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AI-based diagnoses have demonstrated dermatologist-level performance in classifying skin cancer. However, such systems are prone to under-performing when tested on data from minority groups that lack sufficient representation in the training sets. Although data collection and annotation offer the best means for promoting minority groups, these processes are costly and time-consuming. Prior works have suggested that data from majority groups may serve as a valuable information source to supplement the training of diagnosis tools for minority groups. In this work, we propose an effective diffusion-based augmentation framework that maximizes the use of rich information from majority groups to benefit minority groups. Using groups with different skin types as a case study, our results show that the proposed framework can generate synthetic images that improve diagnostic results for the minority groups, even when there is little or no reference data from these target groups. The practical value of our work is evident in medical imaging analysis, where under-diagnosis persists as a problem for certain groups due to insufficient representation.

Generative models for 3D drug design have gained prominence recently for their potential to design ligands directly within protein pockets. Current approaches, however, often suffer from very slow sampling times or generate molecules with poor chemical validity. Addressing these limitations, we propose Semla, a scalable E(3)-equivariant message passing architecture. We further introduce a molecular generation model, SemlaFlow, which is trained using flow matching along with scale optimal transport, a novel extension of equivariant optimal transport. Our model produces state-of-the-art results on benchmark datasets with just 100 sampling steps. Crucially, SemlaFlow samples high quality molecules with as few as 20 steps, corresponding to a two order-of-magnitude speed-up compared to state-of-the-art, without sacrificing performance. Furthermore, we highlight limitations of current evaluation methods for 3D generation and propose new benchmark metrics for unconditional molecular generators. Finally, using these new metrics, we compare our model's ability to generate high quality samples against current approaches and further demonstrate SemlaFlow's strong performance.

Integration of speech into healthcare has intensified privacy concerns due to its potential as a non-invasive biomarker containing individual biometric information. In response, speaker anonymization aims to conceal personally identifiable information while retaining crucial linguistic content. However, the application of anonymization techniques to pathological speech, a critical area where privacy is especially vital, has not been extensively examined. This study investigates anonymization's impact on pathological speech across over 2,700 speakers from multiple German institutions, focusing on privacy, pathological utility, and demographic fairness. We explore both deep-learning-based and signal processing-based anonymization methods, and document substantial privacy improvements across disorders-evidenced by equal error rate increases up to 1933%, with minimal overall impact on utility. Specific disorders such as Dysarthria, Dysphonia, and Cleft Lip and Palate experienced minimal utility changes, while Dysglossia showed slight improvements. Our findings underscore that the impact of anonymization varies substantially across different disorders. This necessitates disorder-specific anonymization strategies to optimally balance privacy with diagnostic utility. Additionally, our fairness analysis revealed consistent anonymization effects across most of the demographics. This study demonstrates the effectiveness of anonymization in pathological speech for enhancing privacy, while also highlighting the importance of customized and disorder-specific approaches to account for inversion attacks.

Retinal blood vessel segmentation can extract clinically relevant information from fundus images. As manual tracing is cumbersome, algorithms based on Convolution Neural Networks have been developed. Such studies have used small publicly available datasets for training and measuring performance, running the risk of overfitting. Here, we provide a rigorous benchmark for various architectural and training choices commonly used in the literature on the largest dataset published to date. We train and evaluate five published models on the publicly available FIVES fundus image dataset, which exceeds previous ones in size and quality and which contains also images from common ophthalmological conditions (diabetic retinopathy, age-related macular degeneration, glaucoma). We compare the performance of different model architectures across different loss functions, levels of image qualitiy and ophthalmological conditions and assess their ability to perform well in the face of disease-induced domain shifts. Given sufficient training data, basic architectures such as U-Net perform just as well as more advanced ones, and transfer across disease-induced domain shifts typically works well for most architectures. However, we find that image quality is a key factor determining segmentation outcomes. When optimizing for segmentation performance, investing into a well curated dataset to train a standard architecture yields better results than tuning a sophisticated architecture on a smaller dataset or one with lower image quality. We distilled the utility of architectural advances in terms of their clinical relevance therefore providing practical guidance for model choices depending on the circumstances of the clinical setting

The objective of this research is to introduce a network specialized in predicting drugs that can be repurposed by investigating real-world evidence sources, such as clinical trials and biomedical literature. Specifically, it aims to generate drug combination therapies for complex diseases (e.g., cancer, Alzheimer's). We present a multilayered network medicine approach, empowered by a highly configured ChatGPT prompt engineering system, which is constructed on the fly to extract drug mentions in clinical trials. Additionally, we introduce a novel algorithm that connects real-world evidence with disease-specific signaling pathways (e.g., KEGG database). This sheds light on the repurposability of drugs if they are found to bind with one or more protein constituents of a signaling pathway. To demonstrate, we instantiated the framework for breast cancer and found that, out of 46 breast cancer signaling pathways, the framework identified 38 pathways that were covered by at least two drugs. This evidence signals the potential for combining those drugs. Specifically, the most covered signaling pathway, ID hsa:2064, was covered by 108 drugs, some of which can be combined. Conversely, the signaling pathway ID hsa:1499 was covered by only two drugs, indicating a significant gap for further research. Our network medicine framework, empowered by GenAI, shows promise in identifying drug combinations with a high degree of specificity, knowing the exact signaling pathways and proteins that serve as targets. It is noteworthy that ChatGPT successfully accelerated the process of identifying drug mentions in clinical trials, though further investigations are required to determine the relationships among the drug mentions.

Personalized medicine based on medical images, including predicting future individualized clinical disease progression and treatment response, would have an enormous impact on healthcare and drug development, particularly for diseases (e.g. multiple sclerosis (MS)) with long term, complex, heterogeneous evolutions and no cure. In this work, we present the first stochastic causal temporal framework to model the continuous temporal evolution of disease progression via Neural Stochastic Differential Equations (NSDE). The proposed causal inference model takes as input the patient's high dimensional images (MRI) and tabular data, and predicts both factual and counterfactual progression trajectories on different treatments in latent space. The NSDE permits the estimation of high-confidence personalized trajectories and treatment effects. Extensive experiments were performed on a large, multi-centre, proprietary dataset of patient 3D MRI and clinical data acquired during several randomized clinical trials for MS treatments. Our results present the first successful uncertainty-based causal Deep Learning (DL) model to: (a) accurately predict future patient MS disability evolution (e.g. EDSS) and treatment effects leveraging baseline MRI, and (b) permit the discovery of subgroups of patients for which the model has high confidence in their response to treatment even in clinical trials which did not reach their clinical endpoints.

Recent strides in automatic speech recognition (ASR) have accelerated their application in the medical domain where their performance on accented medical named entities (NE) such as drug names, diagnoses, and lab results, is largely unknown. We rigorously evaluate multiple ASR models on a clinical English dataset of 93 African accents. Our analysis reveals that despite some models achieving low overall word error rates (WER), errors in clinical entities are higher, potentially posing substantial risks to patient safety. To empirically demonstrate this, we extract clinical entities from transcripts, develop a novel algorithm to align ASR predictions with these entities, and compute medical NE Recall, medical WER, and character error rate. Our results show that fine-tuning on accented clinical speech improves medical WER by a wide margin (25-34 % relative), improving their practical applicability in healthcare environments.

H&E-to-IHC stain translation techniques offer a promising solution for precise cancer diagnosis, especially in low-resource regions where there is a shortage of health professionals and limited access to expensive equipment. Considering the pixel-level misalignment of H&E-IHC image pairs, current research explores the pathological consistency between patches from the same positions of the image pair. However, most of them overemphasize the correspondence between domains or patches, overlooking the side information provided by the non-corresponding objects. In this paper, we propose a Mix-Domain Contrastive Learning (MDCL) method to leverage the supervision information in unpaired H&E-to-IHC stain translation. Specifically, the proposed MDCL method aggregates the inter-domain and intra-domain pathology information by estimating the correlation between the anchor patch and all the patches from the matching images, encouraging the network to learn additional contrastive knowledge from mixed domains. With the mix-domain pathology information aggregation, MDCL enhances the pathological consistency between the corresponding patches and the component discrepancy of the patches from the different positions of the generated IHC image. Extensive experiments on two H&E-to-IHC stain translation datasets, namely MIST and BCI, demonstrate that the proposed method achieves state-of-the-art performance across multiple metrics.

Bayesian predictive probabilities are commonly used for interim monitoring of clinical trials through efficacy and futility stopping rules. Despite their usefulness, calculation of predictive probabilities, particularly in pre-experiment trial simulation, can be a significant challenge. We introduce an approximation for computing predictive probabilities using either a p-value or a posterior probability that significantly reduces this burden. We show the approximation has a high degree of concordance with standard Monte Carlo imputation methods for computing predictive probabilities, and present five simulation studies comparing the approximation to the full predictive probability for a range of primary analysis strategies: dichotomous, time-to-event, and ordinal endpoints, as well as historical borrowing and longitudinal modeling. We find that this faster method of predictive probability approximation works well in all five applications, thus significantly reducing the computational burden of trial simulation, allowing more virtual trials to be simulated to achieve greater precision in estimating trial operating characteristics.

Understanding causality helps to structure interventions to achieve specific goals and enables predictions under interventions. With the growing importance of learning causal relationships, causal discovery tasks have transitioned from using traditional methods to infer potential causal structures from observational data to the field of pattern recognition involved in deep learning. The rapid accumulation of massive data promotes the emergence of causal search methods with brilliant scalability. Existing summaries of causal discovery methods mainly focus on traditional methods based on constraints, scores and FCMs, there is a lack of perfect sorting and elaboration for deep learning-based methods, also lacking some considers and exploration of causal discovery methods from the perspective of variable paradigms. Therefore, we divide the possible causal discovery tasks into three types according to the variable paradigm and give the definitions of the three tasks respectively, define and instantiate the relevant datasets for each task and the final causal model constructed at the same time, then reviews the main existing causal discovery methods for different tasks. Finally, we propose some roadmaps from different perspectives for the current research gaps in the field of causal discovery and point out future research directions.