Uncertainty Estimation in Contrast-Enhanced MR Image Translation with Multi-Axis Fusion

In recent years, deep learning has been applied to a wide range of medical imaging and image processing tasks. In this work, we focus on the estimation of epistemic uncertainty for 3D medical image-to-image translation. We propose a novel model uncertainty quantification method, Multi-Axis Fusion (MAF), which relies on the integration of complementary information derived from multiple views on volumetric image data. The proposed approach is applied to the task of synthesizing contrast enhanced T1-weighted images based on native T1, T2 and T2-FLAIR scans. The quantitative findings indicate a strong correlation ($\rho_{\text healthy} = 0.89$) between the mean absolute image synthetization error and the mean uncertainty score for our MAF method. Hence, we consider MAF as a promising approach to solve the highly relevant task of detecting synthetization failures at inference time.

Fine-grained Appearance Transfer with Diffusion Models

Image-to-image translation (I2I), and particularly its subfield of appearance transfer, which seeks to alter the visual appearance between images while maintaining structural coherence, presents formidable challenges. Despite significant advancements brought by diffusion models, achieving fine-grained transfer remains complex, particularly in terms of retaining detailed structural elements and ensuring information fidelity. This paper proposes an innovative framework designed to surmount these challenges by integrating various aspects of semantic matching, appearance transfer, and latent deviation. A pivotal aspect of our approach is the strategic use of the predicted $x_0$ space by diffusion models within the latent space of diffusion processes. This is identified as a crucial element for the precise and natural transfer of fine-grained details. Our framework exploits this space to accomplish semantic alignment between source and target images, facilitating mask-wise appearance transfer for improved feature acquisition. A significant advancement of our method is the seamless integration of these features into the latent space, enabling more nuanced latent deviations without necessitating extensive model retraining or fine-tuning. The effectiveness of our approach is demonstrated through extensive experiments, which showcase its ability to adeptly handle fine-grained appearance transfers across a wide range of categories and domains. We provide our code at https://github.com/babahui/Fine-grained-Appearance-Transfer

H-Packer: Holographic Rotationally Equivariant Convolutional Neural Network for Protein Side-Chain Packing

Accurately modeling protein 3D structure is essential for the design of functional proteins. An important sub-task of structure modeling is protein side-chain packing: predicting the conformation of side-chains (rotamers) given the protein's backbone structure and amino-acid sequence. Conventional approaches for this task rely on expensive sampling procedures over hand-crafted energy functions and rotamer libraries. Recently, several deep learning methods have been developed to tackle the problem in a data-driven way, albeit with vastly different formulations (from image-to-image translation to directly predicting atomic coordinates). Here, we frame the problem as a joint regression over the side-chains' true degrees of freedom: the dihedral $\chi$ angles. We carefully study possible objective functions for this task, while accounting for the underlying symmetries of the task. We propose Holographic Packer (H-Packer), a novel two-stage algorithm for side-chain packing built on top of two light-weight rotationally equivariant neural networks. We evaluate our method on CASP13 and CASP14 targets. H-Packer is computationally efficient and shows favorable performance against conventional physics-based algorithms and is competitive against alternative deep learning solutions.

CycleGANAS: Differentiable Neural Architecture Search for CycleGAN

We develop a Neural Architecture Search (NAS) framework for CycleGAN that carries out unpaired image-to-image translation task. Extending previous NAS techniques for Generative Adversarial Networks (GANs) to CycleGAN is not straightforward due to the task difference and greater search space. We design architectures that consist of a stack of simple ResNet-based cells and develop a search method that effectively explore the large search space. We show that our framework, called CycleGANAS, not only effectively discovers high-performance architectures that either match or surpass the performance of the original CycleGAN, but also successfully address the data imbalance by individual architecture search for each translation direction. To our best knowledge, it is the first NAS result for CycleGAN and shed light on NAS for more complex structures.

Domain Transfer Through Image-to-Image Translation for Uncertainty-Aware Prostate Cancer Classification

Prostate Cancer (PCa) is often diagnosed using High-resolution 3.0 Tesla(T) MRI, which has been widely established in clinics. However, there are still many medical centers that use 1.5T MRI units in the actual diagnostic process of PCa. In the past few years, deep learning-based models have been proven to be efficient on the PCa classification task and can be successfully used to support radiologists during the diagnostic process. However, training such models often requires a vast amount of data, and sometimes it is unobtainable in practice. Additionally, multi-source MRIs can pose challenges due to cross-domain distribution differences. In this paper, we have presented a novel approach for unpaired image-to-image translation of prostate mp-MRI for classifying clinically significant PCa, to be applied in data-constrained settings. First, we introduce domain transfer, a novel pipeline to translate unpaired 3.0T multi-parametric prostate MRIs to 1.5T, to increase the number of training data. Second, we estimate the uncertainty of our models through an evidential deep learning approach; and leverage the dataset filtering technique during the training process. Furthermore, we introduce a simple, yet efficient Evidential Focal Loss that incorporates the focal loss with evidential uncertainty to train our model. Our experiments demonstrate that the proposed method significantly improves the Area Under ROC Curve (AUC) by over 20% compared to the previous work (98.4% vs. 76.2%). We envision that providing prediction uncertainty to radiologists may help them focus more on uncertain cases and thus expedite the diagnostic process effectively. Our code is available at https://github.com/med-i-lab/DT_UE_PCa

Towards Unsupervised Representation Learning: Learning, Evaluating and Transferring Visual Representations

Unsupervised representation learning aims at finding methods that learn representations from data without annotation-based signals. Abstaining from annotations not only leads to economic benefits but may - and to some extent already does - result in advantages regarding the representation's structure, robustness, and generalizability to different tasks. In the long run, unsupervised methods are expected to surpass their supervised counterparts due to the reduction of human intervention and the inherently more general setup that does not bias the optimization towards an objective originating from specific annotation-based signals. While major advantages of unsupervised representation learning have been recently observed in natural language processing, supervised methods still dominate in vision domains for most tasks. In this dissertation, we contribute to the field of unsupervised (visual) representation learning from three perspectives: (i) Learning representations: We design unsupervised, backpropagation-free Convolutional Self-Organizing Neural Networks (CSNNs) that utilize self-organization- and Hebbian-based learning rules to learn convolutional kernels and masks to achieve deeper backpropagation-free models. (ii) Evaluating representations: We build upon the widely used (non-)linear evaluation protocol to define pretext- and target-objective-independent metrics for measuring and investigating the objective function mismatch between various unsupervised pretext tasks and target tasks. (iii) Transferring representations: We contribute CARLANE, the first 3-way sim-to-real domain adaptation benchmark for 2D lane detection, and a method based on prototypical self-supervised learning. Finally, we contribute a content-consistent unpaired image-to-image translation method that utilizes masks, global and local discriminators, and similarity sampling to mitigate content inconsistencies.

Visible to Thermal image Translation for improving visual task in low light conditions

Several visual tasks, such as pedestrian detection and image-to-image translation, are challenging to accomplish in low light using RGB images. Heat variation of objects in thermal images can be used to overcome this. In this work, an end-to-end framework, which consists of a generative network and a detector network, is proposed to translate RGB image into Thermal ones and compare generated thermal images with real data. We have collected images from two different locations using the Parrot Anafi Thermal drone. After that, we created a two-stream network, preprocessed, augmented, the image data, and trained the generator and discriminator models from scratch. The findings demonstrate that it is feasible to translate RGB training data to thermal data using GAN. As a result, thermal data can now be produced more quickly and affordably, which is useful for security and surveillance applications.

Domain Agnostic Image-to-image Translation using Low-Resolution Conditioning

Generally, image-to-image translation (i2i) methods aim at learning mappings across domains with the assumption that the images used for translation share content (e.g., pose) but have their own domain-specific information (a.k.a. style). Conditioned on a target image, such methods extract the target style and combine it with the source image content, keeping coherence between the domains. In our proposal, we depart from this traditional view and instead consider the scenario where the target domain is represented by a very low-resolution (LR) image, proposing a domain-agnostic i2i method for fine-grained problems, where the domains are related. More specifically, our domain-agnostic approach aims at generating an image that combines visual features from the source image with low-frequency information (e.g. pose, color) of the LR target image. To do so, we present a novel approach that relies on training the generative model to produce images that both share distinctive information of the associated source image and correctly match the LR target image when downscaled. We validate our method on the CelebA-HQ and AFHQ datasets by demonstrating improvements in terms of visual quality. Qualitative and quantitative results show that when dealing with intra-domain image translation, our method generates realistic samples compared to state-of-the-art methods such as StarGAN v2. Ablation studies also reveal that our method is robust to changes in color, it can be applied to out-of-distribution images, and it allows for manual control over the final results.

Optimal Image Transport on Sparse Dictionaries

In this paper, we derive a novel optimal image transport algorithm over sparse dictionaries by taking advantage of Sparse Representation (SR) and Optimal Transport (OT). Concisely, we design a unified optimization framework in which the individual image features (color, textures, styles, etc.) are encoded using sparse representation compactly, and an optimal transport plan is then inferred between two learned dictionaries in accordance with the encoding process. This paradigm gives rise to a simple but effective way for simultaneous image representation and transformation, which is also empirically solvable because of the moderate size of sparse coding and optimal transport sub-problems. We demonstrate its versatility and many benefits to different image-to-image translation tasks, in particular image color transform and artistic style transfer, and show the plausible results for photo-realistic transferred effects.

Zero-shot Image-to-Image Translation

Large-scale text-to-image generative models have shown their remarkable ability to synthesize diverse and high-quality images. However, it is still challenging to directly apply these models for editing real images for two reasons. First, it is hard for users to come up with a perfect text prompt that accurately describes every visual detail in the input image. Second, while existing models can introduce desirable changes in certain regions, they often dramatically alter the input content and introduce unexpected changes in unwanted regions. In this work, we propose pix2pix-zero, an image-to-image translation method that can preserve the content of the original image without manual prompting. We first automatically discover editing directions that reflect desired edits in the text embedding space. To preserve the general content structure after editing, we further propose cross-attention guidance, which aims to retain the cross-attention maps of the input image throughout the diffusion process. In addition, our method does not need additional training for these edits and can directly use the existing pre-trained text-to-image diffusion model. We conduct extensive experiments and show that our method outperforms existing and concurrent works for both real and synthetic image editing.