Contrastive learning has proven useful in many applications where access to labelled data is limited. The lack of annotated data is particularly problematic in medical image segmentation as it is difficult to have clinical experts manually annotate large volumes of data such as cardiac structures in ultrasound images of the heart. In this paper, We propose a self supervised contrastive learning method to segment the left ventricle from echocardiography when limited annotated images exist. Furthermore, we study the effect of contrastive pretraining on two well-known segmentation networks, UNet and DeepLabV3. Our results show that contrastive pretraining helps improve the performance on left ventricle segmentation, particularly when annotated data is scarce. We show how to achieve comparable results to state-of-the-art fully supervised algorithms when we train our models in a self-supervised fashion followed by fine-tuning on just 5\% of the data. We show that our solution outperforms what is currently published on a large public dataset (EchoNet-Dynamic) achieving a Dice score of 0.9252. We also compare the performance of our solution on another smaller dataset (CAMUS) to demonstrate the generalizability of our proposed solution. The code is available at (https://github.com/BioMedIA-MBZUAI/contrastive-echo).
Contrastive learning has made considerable progress in computer vision, outperforming supervised pretraining on a range of downstream datasets. However, is contrastive learning the better choice in all situations? We demonstrate two cases where it is not. First, under sufficiently small pretraining budgets, supervised pretraining on ImageNet consistently outperforms a comparable contrastive model on eight diverse image classification datasets. This suggests that the common practice of comparing pretraining approaches at hundreds or thousands of epochs may not produce actionable insights for th…
EchoPrime: A Multi-Video View-Informed Vision-Language Model for Comprehensive Echocardiography Interpretation
Cedars-Sinai Medical Center（西达赛奈医疗中心）；University of California Los Angeles（加州大学洛杉矶分校）；Stanford University（斯坦福大学）；University of California, San Francisco（加州大学旧金山分校）；San Francisco Veterans Affairs Medical Center（旧金山退伍军人事务医疗中心）
Caltech（加州理工学院）；Google（谷歌）；University of Edinburgh（爱丁堡大学）；Alan Turing Institute（艾伦·图灵研究所）；University of Copenhagen（哥本哈根大学）
Recent self-supervised representation learning techniques have largely closed the gap between supervised and unsupervised learning on ImageNet classification. While the particulars of pretraining on ImageNet are now relatively well understood, the field still lacks widely accepted best practices for replicating this success on other datasets. As a first step in this direction, we study contrastive self-supervised learning on four diverse large-scale datasets. By looking through the lenses of data quantity, data domain, data quality, and task granularity, we provide new insights into the necess…
Medical report generation is a challenging task since it is time-consuming and requires expertise from experienced radiologists. The goal of medical report generation is to accurately capture and describe the image findings. Previous works pretrain their visual encoding neural networks with large datasets in different domains, which cannot learn general visual representation in the specific medical domain. In this work, we propose a medical report generation framework that uses a contrastive learning approach to pretrain the visual encoder and requires no additional meta information. In additi…
Image-level contrastive representation learning has proven to be highly effective as a generic model for transfer learning. Such generality for transfer learning, however, sacrifices specificity if we are interested in a certain downstream task. We argue that this could be sub-optimal and thus advocate a design principle which encourages alignment between the self-supervised pretext task and the downstream task. In this paper, we follow this principle with a pretraining method specifically designed for the task of object detection. We attain alignment in the following three aspects: 1) object-…
Recent advances in contrastive representation learning over paired image-text data have led to models such as CLIP that achieve state-of-the-art performance for zero-shot classification and distributional robustness. Such models typically require joint reasoning in the image and text representation spaces for downstream inference tasks. Contrary to prior beliefs, we demonstrate that the image and text representations learned via a standard contrastive objective are not interchangeable and can lead to inconsistent downstream predictions. To mitigate this issue, we formalize consistency and prop…
Proposal-Contrastive Pretraining for Object Detection from Fewer Data
Université Paris-Saclay（巴黎-萨克雷大学）；CEA（法国原子能委员会）；Université Jean Monnet Saint-Etienne（圣艾蒂安让·莫内大学）；CNRS（法国国家科学研究中心）；Laboratoire Hubert Curien UMR 5516（于贝尔·居里安实验室）；Institut Universitaire de France (IUF)（法国大学研究院）
Fully supervised semantic segmentation learns from dense masks, which requires heavy annotation cost for closed set. In this paper, we use natural language as supervision without any pixel-level annotation for open world segmentation. We call the proposed framework as FreeSeg, where the mask is freely available from raw feature map of pretraining model. Compared with zero-shot or openset segmentation, FreeSeg doesn't require any annotated masks, and it widely predicts categories beyond class-agnostic unsupervised segmentation. Specifically, FreeSeg obtains free mask from Image-Text Similarity …
Recent advances in self-supervised contrastive learning yield good image-level representation, which favors classification tasks but usually neglects pixel-level detailed information, leading to unsatisfactory transfer performance to dense prediction tasks such as semantic segmentation. In this work, we propose a pixel-wise contrastive learning method called CP2 (Copy-Paste Contrastive Pretraining), which facilitates both image- and pixel-level representation learning and therefore is more suitable for downstream dense prediction tasks. In detail, we copy-paste a random crop from an image (the…
DICE: Device-level Integrated Circuits Encoder with Graph Contrastive Pretraining
Electrical and Computer Engineering, The University of Texas at Austin（得克萨斯大学奥斯汀分校电子与计算机工程系）；Computer Science and Engineering, The Chinese University of Hong Kong（香港中文大学计算机科学与工程系）；Computer Science, The University of Hong Kong（香港大学计算机科学系）
Many recent approaches in contrastive learning have worked to close the gap between pretraining on iconic images like ImageNet and pretraining on complex scenes like COCO. This gap exists largely because commonly used random crop augmentations obtain semantically inconsistent content in crowded scene images of diverse objects. Previous works use preprocessing pipelines to localize salient objects for improved cropping, but an end-to-end solution is still elusive. In this work, we propose a framework which accomplishes this goal via joint learning of representations and segmentation. We leverag…
A Supervised Contrastive Learning Pretrain-Finetune Approach for Time Series
School of Operations Research and Information Engineering, Cornell University（康奈尔大学运筹学与信息工程学院）；IBM Research, Thomas J. Watson Research Center（IBM研究部托马斯·J·沃森研究中心）
Wrong Organ, Right Physics: Transferring Echocardiography Pretraining to Lung Ultrasound for Tuberculosis Screening
University of Stellenbosch（斯泰伦博斯大学）；Swiss Federal Institute of Technology (EPFL)（瑞士联邦理工学院（EPFL））；National Teaching Hospital for Tuberculosis and Pulmonary Diseases (CNHU-PPC)（国家结核病与肺病教学医院（CNHU-PPC））；South African Medical Research Council（南非医学研究理事会）；Stellenbosch University（斯泰伦博斯大学）
Contrastive learning is a form of self-supervision that can leverage unlabeled data to produce pretrained models. While contrastive learning has demonstrated promising results on natural image classification tasks, its application to medical imaging tasks like chest X-ray interpretation has been limited. In this work, we propose MoCo-CXR, which is an adaptation of the contrastive learning method Momentum Contrast (MoCo), to produce models with better representations and initializations for the detection of pathologies in chest X-rays. In detecting pleural effusion, we find that linear models t…
Contrastive pretraining techniques for text classification has been largely studied in an unsupervised setting. However, oftentimes labeled data from related tasks which share label semantics with current task is available. We hypothesize that using this labeled data effectively can lead to better generalization on current task. In this paper, we propose a novel way to effectively utilize labeled data from related tasks with a graph based supervised contrastive learning approach. We formulate a token-graph by extrapolating the supervised information from examples to tokens. Our formulation res…
We explore the value of weak labels in learning transferable representations for medical images. Compared to hand-labeled datasets, weak or inexact labels can be acquired in large quantities at significantly lower cost and can provide useful training signals for data-hungry models such as deep neural networks. We consider weak labels in the form of pseudo-labels and propose a semi-weakly supervised contrastive learning (SWCL) framework for representation learning using semi-weakly annotated images. Specifically, we train a semi-supervised model to propagate labels from a small dataset consisti…
Various state-of-the-art self-supervised visual representation learning approaches take advantage of data from multiple sensors by aligning the feature representations across views and/or modalities. In this work, we investigate how aligning representations affects the visual features obtained from cross-view and cross-modal contrastive learning on images and point clouds. On five real-world datasets and on five tasks, we train and evaluate 108 models based on four pretraining variations. We find that cross-modal representation alignment discards complementary visual information, such as color…
Collecting labeled data for the task of semantic segmentation is expensive and time-consuming, as it requires dense pixel-level annotations. While recent Convolutional Neural Network (CNN) based semantic segmentation approaches have achieved impressive results by using large amounts of labeled training data, their performance drops significantly as the amount of labeled data decreases. This happens because deep CNNs trained with the de facto cross-entropy loss can easily overfit to small amounts of labeled data. To address this issue, we propose a simple and effective contrastive learning-base…
This work explores how self-supervised learning can be universally used to discover speaker-specific features towards enabling personalized speech enhancement models. We specifically address the few-shot learning scenario where access to cleaning recordings of a test-time speaker is limited to a few seconds, but noisy recordings of the speaker are abundant. We develop a simple contrastive learning procedure which treats the abundant noisy data as makeshift training targets through pairwise noise injection: the model is pretrained to maximize agreement between pairs of differently deformed iden…
We introduce EfficientCL, a memory-efficient continual pretraining method that applies contrastive learning with novel data augmentation and curriculum learning. For data augmentation, we stack two types of operation sequentially: cutoff and PCA jittering. While pretraining steps proceed, we apply curriculum learning by incrementing the augmentation degree for each difficulty step. After data augmentation is finished, contrastive learning is applied on projected embeddings of original and augmented examples. When finetuned on GLUE benchmark, our model outperforms baseline models, especially fo…
We explore the downstream task performances for graph neural network (GNN) self-supervised learning (SSL) methods trained on subgraphs extracted from relational databases (RDBs). Intuitively, this joint use of SSL and GNNs should allow to leverage more of the available data, which could translate to better results. However, we found that naively porting contrastive SSL techniques can cause ``negative transfer'': linear evaluation on fixed representations from a pretrained model performs worse than on representations from the randomly-initialized model. Based on the conjecture that contrastive …
Contrastive learning has emerged as a competitive pretraining method for object detection. Despite this progress, there has been minimal investigation into the robustness of contrastively pretrained detectors when faced with domain shifts. To address this gap, we conduct an empirical study of contrastive learning and out-of-domain object detection, studying how contrastive view design affects robustness. In particular, we perform a case study of the detection-focused pretext task Instance Localization (InsLoc) and propose strategies to augment views and enhance robustness in appearance-shifted…
Can we inject the pocket-ligand interaction knowledge into the pre-trained model and jointly learn their chemical space? Pretraining molecules and proteins has attracted considerable attention in recent years, while most of these approaches focus on learning one of the chemical spaces and lack the injection of biological knowledge. We propose a co-supervised pretraining (CoSP) framework to simultaneously learn 3D pocket and ligand representations. We use a gated geometric message passing layer to model both 3D pockets and ligands, where each node's chemical features, geometric position and ori…
Revisiting Theory of Contrastive Learning for Domain Generalization
Munich Center for Machine Learning（慕尼黑机器学习中心）；Department of Computer Science, Sharif University of Technology（技术学院计算机科学系）；Department of Statistics, LMU Munich（慕尼黑大学统计系）
Label Informed Contrastive Pretraining for Node Importance Estimation on Knowledge Graphs
Tsinghua University（清华大学）；Fuyao Institute of Technology（福耀科技大学）；Chinese Academy of Sciences（中国科学院）；Southern University of Science and Technology（南方科技大学）；Fuzhou Institute of Data Technology（福州数据技术研究院）
Laboratory for Machine Perception and Learning（机器感知与学习实验室）；University of Central Florida（中佛罗里达大学）
In this paper, we review adversarial pretraining of self-supervised deep networks including both convolutional neural networks and vision transformers. Unlike the adversarial training with access to labeled examples, adversarial pretraining is complicated as it only has access to unlabeled examples. To incorporate adversaries into pretraining models on either input or feature level, we find that existing approaches are largely categorized into two groups: memory-free instance-wise attacks imposing worst-case perturbations on individual examples, and memory-based adversaries shared across examp…
Pretrained language models such as BERT, GPT have shown great effectiveness in language understanding. The auxiliary predictive tasks in existing pretraining approaches are mostly defined on tokens, thus may not be able to capture sentence-level semantics very well. To address this issue, we propose CERT: Contrastive self-supervised Encoder Representations from Transformers, which pretrains language representation models using contrastive self-supervised learning at the sentence level. CERT creates augmentations of original sentences using back-translation. Then it finetunes a pretrained langu…
