TuneVLSeg: Prompt Tuning Benchmark for Vision-Language Segmentation Models

Vision-Language Models (VLMs) have shown impressive performance in vision tasks, but adapting them to new domains often requires expensive fine-tuning. Prompt tuning techniques, including textual, visual, and multimodal prompting, offer efficient alternatives by leveraging learnable prompts. However, their application to Vision-Language Segmentation Models (VLSMs) and evaluation under significant domain shifts remain unexplored. This work presents an open-source benchmarking framework, TuneVLSeg, to integrate various unimodal and multimodal prompt tuning techniques into VLSMs, making prompt tuning usable for downstream segmentation datasets with any number of classes. TuneVLSeg includes $6$ prompt tuning strategies on various prompt depths used in $2$ VLSMs totaling of $8$ different combinations. We test various prompt tuning on $8$ diverse medical datasets, including $3$ radiology datasets (breast tumor, echocardiograph, chest X-ray pathologies) and $5$ non-radiology datasets (polyp, ulcer, skin cancer), and two natural domain segmentation datasets. Our study found that textual prompt tuning struggles under significant domain shifts, from natural-domain images to medical data. Furthermore, visual prompt tuning, with fewer hyperparameters than multimodal prompt tuning, often achieves performance competitive to multimodal approaches, making it a valuable first attempt. Our work advances the understanding and applicability of different prompt-tuning techniques for robust domain-specific segmentation. The source code is available at https://github.com/naamiinepal/tunevlseg.

VLSM-Adapter: Finetuning Vision-Language Segmentation Efficiently with Lightweight Blocks

Foundation Vision-Language Models (VLMs) trained using large-scale open-domain images and text pairs have recently been adapted to develop Vision-Language Segmentation Models (VLSMs) that allow providing text prompts during inference to guide image segmentation. If robust and powerful VLSMs can be built for medical images, it could aid medical professionals in many clinical tasks where they must spend substantial time delineating the target structure of interest. VLSMs for medical images resort to fine-tuning base VLM or VLSM pretrained on open-domain natural image datasets due to fewer annotated medical image datasets; this fine-tuning is resource-consuming and expensive as it usually requires updating all or a significant fraction of the pretrained parameters. Recently, lightweight blocks called adapters have been proposed in VLMs that keep the pretrained model frozen and only train adapters during fine-tuning, substantially reducing the computing resources required. We introduce a novel adapter, VLSM-Adapter, that can fine-tune pretrained vision-language segmentation models using transformer encoders. Our experiments in widely used CLIP-based segmentation models show that with only 3 million trainable parameters, the VLSM-Adapter outperforms state-of-the-art and is comparable to the upper bound end-to-end fine-tuning. The source code is available at: https://github.com/naamiinepal/vlsm-adapter.

AI-Assisted Cervical Cancer Screening

Visual Inspection with Acetic Acid (VIA) remains the most feasible cervical cancer screening test in resource-constrained settings of low- and middle-income countries (LMICs), which are often performed screening camps or primary/community health centers by nurses instead of the preferred but unavailable expert Gynecologist. To address the highly subjective nature of the test, various handheld devices integrating cameras or smartphones have been recently explored to capture cervical images during VIA and aid decision-making via telemedicine or AI models. Most studies proposing AI models retrospectively use a relatively small number of already collected images from specific devices, digital cameras, or smartphones; the challenges and protocol for quality image acquisition during VIA in resource-constrained camp settings, challenges in getting gold standard, data imbalance, etc. are often overlooked. We present a novel approach and describe the end-to-end design process to build a robust smartphone-based AI-assisted system that does not require buying a separate integrated device: the proposed protocol for quality image acquisition in resource-constrained settings, dataset collected from 1,430 women during VIA performed by nurses in screening camps, preprocessing pipeline, and training and evaluation of a deep-learning-based classification model aimed to identify (pre)cancerous lesions. Our work shows that the readily available smartphones and a suitable protocol can capture the cervix images with the required details for the VIA test well; the deep-learning-based classification model provides promising results to assist nurses in VIA screening; and provides a direction for large-scale data collection and validation in resource-constrained settings.

Investigating the Robustness of Vision Transformers against Label Noise in Medical Image Classification

Label noise in medical image classification datasets significantly hampers the training of supervised deep learning methods, undermining their generalizability. The test performance of a model tends to decrease as the label noise rate increases. Over recent years, several methods have been proposed to mitigate the impact of label noise in medical image classification and enhance the robustness of the model. Predominantly, these works have employed CNN-based architectures as the backbone of their classifiers for feature extraction. However, in recent years, Vision Transformer (ViT)-based backbones have replaced CNNs, demonstrating improved performance and a greater ability to learn more generalizable features, especially when the dataset is large. Nevertheless, no prior work has rigorously investigated how transformer-based backbones handle the impact of label noise in medical image classification. In this paper, we investigate the architectural robustness of ViT against label noise and compare it to that of CNNs. We use two medical image classification datasets -- COVID-DU-Ex, and NCT-CRC-HE-100K -- both corrupted by injecting label noise at various rates. Additionally, we show that pretraining is crucial for ensuring ViT's improved robustness against label noise in supervised training.

How does self-supervised pretraining improve robustness against noisy labels across various medical image classification datasets?

Noisy labels can significantly impact medical image classification, particularly in deep learning, by corrupting learned features. Self-supervised pretraining, which doesn't rely on labeled data, can enhance robustness against noisy labels. However, this robustness varies based on factors like the number of classes, dataset complexity, and training size. In medical images, subtle inter-class differences and modality-specific characteristics add complexity. Previous research hasn't comprehensively explored the interplay between self-supervised learning and robustness against noisy labels in medical image classification, considering all these factors. In this study, we address three key questions: i) How does label noise impact various medical image classification datasets? ii) Which types of medical image datasets are more challenging to learn and more affected by label noise? iii) How do different self-supervised pretraining methods enhance robustness across various medical image datasets? Our results show that DermNet, among five datasets (Fetal plane, DermNet, COVID-DU-Ex, MURA, NCT-CRC-HE-100K), is the most challenging but exhibits greater robustness against noisy labels. Additionally, contrastive learning stands out among the eight self-supervised methods as the most effective approach to enhance robustness against noisy labels.

Benchmarking Encoder-Decoder Architectures for Biplanar X-ray to 3D Shape Reconstruction

Various deep learning models have been proposed for 3D bone shape reconstruction from two orthogonal (biplanar) X-ray images. However, it is unclear how these models compare against each other since they are evaluated on different anatomy, cohort and (often privately held) datasets. Moreover, the impact of the commonly optimized image-based segmentation metrics such as dice score on the estimation of clinical parameters relevant in 2D-3D bone shape reconstruction is not well known. To move closer toward clinical translation, we propose a benchmarking framework that evaluates tasks relevant to real-world clinical scenarios, including reconstruction of fractured bones, bones with implants, robustness to population shift, and error in estimating clinical parameters. Our open-source platform provides reference implementations of 8 models (many of whose implementations were not publicly available), APIs to easily collect and preprocess 6 public datasets, and the implementation of automatic clinical parameter and landmark extraction methods. We present an extensive evaluation of 8 2D-3D models on equal footing using 6 public datasets comprising images for four different anatomies. Our results show that attention-based methods that capture global spatial relationships tend to perform better across all anatomies and datasets; performance on clinically relevant subgroups may be overestimated without disaggregated reporting; ribs are substantially more difficult to reconstruct compared to femur, hip and spine; and the dice score improvement does not always bring a corresponding improvement in the automatic estimation of clinically relevant parameters.

Synthetic Boost: Leveraging Synthetic Data for Enhanced Vision-Language Segmentation in Echocardiography

Accurate segmentation is essential for echocardiography-based assessment of cardiovascular diseases (CVDs). However, the variability among sonographers and the inherent challenges of ultrasound images hinder precise segmentation. By leveraging the joint representation of image and text modalities, Vision-Language Segmentation Models (VLSMs) can incorporate rich contextual information, potentially aiding in accurate and explainable segmentation. However, the lack of readily available data in echocardiography hampers the training of VLSMs. In this study, we explore using synthetic datasets from Semantic Diffusion Models (SDMs) to enhance VLSMs for echocardiography segmentation. We evaluate results for two popular VLSMs (CLIPSeg and CRIS) using seven different kinds of language prompts derived from several attributes, automatically extracted from echocardiography images, segmentation masks, and their metadata. Our results show improved metrics and faster convergence when pretraining VLSMs on SDM-generated synthetic images before finetuning on real images. The code, configs, and prompts are available at https://github.com/naamiinepal/synthetic-boost.

Exploring Transfer Learning in Medical Image Segmentation using Vision-Language Models

Medical Image Segmentation is crucial in various clinical applications within the medical domain. While state-of-the-art segmentation models have proven effective, integrating textual guidance to enhance visual features for this task remains an area with limited progress. Existing segmentation models that utilize textual guidance are primarily trained on open-domain images, raising concerns about their direct applicability in the medical domain without manual intervention or fine-tuning. To address these challenges, we propose using multimodal vision-language models for capturing semantic information from image descriptions and images, enabling the segmentation of diverse medical images. This study comprehensively evaluates existing vision language models across multiple datasets to assess their transferability from the open domain to the medical field. Furthermore, we introduce variations of image descriptions for previously unseen images in the dataset, revealing notable variations in model performance based on the generated prompts. Our findings highlight the distribution shift between the open-domain images and the medical domain and show that the segmentation models trained on open-domain images are not directly transferrable to the medical field. But their performance can be increased by finetuning them in the medical datasets. We report the zero-shot and finetuned segmentation performance of 4 Vision Language Models (VLMs) on 11 medical datasets using 9 types of prompts derived from 14 attributes.

Improving Medical Image Classification in Noisy Labels Using Only Self-supervised Pretraining

Noisy labels hurt deep learning-based supervised image classification performance as the models may overfit the noise and learn corrupted feature extractors. For natural image classification training with noisy labeled data, model initialization with contrastive self-supervised pretrained weights has shown to reduce feature corruption and improve classification performance. However, no works have explored: i) how other self-supervised approaches, such as pretext task-based pretraining, impact the learning with noisy label, and ii) any self-supervised pretraining methods alone for medical images in noisy label settings. Medical images often feature smaller datasets and subtle inter class variations, requiring human expertise to ensure correct classification. Thus, it is not clear if the methods improving learning with noisy labels in natural image datasets such as CIFAR would also help with medical images. In this work, we explore contrastive and pretext task-based self-supervised pretraining to initialize the weights of a deep learning classification model for two medical datasets with self-induced noisy labels -- NCT-CRC-HE-100K tissue histological images and COVID-QU-Ex chest X-ray images. Our results show that models initialized with pretrained weights obtained from self-supervised learning can effectively learn better features and improve robustness against noisy labels.

M-VAAL: Multimodal Variational Adversarial Active Learning for Downstream Medical Image Analysis Tasks

Acquiring properly annotated data is expensive in the medical field as it requires experts, time-consuming protocols, and rigorous validation. Active learning attempts to minimize the need for large annotated samples by actively sampling the most informative examples for annotation. These examples contribute significantly to improving the performance of supervised machine learning models, and thus, active learning can play an essential role in selecting the most appropriate information in deep learning-based diagnosis, clinical assessments, and treatment planning. Although some existing works have proposed methods for sampling the best examples for annotation in medical image analysis, they are not task-agnostic and do not use multimodal auxiliary information in the sampler, which has the potential to increase robustness. Therefore, in this work, we propose a Multimodal Variational Adversarial Active Learning (M-VAAL) method that uses auxiliary information from additional modalities to enhance the active sampling. We applied our method to two datasets: i) brain tumor segmentation and multi-label classification using the BraTS2018 dataset, and ii) chest X-ray image classification using the COVID-QU-Ex dataset. Our results show a promising direction toward data-efficient learning under limited annotations.