Yogesh Kumar

Yogesh Kumar, Pekka Marttinen

We introduce eCLIP, an enhanced version of the CLIP model that integrates expert annotations in the form of radiologist eye-gaze heatmaps. It tackles key challenges in contrastive multi-modal medical imaging analysis, notably data scarcity and the "modality gap" -- a significant disparity between image and text embeddings that diminishes the quality of representations and hampers cross-modal interoperability. eCLIP integrates a heatmap processor and leverages mixup augmentation to efficiently utilize the scarce expert annotations, thus boosting the model's learning effectiveness. eCLIP is designed to be generally applicable to any variant of CLIP without requiring any modifications of the core architecture. Through detailed evaluations across several tasks, including zero-shot inference, linear probing, cross-modal retrieval, and Retrieval Augmented Generation (RAG) of radiology reports using a frozen Large Language Model, eCLIP showcases consistent improvements in embedding quality. The outcomes reveal enhanced alignment and uniformity, affirming eCLIP's capability to harness high-quality annotations for enriched multi-modal analysis in the medical imaging domain.

Tianyu Cui, Yogesh Kumar, Pekka Marttinen et al.

Similarity metrics such as representational similarity analysis (RSA) and centered kernel alignment (CKA) have been used to compare layer-wise representations between neural networks. However, these metrics are confounded by the population structure of data items in the input space, leading to spuriously high similarity for even completely random neural networks and inconsistent domain relations in transfer learning. We introduce a simple and generally applicable fix to adjust for the confounder with covariate adjustment regression, which retains the intuitive invariance properties of the original similarity measures. We show that deconfounding the similarity metrics increases the resolution of detecting semantically similar neural networks. Moreover, in real-world applications, deconfounding improves the consistency of representation similarities with domain similarities in transfer learning, and increases correlation with out-of-distribution accuracy.

Yogesh Kumar, Alexander Ilin, Henri Salo et al.

Despite the proven effectiveness of Transformer neural networks across multiple domains, their performance with Electronic Health Records (EHR) can be nuanced. The unique, multidimensional sequential nature of EHR data can sometimes make even simple linear models with carefully engineered features more competitive. Thus, the advantages of Transformers, such as efficient transfer learning and improved scalability are not always fully exploited in EHR applications. Addressing these challenges, we introduce SANSformer, an attention-free sequential model designed with specific inductive biases to cater for the unique characteristics of EHR data. In this work, we aim to forecast the demand for healthcare services, by predicting the number of patient visits to healthcare facilities. The challenge amplifies when dealing with divergent patient subgroups, like those with rare diseases, which are characterized by unique health trajectories and are typically smaller in size. To address this, we employ a self-supervised pretraining strategy, Generative Summary Pretraining (GSP), which predicts future summary statistics based on past health records of a patient. Our models are pretrained on a health registry of nearly one million patients, then fine-tuned for specific subgroup prediction tasks, showcasing the potential to handle the multifaceted nature of EHR data. In evaluation, SANSformer consistently surpasses robust EHR baselines, with our GSP pretraining method notably amplifying model performance, particularly within smaller patient subgroups. Our results illuminate the promising potential of tailored attention-free models and self-supervised pretraining in refining healthcare utilization predictions across various patient demographics.