arXiv subjects

Shekoofeh Azizi

Publications and source records attributed to Shekoofeh Azizi.

27 records · Page 2Linked to original sources

arXiv2022

Large Language Models Encode Clinical Knowledge

Large language models (LLMs) have demonstrated impressive capabilities in natural language understanding and generation, but the quality bar for medical and clinical applications is high. Today, attempts to assess models' clinical knowledge typically rely on automated evaluations on limited benchmarks. There is no standard to evaluate model predictions and reasoning across a breadth of tasks. To address this, we present MultiMedQA, a benchmark combining six existing open question answering datasets spanning professional medical exams, research, and consumer queries; and HealthSearchQA, a new free-response dataset of medical questions searched online. We propose a framework for human evaluation of model answers along multiple axes including factuality, precision, possible harm, and bias. In addition, we evaluate PaLM (a 540-billion parameter LLM) and its instruction-tuned variant, Flan-PaLM, on MultiMedQA. Using a combination of prompting strategies, Flan-PaLM achieves state-of-the-art accuracy on every MultiMedQA multiple-choice dataset (MedQA, MedMCQA, PubMedQA, MMLU clinical topics), including 67.6% accuracy on MedQA (US Medical License Exam questions), surpassing prior state-of-the-art by over 17%. However, human evaluation reveals key gaps in Flan-PaLM responses. To resolve this we introduce instruction prompt tuning, a parameter-efficient approach for aligning LLMs to new domains using a few exemplars. The resulting model, Med-PaLM, performs encouragingly, but remains inferior to clinicians. We show that comprehension, recall of knowledge, and medical reasoning improve with model scale and instruction prompt tuning, suggesting the potential utility of LLMs in medicine. Our human evaluations reveal important limitations of today's models, reinforcing the importance of both evaluation frameworks and method development in creating safe, helpful LLM models for clinical applications.

cs.CL↗

arXiv2022

Joint Debiased Representation and Image Clustering Learning with Self-Supervision

Contrastive learning is among the most successful methods for visual representation learning, and its performance can be further improved by jointly performing clustering on the learned representations. However, existing methods for joint clustering and contrastive learning do not perform well on long-tailed data distributions, as majority classes overwhelm and distort the loss of minority classes, thus preventing meaningful representations to be learned. Motivated by this, we develop a novel joint clustering and contrastive learning framework by adapting the debiased contrastive loss to avoid under-clustering minority classes of imbalanced datasets. We show that our proposed modified debiased contrastive loss and divergence clustering loss improves the performance across multiple datasets and learning tasks. The source code is available at https://anonymous.4open.science/r/SSL-debiased-clustering

cs.CV↗

arXiv2022

Robust and Efficient Medical Imaging with Self-Supervision

Recent progress in Medical Artificial Intelligence (AI) has delivered systems that can reach clinical expert level performance. However, such systems tend to demonstrate sub-optimal "out-of-distribution" performance when evaluated in clinical settings different from the training environment. A common mitigation strategy is to develop separate systems for each clinical setting using site-specific data [1]. However, this quickly becomes impractical as medical data is time-consuming to acquire and expensive to annotate [2]. Thus, the problem of "data-efficient generalization" presents an ongoing difficulty for Medical AI development. Although progress in representation learning shows promise, their benefits have not been rigorously studied, specifically for out-of-distribution settings. To meet these challenges, we present REMEDIS, a unified representation learning strategy to improve robustness and data-efficiency of medical imaging AI. REMEDIS uses a generic combination of large-scale supervised transfer learning with self-supervised learning and requires little task-specific customization. We study a diverse range of medical imaging tasks and simulate three realistic application scenarios using retrospective data. REMEDIS exhibits significantly improved in-distribution performance with up to 11.5% relative improvement in diagnostic accuracy over a strong supervised baseline. More importantly, our strategy leads to strong data-efficient generalization of medical imaging AI, matching strong supervised baselines using between 1% to 33% of retraining data across tasks. These results suggest that REMEDIS can significantly accelerate the life-cycle of medical imaging AI development thereby presenting an important step forward for medical imaging AI to deliver broad impact.

cs.CV↗

arXiv2021

Deep Bregman Divergence for Contrastive Learning of Visual Representations

Deep Bregman divergence measures divergence of data points using neural networks which is beyond Euclidean distance and capable of capturing divergence over distributions. In this paper, we propose deep Bregman divergences for contrastive learning of visual representation where we aim to enhance contrastive loss used in self-supervised learning by training additional networks based on functional Bregman divergence. In contrast to the conventional contrastive learning methods which are solely based on divergences between single points, our framework can capture the divergence between distributions which improves the quality of learned representation. We show the combination of conventional contrastive loss and our proposed divergence loss outperforms baseline and most of the previous methods for self-supervised and semi-supervised learning on multiple classifications and object detection tasks and datasets. Moreover, the learned representations generalize well when transferred to the other datasets and tasks. The source code and our models are available in supplementary and will be released with paper.

cs.CV↗

arXiv2021

Does Your Dermatology Classifier Know What It Doesn't Know? Detecting the Long-Tail of Unseen Conditions

We develop and rigorously evaluate a deep learning based system that can accurately classify skin conditions while detecting rare conditions for which there is not enough data available for training a confident classifier. We frame this task as an out-of-distribution (OOD) detection problem. Our novel approach, hierarchical outlier detection (HOD) assigns multiple abstention classes for each training outlier class and jointly performs a coarse classification of inliers vs. outliers, along with fine-grained classification of the individual classes. We demonstrate the effectiveness of the HOD loss in conjunction with modern representation learning approaches (BiT, SimCLR, MICLe) and explore different ensembling strategies for further improving the results. We perform an extensive subgroup analysis over conditions of varying risk levels and different skin types to investigate how the OOD detection performance changes over each subgroup and demonstrate the gains of our framework in comparison to baselines. Finally, we introduce a cost metric to approximate downstream clinical impact. We use this cost metric to compare the proposed method against a baseline system, thereby making a stronger case for the overall system effectiveness in a real-world deployment scenario.

cs.CV↗

arXiv2021

Big Self-Supervised Models Advance Medical Image Classification

Self-supervised pretraining followed by supervised fine-tuning has seen success in image recognition, especially when labeled examples are scarce, but has received limited attention in medical image analysis. This paper studies the effectiveness of self-supervised learning as a pretraining strategy for medical image classification. We conduct experiments on two distinct tasks: dermatology skin condition classification from digital camera images and multi-label chest X-ray classification, and demonstrate that self-supervised learning on ImageNet, followed by additional self-supervised learning on unlabeled domain-specific medical images significantly improves the accuracy of medical image classifiers. We introduce a novel Multi-Instance Contrastive Learning (MICLe) method that uses multiple images of the underlying pathology per patient case, when available, to construct more informative positive pairs for self-supervised learning. Combining our contributions, we achieve an improvement of 6.7% in top-1 accuracy and an improvement of 1.1% in mean AUC on dermatology and chest X-ray classification respectively, outperforming strong supervised baselines pretrained on ImageNet. In addition, we show that big self-supervised models are robust to distribution shift and can learn efficiently with a small number of labeled medical images.

eess.IV↗

arXiv2020

Contextual Residual Aggregation for Ultra High-Resolution Image Inpainting

Recently data-driven image inpainting methods have made inspiring progress, impacting fundamental image editing tasks such as object removal and damaged image repairing. These methods are more effective than classic approaches, however, due to memory limitations they can only handle low-resolution inputs, typically smaller than 1K. Meanwhile, the resolution of photos captured with mobile devices increases up to 8K. Naive up-sampling of the low-resolution inpainted result can merely yield a large yet blurry result. Whereas, adding a high-frequency residual image onto the large blurry image can generate a sharp result, rich in details and textures. Motivated by this, we propose a Contextual Residual Aggregation (CRA) mechanism that can produce high-frequency residuals for missing contents by weighted aggregating residuals from contextual patches, thus only requiring a low-resolution prediction from the network. Since convolutional layers of the neural network only need to operate on low-resolution inputs and outputs, the cost of memory and computing power is thus well suppressed. Moreover, the need for high-resolution training datasets is alleviated. In our experiments, we train the proposed model on small images with resolutions 512x512 and perform inference on high-resolution images, achieving compelling inpainting quality. Our model can inpaint images as large as 8K with considerable hole sizes, which is intractable with previous learning-based approaches. We further elaborate on the light-weight design of the network architecture, achieving real-time performance on 2K images on a GTX 1080 Ti GPU. Codes are available at: Atlas200dk/sample-imageinpainting-HiFill.

cs.CV↗

arXiv2019

A Kernelized Manifold Mapping to Diminish the Effect of Adversarial Perturbations

The linear and non-flexible nature of deep convolutional models makes them vulnerable to carefully crafted adversarial perturbations. To tackle this problem, we propose a non-linear radial basis convolutional feature mapping by learning a Mahalanobis-like distance function. Our method then maps the convolutional features onto a linearly well-separated manifold, which prevents small adversarial perturbations from forcing a sample to cross the decision boundary. We test the proposed method on three publicly available image classification and segmentation datasets namely, MNIST, ISBI ISIC 2017 skin lesion segmentation, and NIH Chest X-Ray-14. We evaluate the robustness of our method to different gradient (targeted and untargeted) and non-gradient based attacks and compare it to several non-gradient masking defense strategies. Our results demonstrate that the proposed method can increase the resilience of deep convolutional neural networks to adversarial perturbations without accuracy drop on clean data.

cs.CV↗

arXiv2017

Hierarchical Watermarking Framework Based on Analysis of Local Complexity Variations

Increasing production and exchange of multimedia content has increased the need for better protection of copyright by means of watermarking. Different methods have been proposed to satisfy the tradeoff between imperceptibility and robustness as two important characteristics in watermarking while maintaining proper data-embedding capacity. Many watermarking methods use image independent set of parameters. Different images possess different potentials for robust and transparent hosting of watermark data. To overcome this deficiency, in this paper we have proposed a new hierarchical adaptive watermarking framework. At the higher level of hierarchy, complexity of an image is ranked in comparison with complexities of images of a dataset. For a typical dataset of images, the statistical distribution of block complexities is found. At the lower level of the hierarchy, for a single cover image that is to be watermarked, complexities of blocks can be found. Local complexity variation (LCV) among a block and its neighbors is used to adaptively control the watermark strength factor of each block. Such local complexity analysis creates an adaptive embedding scheme, which results in higher transparency by reducing blockiness effects. This two level hierarchy has enabled our method to take advantage of all image blocks to elevate the embedding capacity while preserving imperceptibility. For testing the effectiveness of the proposed framework, contourlet transform (CT) in conjunction with discrete cosine transform (DCT) is used to embed pseudo-random binary sequences as watermark. Experimental results show that the proposed framework elevates the performance the watermarking routine in terms of both robustness and transparency.

cs.MM↗