A General-Purpose Self-Supervised Model for Computational Pathology

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.

Weakly Supervised AI for Efficient Analysis of 3D Pathology Samples

Human tissue and its constituent cells form a microenvironment that is fundamentally three-dimensional (3D). However, the standard-of-care in pathologic diagnosis involves selecting a few two-dimensional (2D) sections for microscopic evaluation, risking sampling bias and misdiagnosis. Diverse methods for capturing 3D tissue morphologies have been developed, but they have yet had little translation to clinical practice; manual and computational evaluations of such large 3D data have so far been impractical and/or unable to provide patient-level clinical insights. Here we present Modality-Agnostic Multiple instance learning for volumetric Block Analysis (MAMBA), a deep-learning-based platform for processing 3D tissue images from diverse imaging modalities and predicting patient outcomes. Archived prostate cancer specimens were imaged with open-top light-sheet microscopy or microcomputed tomography and the resulting 3D datasets were used to train risk-stratification networks based on 5-year biochemical recurrence outcomes via MAMBA. With the 3D block-based approach, MAMBA achieves an area under the receiver operating characteristic curve (AUC) of 0.86 and 0.74, superior to 2D traditional single-slice-based prognostication (AUC of 0.79 and 0.57), suggesting superior prognostication with 3D morphological features. Further analyses reveal that the incorporation of greater tissue volume improves prognostic performance and mitigates risk prediction variability from sampling bias, suggesting the value of capturing larger extents of heterogeneous 3D morphology. With the rapid growth and adoption of 3D spatial biology and pathology techniques by researchers and clinicians, MAMBA provides a general and efficient framework for 3D weakly supervised learning for clinical decision support and can help to reveal novel 3D morphological biomarkers for prognosis and therapeutic response.

Towards a Visual-Language Foundation Model for Computational Pathology

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.

Visual Language Pretrained Multiple Instance Zero-Shot Transfer for Histopathology Images

Contrastive visual language pretraining has emerged as a powerful method for either training new language-aware image encoders or augmenting existing pretrained models with zero-shot visual recognition capabilities. However, existing works typically train on large datasets of image-text pairs and have been designed to perform downstream tasks involving only small to medium sized-images, neither of which are applicable to the emerging field of computational pathology where there are limited publicly available paired image-text datasets and each image can span up to 100,000 x 100,000 pixels. In this paper we present MI-Zero, a simple and intuitive framework for unleashing the zero-shot transfer capabilities of contrastively aligned image and text models on gigapixel histopathology whole slide images, enabling multiple downstream diagnostic tasks to be carried out by pretrained encoders without requiring any additional labels. MI-Zero reformulates zero-shot transfer under the framework of multiple instance learning to overcome the computational challenge of inference on extremely large images. We used over 550k pathology reports and other available in-domain text corpora to pre-train our text encoder. By effectively leveraging strong pre-trained encoders, our best model pretrained on over 33k histopathology image-caption pairs achieves an average median zero-shot accuracy of 70.2% across three different real-world cancer subtyping tasks. Our code is available at: https://github.com/mahmoodlab/MI-Zero.

A Review of Vision-Language Models and their Performance on the Hateful Memes Challenge

Moderation of social media content is currently a highly manual task, yet there is too much content posted daily to do so effectively. With the advent of a number of multimodal models, there is the potential to reduce the amount of manual labor for this task. In this work, we aim to explore different models and determine what is most effective for the Hateful Memes Challenge, a challenge by Meta designed to further machine learning research in content moderation. Specifically, we explore the differences between early fusion and late fusion models in classifying multimodal memes containing text and images. We first implement a baseline using unimodal models for text and images separately using BERT and ResNet-152, respectively. The outputs from these unimodal models were then concatenated together to create a late fusion model. In terms of early fusion models, we implement ConcatBERT, VisualBERT, ViLT, CLIP, and BridgeTower. It was found that late fusion performed significantly worse than early fusion models, with the best performing model being CLIP which achieved an AUROC of 70.06. The code for this work is available at https://github.com/bzhao18/CS-7643-Project.

A Robot for Nondestructive Assay of Holdup Deposits in Gaseous Diffusion Piping

Miles of contaminated pipe must be measured, foot by foot, as part of the decommissioning effort at deactivated gaseous diffusion enrichment facilities. The current method requires cutting away asbestos-lined thermal enclosures and performing repeated, elevated operations to manually measure pipe from the outside. The RadPiper robot, part of the Pipe Crawling Activity Measurement System (PCAMS) developed by Carnegie Mellon University and commissioned for use at the DOE Portsmouth Gaseous Diffusion Enrichment Facility, automatically measures U-235 in pipes from the inside. This improves certainty, increases safety, and greatly reduces measurement time. The heart of the RadPiper robot is a sodium iodide scintillation detector in an innovative disc-collimated assembly. By measuring from inside pipes, the robot significantly increases its count rate relative to external through-pipe measurements. The robot also provides imagery, models interior pipe geometry, and precisely measures distance in order to localize radiation measurements. Data collected by this system provides insight into pipe interiors that is simply not possible from exterior measurements, all while keeping operators safer. This paper describes the technical details of the PCAMS RadPiper robot. Key features for this robot include precision distance measurement, in-pipe obstacle detection, ability to transform for two pipe sizes, and robustness in autonomous operation. Test results demonstrating the robot's functionality are presented, including deployment tolerance tests, safeguarding tests, and localization tests. Integrated robot tests are also shown.

WALL-E: An Efficient Reinforcement Learning Research Framework

There are two halves to RL systems: experience collection time and policy learning time. For a large number of samples in rollouts, experience collection time is the major bottleneck. Thus, it is necessary to speed up the rollout generation time with multi-process architecture support. Our work, dubbed WALL-E, utilizes multiple rollout samplers running in parallel to rapidly generate experience. Due to our parallel samplers, we experience not only faster convergence times, but also higher average reward thresholds. For example, on the MuJoCo HalfCheetah-v2 task, with $N = 10$ parallel sampler processes, we are able to achieve much higher average return than those from using only a single process architecture.