Slide-Level Prompt Learning with Vision Language Models for Few-Shot Multiple Instance Learning in Histopathology

In this paper, we address the challenge of few-shot classification in histopathology whole slide images (WSIs) by utilizing foundational vision-language models (VLMs) and slide-level prompt learning. Given the gigapixel scale of WSIs, conventional multiple instance learning (MIL) methods rely on aggregation functions to derive slide-level (bag-level) predictions from patch representations, which require extensive bag-level labels for training. In contrast, VLM-based approaches excel at aligning visual embeddings of patches with candidate class text prompts but lack essential pathological prior knowledge. Our method distinguishes itself by utilizing pathological prior knowledge from language models to identify crucial local tissue types (patches) for WSI classification, integrating this within a VLM-based MIL framework. Our approach effectively aligns patch images with tissue types, and we fine-tune our model via prompt learning using only a few labeled WSIs per category. Experimentation on real-world pathological WSI datasets and ablation studies highlight our method's superior performance over existing MIL- and VLM-based methods in few-shot WSI classification tasks. Our code is publicly available at https://github.com/LTS5/SLIP.

Gene42: Long-Range Genomic Foundation Model With Dense Attention

We introduce Gene42, a novel family of Genomic Foundation Models (GFMs) designed to manage context lengths of up to 192,000 base pairs (bp) at a single-nucleotide resolution. Gene42 models utilize a decoder-only (LLaMA-style) architecture with a dense self-attention mechanism. Initially trained on fixed-length sequences of 4,096 bp, our models underwent continuous pretraining to extend the context length to 192,000 bp. This iterative extension allowed for the comprehensive processing of large-scale genomic data and the capture of intricate patterns and dependencies within the human genome. Gene42 is the first dense attention model capable of handling such extensive long context lengths in genomics, challenging state-space models that often rely on convolutional operators among other mechanisms. Our pretrained models exhibit notably low perplexity values and high reconstruction accuracy, highlighting their strong ability to model genomic data. Extensive experiments on various genomic benchmarks have demonstrated state-of-the-art performance across multiple tasks, including biotype classification, regulatory region identification, chromatin profiling prediction, variant pathogenicity prediction, and species classification. The models are publicly available at huggingface.co/inceptionai.

MedUnA: Language guided Unsupervised Adaptation of Vision-Language Models for Medical Image Classification

In medical image classification, supervised learning is challenging due to the lack of labeled medical images. Contrary to the traditional \textit{modus operandi} of pre-training followed by fine-tuning, this work leverages the visual-textual alignment within Vision-Language models (\texttt{VLMs}) to facilitate the unsupervised learning. Specifically, we propose \underline{Med}ical \underline{Un}supervised \underline{A}daptation (\texttt{MedUnA}), constituting two-stage training: Adapter Pre-training, and Unsupervised Learning. In the first stage, we use descriptions generated by a Large Language Model (\texttt{LLM}) corresponding to class labels, which are passed through the text encoder \texttt{BioBERT}. The resulting text embeddings are then aligned with the class labels by training a lightweight \texttt{adapter}. We choose \texttt{\texttt{LLMs}} because of their capability to generate detailed, contextually relevant descriptions to obtain enhanced text embeddings. In the second stage, the trained \texttt{adapter} is integrated with the visual encoder of \texttt{MedCLIP}. This stage employs a contrastive entropy-based loss and prompt tuning to align visual embeddings. We incorporate self-entropy minimization into the overall training objective to ensure more confident embeddings, which are crucial for effective unsupervised learning and alignment. We evaluate the performance of \texttt{MedUnA} on three different kinds of data modalities - chest X-rays, eye fundus and skin lesion images. The results demonstrate significant accuracy gain on average compared to the baselines across different datasets, highlighting the efficacy of our approach.

Characterizing Continual Learning Scenarios and Strategies for Audio Analysis

Audio analysis is useful in many application scenarios. The state-of-the-art audio analysis approaches assume that the data distribution at training and deployment time will be the same. However, due to various real-life environmental factors, the data may encounter drift in its distribution or can encounter new classes in the late future. Thus, a one-time trained model might not perform adequately. In this paper, we characterize continual learning (CL) approaches in audio analysis. In this paper, we characterize continual learning (CL) approaches, intended to tackle catastrophic forgetting arising due to drifts. As there is no CL dataset for audio analysis, we use DCASE 2020 to 2023 datasets to create various CL scenarios for audio-based monitoring tasks. We have investigated the following CL and non-CL approaches: EWC, LwF, SI, GEM, A-GEM, GDumb, Replay, Naive, cumulative, and joint training. The study is very beneficial for researchers and practitioners working in the area of audio analysis for developing adaptive models. We observed that Replay achieved better results than other methods in the DCASE challenge data. It achieved an accuracy of 70.12% for the domain incremental scenario and an accuracy of 96.98% for the class incremental scenario.

Envisioning MedCLIP: A Deep Dive into Explainability for Medical Vision-Language Models

Explaining Deep Learning models is becoming increasingly important in the face of daily emerging multimodal models, particularly in safety-critical domains like medical imaging. However, the lack of detailed investigations into the performance of explainability methods on these models is widening the gap between their development and safe deployment. In this work, we analyze the performance of various explainable AI methods on a vision-language model, MedCLIP, to demystify its inner workings. We also provide a simple methodology to overcome the shortcomings of these methods. Our work offers a different new perspective on the explainability of a recent well-known VLM in the medical domain and our assessment method is generalizable to other current and possible future VLMs.

XReal: Realistic Anatomy and Pathology-Aware X-ray Generation via Controllable Diffusion Model

Large-scale generative models have demonstrated impressive capacity in producing visually compelling images, with increasing applications in medical imaging. However, they continue to grapple with the challenge of image hallucination and the generation of anatomically inaccurate outputs. These limitations are mainly due to the sole reliance on textual inputs and lack of spatial control over the generated images, hindering the potential usefulness of such models in real-life settings. We present XReal, a novel controllable diffusion model for generating realistic chest X-ray images through precise anatomy and pathology location control. Our lightweight method can seamlessly integrate spatial control in a pre-trained text-to-image diffusion model without fine-tuning, retaining its existing knowledge while enhancing its generation capabilities. XReal outperforms state-of-the-art x-ray diffusion models in quantitative and qualitative metrics while showing 13% and 10% anatomy and pathology realism gain, respectively, based on the expert radiologist evaluation. Our model holds promise for advancing generative models in medical imaging, offering greater precision and adaptability while inviting further exploration in this evolving field. A large synthetically generated data with annotations and code is publicly available at https://github.com/BioMedIA-MBZUAI/XReal.

Prompt-driven Latent Domain Generalization for Medical Image Classification

Deep learning models for medical image analysis easily suffer from distribution shifts caused by dataset artifacts bias, camera variations, differences in the imaging station, etc., leading to unreliable diagnoses in real-world clinical settings. Domain generalization (DG) methods, which aim to train models on multiple domains to perform well on unseen domains, offer a promising direction to solve the problem. However, existing DG methods assume domain labels of each image are available and accurate, which is typically feasible for only a limited number of medical datasets. To address these challenges, we propose a novel DG framework for medical image classification without relying on domain labels, called Prompt-driven Latent Domain Generalization (PLDG). PLDG consists of unsupervised domain discovery and prompt learning. This framework first discovers pseudo domain labels by clustering the bias-associated style features, then leverages collaborative domain prompts to guide a Vision Transformer to learn knowledge from discovered diverse domains. To facilitate cross-domain knowledge learning between different prompts, we introduce a domain prompt generator that enables knowledge sharing between domain prompts and a shared prompt. A domain mixup strategy is additionally employed for more flexible decision margins and mitigates the risk of incorrect domain assignments. Extensive experiments on three medical image classification tasks and one debiasing task demonstrate that our method can achieve comparable or even superior performance than conventional DG algorithms without relying on domain labels. Our code will be publicly available upon the paper is accepted.

Domain Generalization by Learning from Privileged Medical Imaging Information

Learning the ability to generalize knowledge between similar contexts is particularly important in medical imaging as data distributions can shift substantially from one hospital to another, or even from one machine to another. To strengthen generalization, most state-of-the-art techniques inject knowledge of the data distribution shifts by enforcing constraints on learned features or regularizing parameters. We offer an alternative approach: Learning from Privileged Medical Imaging Information (LPMII). We show that using some privileged information such as tumor shape or location leads to stronger domain generalization ability than current state-of-the-art techniques. This paper demonstrates that by using privileged information to predict the severity of intra-layer retinal fluid in optical coherence tomography scans, the classification accuracy of a deep learning model operating on out-of-distribution data improves from $0.911$ to $0.934$. This paper provides a strong starting point for using privileged information in other medical problems requiring generalization.

AMAE: Adaptation of Pre-Trained Masked Autoencoder for Dual-Distribution Anomaly Detection in Chest X-Rays

Unsupervised anomaly detection in medical images such as chest radiographs is stepping into the spotlight as it mitigates the scarcity of the labor-intensive and costly expert annotation of anomaly data. However, nearly all existing methods are formulated as a one-class classification trained only on representations from the normal class and discard a potentially significant portion of the unlabeled data. This paper focuses on a more practical setting, dual distribution anomaly detection for chest X-rays, using the entire training data, including both normal and unlabeled images. Inspired by a modern self-supervised vision transformer model trained using partial image inputs to reconstruct missing image regions -- we propose AMAE, a two-stage algorithm for adaptation of the pre-trained masked autoencoder (MAE). Starting from MAE initialization, AMAE first creates synthetic anomalies from only normal training images and trains a lightweight classifier on frozen transformer features. Subsequently, we propose an adaptation strategy to leverage unlabeled images containing anomalies. The adaptation scheme is accomplished by assigning pseudo-labels to unlabeled images and using two separate MAE based modules to model the normative and anomalous distributions of pseudo-labeled images. The effectiveness of the proposed adaptation strategy is evaluated with different anomaly ratios in an unlabeled training set. AMAE leads to consistent performance gains over competing self-supervised and dual distribution anomaly detection methods, setting the new state-of-the-art on three public chest X-ray benchmarks: RSNA, NIH-CXR, and VinDr-CXR.

TPMIL: Trainable Prototype Enhanced Multiple Instance Learning for Whole Slide Image Classification

Digital pathology based on whole slide images (WSIs) plays a key role in cancer diagnosis and clinical practice. Due to the high resolution of the WSI and the unavailability of patch-level annotations, WSI classification is usually formulated as a weakly supervised problem, which relies on multiple instance learning (MIL) based on patches of a WSI. In this paper, we aim to learn an optimal patch-level feature space by integrating prototype learning with MIL. To this end, we develop a Trainable Prototype enhanced deep MIL (TPMIL) framework for weakly supervised WSI classification. In contrast to the conventional methods which rely on a certain number of selected patches for feature space refinement, we softly cluster all the instances by allocating them to their corresponding prototypes. Additionally, our method is able to reveal the correlations between different tumor subtypes through distances between corresponding trained prototypes. More importantly, TPMIL also enables to provide a more accurate interpretability based on the distance of the instances from the trained prototypes which serves as an alternative to the conventional attention score-based interpretability. We test our method on two WSI datasets and it achieves a new SOTA. GitHub repository: https://github.com/LitaoYang-Jet/TPMIL