Anand Sampat

Dinkar Juyal, Siddhant Shingi, Syed Ashar Javed et al.

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.

Tan H. Nguyen, Dinkar Juyal, Jin Li et al.

Differences in staining and imaging procedures can cause significant color variations in histopathology images, leading to poor generalization when deploying deep-learning models trained from a different data source. Various color augmentation methods have been proposed to generate synthetic images during training to make models more robust, eliminating the need for stain normalization during test time. Many color augmentation methods leverage domain labels to generate synthetic images. This approach causes three significant challenges to scaling such a model. Firstly, incorporating data from a new domain into deep-learning models trained on existing domain labels is not straightforward. Secondly, dependency on domain labels prevents the use of pathology images without domain labels to improve model performance. Finally, implementation of these methods becomes complicated when multiple domain labels (e.g., patient identification, medical center, etc) are associated with a single image. We introduce ContriMix, a novel domain label free stain color augmentation method based on DRIT++, a style-transfer method. Contrimix leverages sample stain color variation within a training minibatch and random mixing to extract content and attribute information from pathology images. This information can be used by a trained ContriMix model to create synthetic images to improve the performance of existing classifiers. ContriMix outperforms competing methods on the Camelyon17-WILDS dataset. Its performance is consistent across different slides in the test set while being robust to the color variation from rare substances in pathology images. We make our code and trained ContriMix models available for research use. The code for ContriMix can be found at https://gitlab.com/huutan86/contrimix

Jin Li, Deepta Rajan, Chintan Shah et al.

Histopathology images are gigapixel-sized and include features and information at different resolutions. Collecting annotations in histopathology requires highly specialized pathologists, making it expensive and time-consuming. Self-training can alleviate annotation constraints by learning from both labeled and unlabeled data, reducing the amount of annotations required from pathologists. We study the design of teacher-student self-training systems for Non-alcoholic Steatohepatitis (NASH) using clinical histopathology datasets with limited annotations. We evaluate the models on in-distribution and out-of-distribution test data under clinical data shifts. We demonstrate that through self-training, the best student model statistically outperforms the teacher with a $3\%$ absolute difference on the macro F1 score. The best student model also approaches the performance of a fully supervised model trained with twice as many annotations.

Swayambhoo Jain, Ravi Raju, Bo Li et al.

Large Language Models (LLMs) have achieved remarkable advancements, but their monolithic nature presents challenges in terms of scalability, cost, and customization. This paper introduces the Composition of Experts (CoE), a modular compound AI system leveraging multiple expert LLMs. CoE leverages a router to dynamically select the most appropriate expert for a given input, enabling efficient utilization of resources and improved performance. We formulate the general problem of training a CoE and discuss inherent complexities associated with it. We propose a two-step routing approach to address these complexities that first uses a router to classify the input into distinct categories followed by a category-to-expert mapping to obtain desired experts. CoE offers a flexible and cost-effective solution to build compound AI systems. Our empirical evaluation demonstrates the effectiveness of CoE in achieving superior performance with reduced computational overhead. Given that CoE comprises of many expert LLMs it has unique system requirements for cost-effective serving. We present an efficient implementation of CoE leveraging SambaNova SN40L RDUs unique three-tiered memory architecture. CoEs obtained using open weight LLMs Qwen/Qwen2-7B-Instruct, google/gemma-2-9b-it, google/gemma-2-27b-it, meta-llama/Llama-3.1-70B-Instruct and Qwen/Qwen2-72B-Instruct achieve a score of $59.4$ with merely $31$ billion average active parameters on Arena-Hard and a score of $9.06$ with $54$ billion average active parameters on MT-Bench.

Sai Chowdary Gullapally, Yibo Zhang, Nitin Kumar Mittal et al.

Machine learning algorithms have the potential to improve patient outcomes in digital pathology. However, generalization of these tools is currently limited by sensitivity to variations in tissue preparation, staining procedures and scanning equipment that lead to domain shift in digitized slides. To overcome this limitation and improve model generalization, we studied the effectiveness of two Synthetic DOmain-Targeted Augmentation (S-DOTA) methods, namely CycleGAN-enabled Scanner Transform (ST) and targeted Stain Vector Augmentation (SVA), and compared them against the International Color Consortium (ICC) profile-based color calibration (ICC Cal) method and a baseline method using traditional brightness, color and noise augmentations. We evaluated the ability of these techniques to improve model generalization to various tasks and settings: four models, two model types (tissue segmentation and cell classification), two loss functions, six labs, six scanners, and three indications (hepatocellular carcinoma (HCC), nonalcoholic steatohepatitis (NASH), prostate adenocarcinoma). We compared these methods based on the macro-averaged F1 scores on in-distribution (ID) and out-of-distribution (OOD) test sets across multiple domains, and found that S-DOTA methods (i.e., ST and SVA) led to significant improvements over ICC Cal and baseline on OOD data while maintaining comparable performance on ID data. Thus, we demonstrate that S-DOTA may help address generalization due to domain shift in real world applications.