Uddeshya Upadhyay

Uddeshya Upadhyay, Shyamgopal Karthik, Yanbei Chen et al.

High-quality calibrated uncertainty estimates are crucial for numerous real-world applications, especially for deep learning-based deployed ML systems. While Bayesian deep learning techniques allow uncertainty estimation, training them with large-scale datasets is an expensive process that does not always yield models competitive with non-Bayesian counterparts. Moreover, many of the high-performing deep learning models that are already trained and deployed are non-Bayesian in nature and do not provide uncertainty estimates. To address these issues, we propose BayesCap that learns a Bayesian identity mapping for the frozen model, allowing uncertainty estimation. BayesCap is a memory-efficient method that can be trained on a small fraction of the original dataset, enhancing pretrained non-Bayesian computer vision models by providing calibrated uncertainty estimates for the predictions without (i) hampering the performance of the model and (ii) the need for expensive retraining the model from scratch. The proposed method is agnostic to various architectures and tasks. We show the efficacy of our method on a wide variety of tasks with a diverse set of architectures, including image super-resolution, deblurring, inpainting, and crucial application such as medical image translation. Moreover, we apply the derived uncertainty estimates to detect out-of-distribution samples in critical scenarios like depth estimation in autonomous driving. Code is available at https://github.com/ExplainableML/BayesCap.

Sebastian Bordt, Uddeshya Upadhyay, Zeynep Akata et al.

When do gradient-based explanation algorithms provide perceptually-aligned explanations? We propose a criterion: the feature attributions need to be aligned with the tangent space of the data manifold. To provide evidence for this hypothesis, we introduce a framework based on variational autoencoders that allows to estimate and generate image manifolds. Through experiments across a range of different datasets -- MNIST, EMNIST, CIFAR10, X-ray pneumonia and Diabetic Retinopathy detection -- we demonstrate that the more a feature attribution is aligned with the tangent space of the data, the more perceptually-aligned it tends to be. We then show that the attributions provided by popular post-hoc methods such as Integrated Gradients and SmoothGrad are more strongly aligned with the data manifold than the raw gradient. Adversarial training also improves the alignment of model gradients with the data manifold. As a consequence, we suggest that explanation algorithms should actively strive to align their explanations with the data manifold. This is an extended version of a CVPR Workshop paper. Code is available at https://github.com/tml-tuebingen/explanations-manifold.

Uddeshya Upadhyay, Shyamgopal Karthik, Massimiliano Mancini et al.

Large-scale vision-language models (VLMs) like CLIP successfully find correspondences between images and text. Through the standard deterministic mapping process, an image or a text sample is mapped to a single vector in the embedding space. This is problematic: as multiple samples (images or text) can abstract the same concept in the physical world, deterministic embeddings do not reflect the inherent ambiguity in the embedding space. We propose ProbVLM, a probabilistic adapter that estimates probability distributions for the embeddings of pre-trained VLMs via inter/intra-modal alignment in a post-hoc manner without needing large-scale datasets or computing. On four challenging datasets, i.e., COCO, Flickr, CUB, and Oxford-flowers, we estimate the multi-modal embedding uncertainties for two VLMs, i.e., CLIP and BLIP, quantify the calibration of embedding uncertainties in retrieval tasks and show that ProbVLM outperforms other methods. Furthermore, we propose active learning and model selection as two real-world downstream tasks for VLMs and show that the estimated uncertainty aids both tasks. Lastly, we present a novel technique for visualizing the embedding distributions using a large-scale pre-trained latent diffusion model. Code is available at https://github.com/ExplainableML/ProbVLM.

Uddeshya Upadhyay, Jae Myung Kim, Cordelia Schmidt et al.

Recent advances in deep learning have shown that uncertainty estimation is becoming increasingly important in applications such as medical imaging, natural language processing, and autonomous systems. However, accurately quantifying uncertainty remains a challenging problem, especially in regression tasks where the output space is continuous. Deep learning approaches that allow uncertainty estimation for regression problems often converge slowly and yield poorly calibrated uncertainty estimates that can not be effectively used for quantification. Recently proposed post hoc calibration techniques are seldom applicable to regression problems and often add overhead to an already slow model training phase. This work presents a fast calibrated uncertainty estimation method for regression tasks called Likelihood Annealing, that consistently improves the convergence of deep regression models and yields calibrated uncertainty without any post hoc calibration phase. Unlike previous methods for calibrated uncertainty in regression that focus only on low-dimensional regression problems, our method works well on a broad spectrum of regression problems, including high-dimensional regression.Our empirical analysis shows that our approach is generalizable to various network architectures, including multilayer perceptrons, 1D/2D convolutional networks, and graph neural networks, on five vastly diverse tasks, i.e., chaotic particle trajectory denoising, physical property prediction of molecules using 3D atomistic representation, natural image super-resolution, and medical image translation using MRI.

Uddeshya Upadhyay, Sairam Bade, Arjun Puranik et al.

The automated analysis of medical time series, such as the electrocardiogram (ECG), electroencephalogram (EEG), pulse oximetry, etc, has the potential to serve as a valuable tool for diagnostic decisions, allowing for remote monitoring of patients and more efficient use of expensive and time-consuming medical procedures. Deep neural networks (DNNs) have been demonstrated to process such signals effectively. However, previous research has primarily focused on classifying medical time series rather than attempting to regress the continuous-valued physiological parameters central to diagnosis. One significant challenge in this regard is the imbalanced nature of the dataset, as a low prevalence of abnormal conditions can lead to heavily skewed data that results in inaccurate predictions and a lack of certainty in such predictions when deployed. To address these challenges, we propose HypUC, a framework for imbalanced probabilistic regression in medical time series, making several contributions. (i) We introduce a simple kernel density-based technique to tackle the imbalanced regression problem with medical time series. (ii) Moreover, we employ a probabilistic regression framework that allows uncertainty estimation for the predicted continuous values. (iii) We also present a new approach to calibrate the predicted uncertainty further. (iv) Finally, we demonstrate a technique to use calibrated uncertainty estimates to improve the predicted continuous value and show the efficacy of the calibrated uncertainty estimates to flag unreliable predictions. HypUC is evaluated on a large, diverse, real-world dataset of ECGs collected from millions of patients, outperforming several conventional baselines on various diagnostic tasks, suggesting a potential use-case for the reliable clinical deployment of deep learning models.

Aditya Aggarwal, Siddhartha Gairola, Uddeshya Upadhyay et al.

Refractive error is the most common eye disorder and is the key cause behind correctable visual impairment, responsible for nearly 80% of the visual impairment in the US. Refractive error can be diagnosed using multiple methods, including subjective refraction, retinoscopy, and autorefractors. Although subjective refraction is the gold standard, it requires cooperation from the patient and hence is not suitable for infants, young children, and developmentally delayed adults. Retinoscopy is an objective refraction method that does not require any input from the patient. However, retinoscopy requires a lens kit and a trained examiner, which limits its use for mass screening. In this work, we automate retinoscopy by attaching a smartphone to a retinoscope and recording retinoscopic videos with the patient wearing a custom pair of paper frames. We develop a video processing pipeline that takes retinoscopic videos as input and estimates the net refractive error based on our proposed extension of the retinoscopy mathematical model. Our system alleviates the need for a lens kit and can be performed by an untrained examiner. In a clinical trial with 185 eyes, we achieved a sensitivity of 91.0% and specificity of 74.0% on refractive error diagnosis. Moreover, the mean absolute error of our approach was 0.75$\pm$0.67D on net refractive error estimation compared to subjective refraction measurements. Our results indicate that our approach has the potential to be used as a retinoscopy-based refractive error screening tool in real-world medical settings.

Uddeshya Upadhyay, Yanbei Chen, Zeynep Akata

Unpaired image-to-image translation refers to learning inter-image-domain mapping without corresponding image pairs. Existing methods learn deterministic mappings without explicitly modelling the robustness to outliers or predictive uncertainty, leading to performance degradation when encountering unseen perturbations at test time. To address this, we propose a novel probabilistic method based on Uncertainty-aware Generalized Adaptive Cycle Consistency (UGAC), which models the per-pixel residual by generalized Gaussian distribution, capable of modelling heavy-tailed distributions. We compare our model with a wide variety of state-of-the-art methods on various challenging tasks including unpaired image translation of natural images, using standard datasets, spanning autonomous driving, maps, facades, and also in medical imaging domain consisting of MRI. Experimental results demonstrate that our method exhibits stronger robustness towards unseen perturbations in test data. Code is released here: https://github.com/ExplainableML/UncertaintyAwareCycleConsistency.

Uddeshya Upadhyay, Yanbei Chen, Tobias Hepp et al.

Image-to-image translation plays a vital role in tackling various medical imaging tasks such as attenuation correction, motion correction, undersampled reconstruction, and denoising. Generative adversarial networks have been shown to achieve the state-of-the-art in generating high fidelity images for these tasks. However, the state-of-the-art GAN-based frameworks do not estimate the uncertainty in the predictions made by the network that is essential for making informed medical decisions and subsequent revision by medical experts and has recently been shown to improve the performance and interpretability of the model. In this work, we propose an uncertainty-guided progressive learning scheme for image-to-image translation. By incorporating aleatoric uncertainty as attention maps for GANs trained in a progressive manner, we generate images of increasing fidelity progressively. We demonstrate the efficacy of our model on three challenging medical image translation tasks, including PET to CT translation, undersampled MRI reconstruction, and MRI motion artefact correction. Our model generalizes well in three different tasks and improves performance over state of the art under full-supervision and weak-supervision with limited data. Code is released here: https://github.com/ExplainableML/UncerGuidedI2I

Uddeshya Upadhyay

Deep neural networks (DNNs) are increasingly being used in autonomous systems. However, DNNs do not generalize well to domain shift. Adapting to a continuously evolving environment is a safety-critical challenge inevitably faced by all autonomous systems deployed to the real world. Recent work on test-time training proposes methods that adapt to a new test distribution on the fly by optimizing the DNN model for each test input using self-supervision. However, these techniques result in a sharp increase in inference time as multiple forward and backward passes are required for a single test sample (for test-time training) before finally making the prediction based on the fine-tuned features. This is undesirable for real-world robotics applications where these models may be deployed to resource constraint hardware with strong latency requirements. In this work, we propose a new framework (called UT$^3$) that leverages test-time training for improved performance in the presence of continuous domain shift while also decreasing the inference time, making it suitable for real-world applications. Our method proposes an uncertainty-aware self-supervision task for efficient test-time training that leverages the quantified uncertainty to selectively apply the training leading to sharp improvements in the inference time while performing comparably to standard test-time training protocol. Our proposed protocol offers a continuous setting to identify the selected keyframes, allowing the end-user to control how often to apply test-time training. We demonstrate the efficacy of our method on a dense regression task - monocular depth estimation.

Vikrant Rangnekar, Uddeshya Upadhyay, Zeynep Akata et al.

Dense regression is a widely used approach in computer vision for tasks such as image super-resolution, enhancement, depth estimation, etc. However, the high cost of annotation and labeling makes it challenging to achieve accurate results. We propose incorporating active learning into dense regression models to address this problem. Active learning allows models to select the most informative samples for labeling, reducing the overall annotation cost while improving performance. Despite its potential, active learning has not been widely explored in high-dimensional computer vision regression tasks like super-resolution. We address this research gap and propose a new framework called USIM-DAL that leverages the statistical properties of colour images to learn informative priors using probabilistic deep neural networks that model the heteroscedastic predictive distribution allowing uncertainty quantification. Moreover, the aleatoric uncertainty from the network serves as a proxy for error that is used for active learning. Our experiments on a wide variety of datasets spanning applications in natural images (visual genome, BSD100), medical imaging (histopathology slides), and remote sensing (satellite images) demonstrate the efficacy of the newly proposed USIM-DAL and superiority over several dense regression active learning methods.

Uddeshya Upadhyay, Viswanath P. Sudarshan, Suyash P. Awate

Image-to-image translation is an ill-posed problem as unique one-to-one mapping may not exist between the source and target images. Learning-based methods proposed in this context often evaluate the performance on test data that is similar to the training data, which may be impractical. This demands robust methods that can quantify uncertainty in the prediction for making informed decisions, especially for critical areas such as medical imaging. Recent works that employ conditional generative adversarial networks (GANs) have shown improved performance in learning photo-realistic image-to-image mappings between the source and the target images. However, these methods do not focus on (i)~robustness of the models to out-of-distribution (OOD)-noisy data and (ii)~uncertainty quantification. This paper proposes a GAN-based framework that (i)~models an adaptive loss function for robustness to OOD-noisy data that automatically tunes the spatially varying norm for penalizing the residuals and (ii)~estimates the per-voxel uncertainty in the predictions. We demonstrate our method on two key applications in medical imaging: (i)~undersampled magnetic resonance imaging (MRI) reconstruction (ii)~MRI modality propagation. Our experiments with two different real-world datasets show that the proposed method (i)~is robust to OOD-noisy test data and provides improved accuracy and (ii)~quantifies voxel-level uncertainty in the predictions.

Viswanath P. Sudarshan, Uddeshya Upadhyay, Gary F. Egan et al.

Radiation exposure in positron emission tomography (PET) imaging limits its usage in the studies of radiation-sensitive populations, e.g., pregnant women, children, and adults that require longitudinal imaging. Reducing the PET radiotracer dose or acquisition time reduces photon counts, which can deteriorate image quality. Recent deep-neural-network (DNN) based methods for image-to-image translation enable the mapping of low-quality PET images (acquired using substantially reduced dose), coupled with the associated magnetic resonance imaging (MRI) images, to high-quality PET images. However, such DNN methods focus on applications involving test data that match the statistical characteristics of the training data very closely and give little attention to evaluating the performance of these DNNs on new out-of-distribution (OOD) acquisitions. We propose a novel DNN formulation that models the (i) underlying sinogram-based physics of the PET imaging system and (ii) the uncertainty in the DNN output through the per-voxel heteroscedasticity of the residuals between the predicted and the high-quality reference images. Our sinogram-based uncertainty-aware DNN framework, namely, suDNN, estimates a standard-dose PET image using multimodal input in the form of (i) a low-dose/low-count PET image and (ii) the corresponding multi-contrast MRI images, leading to improved robustness of suDNN to OOD acquisitions. Results on in vivo simultaneous PET-MRI, and various forms of OOD data in PET-MRI, show the benefits of suDNN over the current state of the art, quantitatively and qualitatively.

Uddeshya Upadhyay, Suyash Awate

Deep neural networks for image quality enhancement typically need large quantities of highly-curated training data comprising pairs of low-quality images and their corresponding high-quality images. While high-quality image acquisition is typically expensive and time-consuming, medium-quality images are faster to acquire, at lower equipment costs, and available in larger quantities. Thus, we propose a novel generative adversarial network (GAN) that can leverage training data at multiple levels of quality (e.g., high and medium quality) to improve performance while limiting costs of data curation. We apply our mixed-supervision GAN to (i) super-resolve histopathology images and (ii) enhance laparoscopy images by combining super-resolution and surgical smoke removal. Results on large clinical and pre-clinical datasets show the benefits of our mixed-supervision GAN over the state of the art.

Uddeshya Upadhyay, Yanbei Chen, Zeynep Akata

Unpaired image-to-image translation refers to learning inter-image-domain mapping in an unsupervised manner. Existing methods often learn deterministic mappings without explicitly modelling the robustness to outliers or predictive uncertainty, leading to performance degradation when encountering unseen out-of-distribution (OOD) patterns at test time. To address this limitation, we propose a novel probabilistic method called Uncertainty-aware Generalized Adaptive Cycle Consistency (UGAC), which models the per-pixel residual by generalized Gaussian distribution, capable of modelling heavy-tailed distributions. We compare our model with a wide variety of state-of-the-art methods on two challenging tasks: unpaired image denoising in the natural image and unpaired modality prorogation in medical image domains. Experimental results demonstrate that our model offers superior image generation quality compared to recent methods in terms of quantitative metrics such as signal-to-noise ratio and structural similarity. Our model also exhibits stronger robustness towards OOD test data.

Uddeshya Upadhyay, Nikunj Shah, Sucheta Ravikanti et al.

Recent times have witnessed sharp improvements in reinforcement learning tasks using deep reinforcement learning techniques like Deep Q Networks, Policy Gradients, Actor Critic methods which are based on deep learning based models and back-propagation of gradients to train such models. An active area of research in reinforcement learning is about training agents to play complex video games, which so far has been something accomplished only by human intelligence. Some state of the art performances in video game playing using deep reinforcement learning are obtained by processing the sequence of frames from video games, passing them through a convolutional network to obtain features and then using recurrent neural networks to figure out the action leading to optimal rewards. The recurrent neural network will learn to extract the meaningful signal out of the sequence of such features. In this work, we propose a method utilizing a transformer network which have recently replaced RNNs in Natural Language Processing (NLP), and perform experiments to compare with existing methods.

Uddeshya Upadhyay, Suyash P. Awate

Super-resolution using deep neural networks typically relies on highly curated training sets that are often unavailable in clinical deployment scenarios. Using loss functions that assume Gaussian-distributed residuals makes the learning sensitive to corruptions in clinical training sets. We propose novel loss functions that are robust to corruptions in training sets by modeling heavy-tailed non-Gaussian distributions on the residuals. We propose a loss based on an autoencoder-based manifold-distance between the super-resolved and high-resolution images, to reproduce realistic textural content in super-resolved images. We propose to learn to super-resolve images to match human perceptions of structure, luminance, and contrast. Results on a large clinical dataset shows the advantages of each of our contributions, where our framework improves over the state of the art.

Uddeshya Upadhyay, Arjun Jain

Many biological data analysis processes like Cytometry or Next Generation Sequencing (NGS) produce massive amounts of data which needs to be processed in batches for down-stream analysis. Such datasets are prone to technical variations due to difference in handling the batches possibly at different times, by different experimenters or under other different conditions. This adds variation to the batches coming from the same source sample. These variations are known as Batch Effects. It is possible that these variations and natural variations due to biology confound but such situations can be avoided by performing experiments in a carefully planned manner. Batch effects can hamper downstream analysis and may also cause results to be inconclusive. Thus, it is essential to correct for these effects. This can be solved using a novel Generative Adversarial Networks (GANs) based framework that is proposed here, advantage of using this framework over other prior approaches is that here it is not required to choose a reproducing kernel and define its parameters. Results of the framework on a mass cytometry dataset are reported.