC) subjects. METAFormer employs a multi-atlas approach, where flattened connectivity matrices from the AAL, CC200, and DOS160 atlases serve as input to the transformer encoder. Notably, we demonstrate that self-supervised pretraining, involving the reconstruction of masked values from the input, significantly enhances classification performance without the need for additional or separate training data. Through stratified cross-validation, we evaluate the proposed framework and show that it surpasses state-of-the-art performance on the ABIDE I dataset, with an average accuracy of 83.7% and an AUC-score of 0.832. The code for our framework is available at https://github.com/Lugges991/METAFormer

In this work we introduce Labrador, a pre-trained Transformer model for laboratory data. Labrador and BERT were pre-trained on a corpus of 100 million lab test results from electronic health records (EHRs) and evaluated on various downstream outcome prediction tasks. Both models demonstrate mastery of the pre-training task but neither consistently outperform XGBoost on downstream supervised tasks. Our ablation studies reveal that transfer learning shows limited effectiveness for BERT and achieves marginal success with Labrador. We explore the reasons for the failure of transfer learning and suggest that the data generating process underlying each patient cannot be characterized sufficiently using labs alone, among other factors. We encourage future work to focus on joint modeling of multiple EHR data categories and to include tree-based baselines in their evaluations.

Clinical data in hospitals are increasingly accessible for research through clinical data warehouses, however these documents are unstructured. It is therefore necessary to extract information from medical reports to conduct clinical studies. Transfer learning with BERT-like models such as CamemBERT has allowed major advances, especially for named entity recognition. However, these models are trained for plain language and are less efficient on biomedical data. This is why we propose a new French public biomedical dataset on which we have continued the pre-training of CamemBERT. Thus, we introduce a first version of CamemBERT-bio, a specialized public model for the French biomedical domain that shows 2.54 points of F1 score improvement on average on different biomedical named entity recognition tasks. Our findings demonstrate the success of continual pre-training from a French model and contrast with recent proposals on the same domain and language. One of our key contributions highlights the importance of using a standard evaluation protocol that enables a clear view of the current state-of-the-art for French biomedical models.

The current state of adoption of well-structured electronic health records and integration of digital methods for storing medical patient data in structured formats can often considered as inferior compared to the use of traditional, unstructured text based patient data documentation. Data mining in the field of medical data analysis often needs to rely solely on processing of unstructured data to retrieve relevant data. In natural language processing (NLP), statistical models have been shown successful in various tasks like part-of-speech tagging, relation extraction (RE) and named entity recognition (NER). In this work, we present GERNERMED, the first open, neural NLP model for NER tasks dedicated to detect medical entity types in German text data. Here, we avoid the conflicting goals of protection of sensitive patient data from training data extraction and the publication of the statistical model weights by training our model on a custom dataset that was translated from publicly available datasets in foreign language by a pretrained neural machine translation model. The sample code and the statistical model is available at: https://github.com/frankkramer-lab/GERNERMED

A brain tumour is a mass or cluster of abnormal cells in the brain, which has the possibility of becoming life-threatening because of its ability to invade neighbouring tissues and also form metastases. An accurate diagnosis is essential for successful treatment planning and magnetic resonance imaging is the principal imaging modality for diagnostic of brain tumours and their extent. Deep Learning methods in computer vision applications have shown significant improvement in recent years, most of which can be credited to the fact that a sizeable amount of data is available to train models on, and the improvements in the model architectures yielding better approximations in a supervised setting. Classifying tumours using such deep learning methods has made significant progress with the availability of open datasets with reliable annotations. Typically those methods are either 3D models, which use 3D volumetric MRIs or even 2D models considering each slice separately. However, by treating the slice spatial dimension separately, spatiotemporal models can be employed as spatiospatial models for this task. These models have the capabilities of learning specific spatial and temporal relationship, while reducing computational costs. This paper uses two spatiotemporal models, ResNet (2+1)D and ResNet Mixed Convolution, to classify different types of brain tumours. It was observed that both these models performed superior to the pure 3D convolutional model, ResNet18. Furthermore, it was also observed that pre-training the models on a different, even unrelated dataset before training them for the task of tumour classification improves the performance. Finally, Pre-trained ResNet Mixed Convolution was observed to be the best model in these experiments, achieving a macro F1-score of 0.93 and a test accuracy of 96.98\%, while at the same time being the model with the least computational cost.

The accelerated adoption of digital pathology and advances in deep learning have enabled the development of powerful models for various pathology tasks across a diverse array of diseases and patient cohorts. However, model training is often difficult due to label scarcity in the medical domain and the model's usage is limited by the specific task and disease for which it is trained. Additionally, most models in histopathology leverage only image data, a stark contrast to how humans teach each other and reason about histopathologic entities. We introduce CONtrastive learning from Captions for Histopathology (CONCH), a visual-language foundation model developed using diverse sources of histopathology images, biomedical text, and notably over 1.17 million image-caption pairs via task-agnostic pretraining. Evaluated on a suite of 13 diverse benchmarks, CONCH can be transferred to a wide range of downstream tasks involving either or both histopathology images and text, achieving state-of-the-art performance on histology image classification, segmentation, captioning, text-to-image and image-to-text retrieval. CONCH represents a substantial leap over concurrent visual-language pretrained systems for histopathology, with the potential to directly facilitate a wide array of machine learning-based workflows requiring minimal or no further supervised fine-tuning.

This paper introduces the Pandemic PACT Advanced Categorisation Engine (PPACE) along with its associated dataset. PPACE is a fine-tuned model developed to automatically classify research abstracts from funded biomedical projects according to WHO-aligned research priorities. This task is crucial for monitoring research trends and identifying gaps in global health preparedness and response. Our approach builds on human-annotated projects, which are allocated one or more categories from a predefined list. A large language model is then used to generate `rationales' explaining the reasoning behind these annotations. This augmented data, comprising expert annotations and rationales, is subsequently used to fine-tune a smaller, more efficient model. Developed as part of the Pandemic PACT project, which aims to track and analyse research funding and clinical evidence for a wide range of diseases with outbreak potential, PPACE supports informed decision-making by research funders, policymakers, and independent researchers. We introduce and release both the trained model and the instruction-based dataset used for its training. Our evaluation shows that PPACE significantly outperforms its baselines. The release of PPACE and its associated dataset offers valuable resources for researchers in multilabel biomedical document classification and supports advancements in aligning biomedical research with key global health priorities.

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.

Obtaining large pre-trained models that can be fine-tuned to new tasks with limited annotated samples has remained an open challenge for medical imaging data. While pre-trained deep networks on ImageNet and vision-language foundation models trained on web-scale data are prevailing approaches, their effectiveness on medical tasks is limited due to the significant domain shift between natural and medical images. To bridge this gap, we introduce LVM-Med, the first family of deep networks trained on large-scale medical datasets. We have collected approximately 1.3 million medical images from 55 publicly available datasets, covering a large number of organs and modalities such as CT, MRI, X-ray, and Ultrasound. We benchmark several state-of-the-art self-supervised algorithms on this dataset and propose a novel self-supervised contrastive learning algorithm using a graph-matching formulation. The proposed approach makes three contributions: (i) it integrates prior pair-wise image similarity metrics based on local and global information; (ii) it captures the structural constraints of feature embeddings through a loss function constructed via a combinatorial graph-matching objective; and (iii) it can be trained efficiently end-to-end using modern gradient-estimation techniques for black-box solvers. We thoroughly evaluate the proposed LVM-Med on 15 downstream medical tasks ranging from segmentation and classification to object detection, and both for the in and out-of-distribution settings. LVM-Med empirically outperforms a number of state-of-the-art supervised, self-supervised, and foundation models. For challenging tasks such as Brain Tumor Classification or Diabetic Retinopathy Grading, LVM-Med improves previous vision-language models trained on 1 billion masks by 6-7% while using only a ResNet-50.

Natural language processing (NLP) is becoming an important means for automatic recognition of human traits and states, such as intoxication, presence of psychiatric disorders, presence of airway disorders and states of stress. Such applications have the potential to be an important pillar for online help lines, and may gradually be introduced into eHealth modules. However, NLP is language specific and for languages such as Dutch, NLP models are scarce. As a result, recent Dutch NLP models have a low capture of long range semantic dependencies over sentences. To overcome this, here we present belabBERT, a new Dutch language model extending the RoBERTa architecture. belabBERT is trained on a large Dutch corpus (+32 GB) of web crawled texts. We applied belabBERT to the classification of psychiatric illnesses. First, we evaluated the strength of text-based classification using belabBERT, and compared the results to the existing RobBERT model. Then, we compared the performance of belabBERT to audio classification for psychiatric disorders. Finally, a brief exploration was performed, extending the framework to a hybrid text- and audio-based classification. Our results show that belabBERT outperformed the current best text classification network for Dutch, RobBERT. belabBERT also outperformed classification based on audio alone.

The extreme multi-label classification (XMC) task aims at tagging content with a subset of labels from an extremely large label set. The label vocabulary is typically defined in advance by domain experts and assumed to capture all necessary tags. However in real world scenarios this label set, although large, is often incomplete and experts frequently need to refine it. To develop systems that simplify this process, we introduce the task of open vocabulary XMC (OXMC): given a piece of content, predict a set of labels, some of which may be outside of the known tag set. Hence, in addition to not having training data for some labels - as is the case in zero-shot classification - models need to invent some labels on-the-fly. We propose GROOV, a fine-tuned seq2seq model for OXMC that generates the set of labels as a flat sequence and is trained using a novel loss independent of predicted label order. We show the efficacy of the approach, experimenting with popular XMC datasets for which GROOV is able to predict meaningful labels outside the given vocabulary while performing on par with state-of-the-art solutions for known labels.

Pulmonary Hypertension (PH) is a severe disease characterized by an elevated pulmonary artery pressure. The gold standard for PH diagnosis is measurement of mean Pulmonary Artery Pressure (mPAP) during an invasive Right Heart Catheterization. In this paper, we investigate noninvasive approach to PH detection utilizing Magnetic Resonance Imaging, Computer Models and Machine Learning. We show using the ablation study, that physics-informed feature engineering based on models of blood circulation increases the performance of Gradient Boosting Decision Trees-based algorithms for classification of PH and regression of values of mPAP. We compare results of regression (with thresholding of estimated mPAP) and classification and demonstrate that metrics achieved in both experiments are comparable. The predicted mPAP values are more informative to the physicians than the probability of PH returned by classification models. They provide the intuitive explanation of the outcome of the machine learning model (clinicians are accustomed to the mPAP metric, contrary to the PH probability).

Pre-training large-scale neural language models on raw texts has made a significant contribution to improving transfer learning in natural language processing (NLP). With the introduction of transformer-based language models, such as bidirectional encoder representations from transformers (BERT), the performance of information extraction from a free text by NLP has significantly improved for both the general domain and medical domain; however, it is difficult to train specific BERT models that perform well for domains in which there are few publicly available databases of high quality and large size. We hypothesized that this problem can be addressed by up-sampling a domain-specific corpus and using it for pre-training with a larger corpus in a balanced manner. Our proposed method consists of a single intervention with one option: simultaneous pre-training after up-sampling and amplified vocabulary. We conducted three experiments and evaluated the resulting products. We confirmed that our Japanese medical BERT outperformed conventional baselines and the other BERT models in terms of the medical document classification task and that our English BERT pre-trained using both the general and medical-domain corpora performed sufficiently well for practical use in terms of the biomedical language understanding evaluation (BLUE) benchmark. Moreover, our enhanced biomedical BERT model, in which clinical notes were not used during pre-training, showed that both the clinical and biomedical scores of the BLUE benchmark were 0.3 points above that of the ablation model trained without our proposed method. Well-balanced pre-training by up-sampling instances derived from a corpus appropriate for the target task allows us to construct a high-performance BERT model.

This paper presents our team's participation in the MEDIQA-ClinicalNLP2024 shared task B. We present a novel approach to diagnosing clinical dermatology cases by integrating large multimodal models, specifically leveraging the capabilities of GPT-4V under a retriever and a re-ranker framework. Our investigation reveals that GPT-4V, when used as a retrieval agent, can accurately retrieve the correct skin condition 85% of the time using dermatological images and brief patient histories. Additionally, we empirically show that Naive Chain-of-Thought (CoT) works well for retrieval while Medical Guidelines Grounded CoT is required for accurate dermatological diagnosis. Further, we introduce a Multi-Agent Conversation (MAC) framework and show its superior performance and potential over the best CoT strategy. The experiments suggest that using naive CoT for retrieval and multi-agent conversation for critique-based diagnosis, GPT-4V can lead to an early and accurate diagnosis of dermatological conditions. The implications of this work extend to improving diagnostic workflows, supporting dermatological education, and enhancing patient care by providing a scalable, accessible, and accurate diagnostic tool.

Diabetic foot ulcers are a common manifestation of lesions on the diabetic foot, a syndrome acquired as a long-term complication of diabetes mellitus. Accompanying neuropathy and vascular damage promote acquisition of pressure injuries and tissue death due to ischaemia. Affected areas are prone to infections, hindering the healing progress. The research at hand investigates an approach on classification of infection and ischaemia, conducted as part of the Diabetic Foot Ulcer Challenge (DFUC) 2021. Different models of the EfficientNet family are utilized in ensembles. An extension strategy for the training data is applied, involving pseudo-labeling for unlabeled images, and extensive generation of synthetic images via pix2pixHD to cope with severe class imbalances. The resulting extended training dataset features 8.68 times the size of the baseline and shows a real to synthetic image ratio of 1:3. Performances of models and ensembles trained on the baseline and extended training dataset are compared. Synthetic images featured a broad qualitative variety. Results show that models trained on the extended training dataset as well as their ensemble benefit from the large extension. F1-Scores for rare classes receive outstanding boosts, while those for common classes are either not harmed or boosted moderately. A critical discussion concretizes benefits and identifies limitations, suggesting improvements. The work concludes that classification performance of individual models as well as that of ensembles can be boosted utilizing synthetic images. Especially performance for rare classes benefits notably.

We present PubMed 200k RCT, a new dataset based on PubMed for sequential sentence classification. The dataset consists of approximately 200,000 abstracts of randomized controlled trials, totaling 2.3 million sentences. Each sentence of each abstract is labeled with their role in the abstract using one of the following classes: background, objective, method, result, or conclusion. The purpose of releasing this dataset is twofold. First, the majority of datasets for sequential short-text classification (i.e., classification of short texts that appear in sequences) are small: we hope that releasing a new large dataset will help develop more accurate algorithms for this task. Second, from an application perspective, researchers need better tools to efficiently skim through the literature. Automatically classifying each sentence in an abstract would help researchers read abstracts more efficiently, especially in fields where abstracts may be long, such as the medical field.

Automated interpretation of electrocardiograms (ECG) has garnered significant attention with the advancements in machine learning methodologies. Despite the growing interest, most current studies focus solely on classification or regression tasks, which overlook a crucial aspect of clinical cardio-disease diagnosis: the diagnostic report generated by experienced human clinicians. In this paper, we introduce a novel approach to ECG interpretation, leveraging recent breakthroughs in Large Language Models (LLMs) and Vision-Transformer (ViT) models. Rather than treating ECG diagnosis as a classification or regression task, we propose an alternative method of automatically identifying the most similar clinical cases based on the input ECG data. Also, since interpreting ECG as images is more affordable and accessible, we process ECG as encoded images and adopt a vision-language learning paradigm to jointly learn vision-language alignment between encoded ECG images and ECG diagnosis reports. Encoding ECG into images can result in an efficient ECG retrieval system, which will be highly practical and useful in clinical applications. More importantly, our findings could serve as a crucial resource for providing diagnostic services in underdeveloped regions.

Predicting disease trajectories from electronic health records (EHRs) is a complex task due to major challenges such as data non-stationarity, high granularity of medical codes, and integration of multimodal data. EHRs contain both structured data, such as diagnostic codes, and unstructured data, such as clinical notes, which hold essential information often overlooked. Current models, primarily based on structured data, struggle to capture the complete medical context of patients, resulting in a loss of valuable information. To address this issue, we propose an approach that integrates unstructured clinical notes into transformer-based deep learning models for sequential disease prediction. This integration enriches the representation of patients' medical histories, thereby improving the accuracy of diagnosis predictions. Experiments on MIMIC-IV datasets demonstrate that the proposed approach outperforms traditional models relying solely on structured data.

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.

Electronic health records (EHR) contain narrative notes that provide extensive details on the medical condition and management of patients. Natural language processing (NLP) of clinical notes can use observed frequencies of clinical terms as predictive features for downstream applications such as clinical decision making and patient trajectory prediction. However, due to the vast number of highly similar and related clinical concepts, a more effective modeling strategy is to represent clinical terms as semantic embeddings via representation learning and use the low dimensional embeddings as feature vectors for predictive modeling. To achieve efficient representation, fine-tuning pretrained language models with biomedical knowledge graphs may generate better embeddings for biomedical terms than those from standard language models alone. These embeddings can effectively discriminate synonymous pairs of from those that are unrelated. However, they often fail to capture different degrees of similarity or relatedness for concepts that are hierarchical in nature. To overcome this limitation, we propose HiPrBERT, a novel biomedical term representation model trained on additionally complied data that contains hierarchical structures for various biomedical terms. We modify an existing contrastive loss function to extract information from these hierarchies. Our numerical experiments demonstrate that HiPrBERT effectively learns the pair-wise distance from hierarchical information, resulting in a substantially more informative embeddings for further biomedical applications

One essential task in information extraction from the medical corpus is drug name recognition. Compared with text sources come from other domains, the medical text is special and has unique characteristics. In addition, the medical text mining poses more challenges, e.g., more unstructured text, the fast growing of new terms addition, a wide range of name variation for the same drug. The mining is even more challenging due to the lack of labeled dataset sources and external knowledge, as well as multiple token representations for a single drug name that is more common in the real application setting. Although many approaches have been proposed to overwhelm the task, some problems remained with poor F-score performance (less than 0.75). This paper presents a new treatment in data representation techniques to overcome some of those challenges. We propose three data representation techniques based on the characteristics of word distribution and word similarities as a result of word embedding training. The first technique is evaluated with the standard NN model, i.e., MLP (Multi-Layer Perceptrons). The second technique involves two deep network classifiers, i.e., DBN (Deep Belief Networks), and SAE (Stacked Denoising Encoders). The third technique represents the sentence as a sequence that is evaluated with a recurrent NN model, i.e., LSTM (Long Short Term Memory). In extracting the drug name entities, the third technique gives the best F-score performance compared to the state of the art, with its average F-score being 0.8645.

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.

We pretrain METAGENE-1, a 7-billion-parameter autoregressive transformer model, which we refer to as a metagenomic foundation model, on a novel corpus of diverse metagenomic DNA and RNA sequences comprising over 1.5 trillion base pairs. This dataset is sourced from a large collection of human wastewater samples, processed and sequenced using deep metagenomic (next-generation) sequencing methods. Unlike genomic models that focus on individual genomes or curated sets of specific species, the aim of METAGENE-1 is to capture the full distribution of genomic information present within this wastewater, to aid in tasks relevant to pandemic monitoring and pathogen detection. We carry out byte-pair encoding (BPE) tokenization on our dataset, tailored for metagenomic sequences, and then pretrain our model. In this paper, we first detail the pretraining dataset, tokenization strategy, and model architecture, highlighting the considerations and design choices that enable the effective modeling of metagenomic data. We then show results of pretraining this model on our metagenomic dataset, providing details about our losses, system metrics, and training stability over the course of pretraining. Finally, we demonstrate the performance of METAGENE-1, which achieves state-of-the-art results on a set of genomic benchmarks and new evaluations focused on human-pathogen detection and genomic sequence embedding, showcasing its potential for public health applications in pandemic monitoring, biosurveillance, and early detection of emerging health threats.

Survey data can contain a high number of features while having a comparatively low quantity of examples. Machine learning models that attempt to predict outcomes from survey data under these conditions can overfit and result in poor generalizability. One remedy to this issue is feature selection, which attempts to select an optimal subset of features to learn upon. A relatively unexplored source of information in the feature selection process is the usage of textual names of features, which may be semantically indicative of which features are relevant to a target outcome. The relationships between feature names and target names can be evaluated using language models (LMs) to produce semantic textual similarity (STS) scores, which can then be used to select features. We examine the performance using STS to select features directly and in the minimal-redundancy-maximal-relevance (mRMR) algorithm. The performance of STS as a feature selection metric is evaluated against preliminary survey data collected as a part of a clinical study on persistent post-surgical pain (PPSP). The results suggest that features selected with STS can result in higher performance models compared to traditional feature selection algorithms.

WHO has declared that more than 2.2 billion people worldwide are suffering from visual disorders, such as media haze, glaucoma, and drusen. At least 1 billion of these cases could have been either prevented or successfully treated, yet they remain unaddressed due to poverty, a lack of specialists, inaccurate ocular fundus diagnoses by ophthalmologists, or the presence of a rare disease. To address this, the research has developed the Hybrid Trio-Network Model Algorithm for accurately diagnosing 12 distinct common and rare eye diseases. This algorithm utilized the RFMiD dataset of 3,200 fundus images and the Binary Relevance Method to detect diseases separately, ensuring expandability and avoiding incorrect correlations. Each detector, incorporating finely tuned hyperparameters to optimize performance, consisted of three feature components: A classical transfer learning CNN model, a two-stage CNN model, and a Siamese Network. The diagnosis was made using features extracted through this Trio-Model with Ensembled Machine Learning algorithms. The proposed model achieved an average accuracy of 97% and an AUC score of 0.96. Compared to past benchmark studies, an increase of over 10% in the F1-score was observed for most diseases. Furthermore, using the Siamese Network, the model successfully made predictions in diseases like optic disc pallor, which past studies failed to predict due to low confidence. This diagnostic tool presents a stable, adaptive, cost-effective, efficient, accessible, and fast solution for globalizing early detection of both common and rare diseases.

In an effort to catalog insect biodiversity, we propose a new large dataset of hand-labelled insect images, the BIOSCAN-Insect Dataset. Each record is taxonomically classified by an expert, and also has associated genetic information including raw nucleotide barcode sequences and assigned barcode index numbers, which are genetically-based proxies for species classification. This paper presents a curated million-image dataset, primarily to train computer-vision models capable of providing image-based taxonomic assessment, however, the dataset also presents compelling characteristics, the study of which would be of interest to the broader machine learning community. Driven by the biological nature inherent to the dataset, a characteristic long-tailed class-imbalance distribution is exhibited. Furthermore, taxonomic labelling is a hierarchical classification scheme, presenting a highly fine-grained classification problem at lower levels. Beyond spurring interest in biodiversity research within the machine learning community, progress on creating an image-based taxonomic classifier will also further the ultimate goal of all BIOSCAN research: to lay the foundation for a comprehensive survey of global biodiversity. This paper introduces the dataset and explores the classification task through the implementation and analysis of a baseline classifier.

With the widespread application of artificial intelligence (AI), particularly deep learning (DL) and vision-based large language models (VLLMs), in skin disease diagnosis, the need for interpretability becomes crucial. However, existing dermatology datasets are limited in their inclusion of concept-level meta-labels, and none offer rich medical descriptions in natural language. This deficiency impedes the advancement of LLM-based methods in dermatological diagnosis. To address this gap and provide a meticulously annotated dermatology dataset with comprehensive natural language descriptions, we introduce SkinCAP: a multi-modal dermatology dataset annotated with rich medical captions. SkinCAP comprises 4,000 images sourced from the Fitzpatrick 17k skin disease dataset and the Diverse Dermatology Images dataset, annotated by board-certified dermatologists to provide extensive medical descriptions and captions. Notably, SkinCAP represents the world's first such dataset and is publicly available at https://huggingface.co/datasets/joshuachou/SkinCAP.

Pre-training (PT) followed by fine-tuning (FT) is an effective method for training neural networks, and has led to significant performance improvements in many domains. PT can incorporate various design choices such as task and data reweighting strategies, augmentation policies, and noise models, all of which can significantly impact the quality of representations learned. The hyperparameters introduced by these strategies therefore must be tuned appropriately. However, setting the values of these hyperparameters is challenging. Most existing methods either struggle to scale to high dimensions, are too slow and memory-intensive, or cannot be directly applied to the two-stage PT and FT learning process. In this work, we propose an efficient, gradient-based algorithm to meta-learn PT hyperparameters. We formalize the PT hyperparameter optimization problem and propose a novel method to obtain PT hyperparameter gradients by combining implicit differentiation and backpropagation through unrolled optimization. We demonstrate that our method improves predictive performance on two real-world domains. First, we optimize high-dimensional task weighting hyperparameters for multitask pre-training on protein-protein interaction graphs and improve AUROC by up to 3.9%. Second, we optimize a data augmentation neural network for self-supervised PT with SimCLR on electrocardiography data and improve AUROC by up to 1.9%.

Medical multiple-choice question answering (MCQA) is particularly difficult. Questions may describe patient symptoms and ask for the correct diagnosis, which requires domain knowledge and complex reasoning. Standard language modeling pretraining alone is not sufficient to achieve the best results. jin2020disease showed that focusing masked language modeling on disease name prediction when using medical encyclopedic paragraphs as input leads to considerable MCQA accuracy improvement. In this work, we show that (1) fine-tuning on generated MCQA dataset outperforms the masked language modeling based objective and (2) correctly masking the cues to the answers is critical for good performance. We release new pretraining datasets and achieve state-of-the-art results on 4 MCQA datasets, notably +5.7\% with base-size model on MedQA-USMLE.

Existing models based on artificial neural networks (ANNs) for sentence classification often do not incorporate the context in which sentences appear, and classify sentences individually. However, traditional sentence classification approaches have been shown to greatly benefit from jointly classifying subsequent sentences, such as with conditional random fields. In this work, we present an ANN architecture that combines the effectiveness of typical ANN models to classify sentences in isolation, with the strength of structured prediction. Our model achieves state-of-the-art results on two different datasets for sequential sentence classification in medical abstracts.

Document clustering is a text mining technique used to provide better document search and browsing in digital libraries or online corpora. A lot of research has been done on biomedical document clustering that is based on using existing ontology. But, associations and co-occurrences of the medical concepts are not well represented by using ontology. In this research, a vector representation of concepts of diseases and similarity measurement between concepts are proposed. They identify the closest concepts of diseases in the context of a corpus. Each document is represented by using the vector space model. A weight scheme is proposed to consider both local content and associations between concepts. A Self-Organizing Map is used as document clustering algorithm. The vector projection and visualization features of SOM enable visualization and analysis of the clusters distributions and relationships on the two dimensional space. The experimental results show that the proposed document clustering framework generates meaningful clusters and facilitate visualization of the clusters based on the concepts of diseases.

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.

Nowadays the medical domain is receiving more and more attention in applications involving Artificial Intelligence. Clinicians have to deal with an enormous amount of unstructured textual data to make a conclusion about patients' health in their everyday life. Argument mining helps to provide a structure to such data by detecting argumentative components in the text and classifying the relations between them. However, as it is the case for many tasks in Natural Language Processing in general and in medical text processing in particular, the large majority of the work on computational argumentation has been done only for English. This is also the case with the only dataset available for argumentation in the medical domain, namely, the annotated medical data of abstracts of Randomized Controlled Trials (RCT) from the MEDLINE database. In order to mitigate the lack of annotated data for other languages, we empirically investigate several strategies to perform argument mining and classification in medical texts for a language for which no annotated data is available. This project shows that automatically translating and project annotations from English to a target language (Spanish) is an effective way to generate annotated data without manual intervention. Furthermore, our experiments demonstrate that the translation and projection approach outperforms zero-shot cross-lingual approaches using a large masked multilingual language model. Finally, we show how the automatically generated data in Spanish can also be used to improve results in the original English evaluation setting.

In healthcare, medical image segmentation is crucial for accurate disease diagnosis and the development of effective treatment strategies. Early detection can significantly aid in managing diseases and potentially prevent their progression. Machine learning, particularly deep convolutional neural networks, has emerged as a promising approach to addressing segmentation challenges. Traditional methods like U-Net use encoding blocks for local representation modeling and decoding blocks to uncover semantic relationships. However, these models often struggle with multi-scale objects exhibiting significant variations in texture and shape, and they frequently fail to capture long-range dependencies in the input data. Transformers designed for sequence-to-sequence predictions have been proposed as alternatives, utilizing global self-attention mechanisms. Yet, they can sometimes lack precise localization due to insufficient granular details. To overcome these limitations, we introduce TransDAE: a novel approach that reimagines the self-attention mechanism to include both spatial and channel-wise associations across the entire feature space, while maintaining computational efficiency. Additionally, TransDAE enhances the skip connection pathway with an inter-scale interaction module, promoting feature reuse and improving localization accuracy. Remarkably, TransDAE outperforms existing state-of-the-art methods on the Synaps multi-organ dataset, even without relying on pre-trained weights.

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.

Objective:Develop and validate an algorithm for analyzing the layout of PDF clinical documents to improve the performance of downstream natural language processing tasks. Materials and Methods: We designed an algorithm to process clinical PDF documents and extract only clinically relevant text. The algorithm consists of several steps: initial text extraction using a PDF parser, followed by classification into categories such as body text, left notes, and footers using a Transformer deep neural network architecture, and finally an aggregation step to compile the lines of a given label in the text. We evaluated the technical performance of the body text extraction algorithm by applying it to a random sample of documents that were annotated. Medical performance was evaluated by examining the extraction of medical concepts of interest from the text in their respective sections. Finally, we tested an end-to-end system on a medical use case of automatic detection of acute infection described in the hospital report. Results:Our algorithm achieved per-line precision, recall, and F1 score of 98.4, 97.0, and 97.7, respectively, for body line extraction. The precision, recall, and F1 score per document for the acute infection detection algorithm were 82.54 (95CI 72.86-91.60), 85.24 (95CI 76.61-93.70), 83.87 (95CI 76, 92-90.08) with exploitation of the results of the advanced body extraction algorithm, respectively. Conclusion:We have developed and validated a system for extracting body text from clinical documents in PDF format by identifying their layout. We were able to demonstrate that this preprocessing allowed us to obtain better performances for a common downstream task, i.e., the extraction of medical concepts in their respective sections, thus proving the interest of this method on a clinical use case.

Colon Cancer is one of the most common types of cancer. The treatment is planned to depend on the grade or stage of cancer. One of the preconditions for grading of colon cancer is to segment the glandular structures of tissues. Manual segmentation method is very time-consuming, and it leads to life risk for the patients. The principal objective of this project is to assist the pathologist to accurate detection of colon cancer. In this paper, the authors have proposed an algorithm for an automatic segmentation of glands in colon histology using local intensity and texture features. Here the dataset images are cropped into patches with different window sizes and taken the intensity of those patches, and also calculated texture-based features. Random forest classifier has been used to classify this patch into different labels. A multilevel random forest technique in a hierarchical way is proposed. This solution is fast, accurate and it is very much applicable in a clinical setup.

Deep neural networks are often applied to medical images to automate the problem of medical diagnosis. However, a more clinically relevant question that practitioners usually face is how to predict the future trajectory of a disease. Current methods for prognosis or disease trajectory forecasting often require domain knowledge and are complicated to apply. In this paper, we formulate the prognosis prediction problem as a one-to-many prediction problem. Inspired by a clinical decision-making process with two agents -- a radiologist and a general practitioner -- we predict prognosis with two transformer-based components that share information with each other. The first transformer in this framework aims to analyze the imaging data, and the second one leverages its internal states as inputs, also fusing them with auxiliary clinical data. The temporal nature of the problem is modeled within the transformer states, allowing us to treat the forecasting problem as a multi-task classification, for which we propose a novel loss. We show the effectiveness of our approach in predicting the development of structural knee osteoarthritis changes and forecasting Alzheimer's disease clinical status directly from raw multi-modal data. The proposed method outperforms multiple state-of-the-art baselines with respect to performance and calibration, both of which are needed for real-world applications. An open-source implementation of our method is made publicly available at https://github.com/Oulu-IMEDS/CLIMATv2.