Attention-based Interpretable Regression of Gene Expression in Histology

Interpretability of deep learning is widely used to evaluate the reliability of medical imaging models and reduce the risks of inaccurate patient recommendations. For models exceeding human performance, e.g. predicting RNA structure from microscopy images, interpretable modelling can be further used to uncover highly non-trivial patterns which are otherwise imperceptible to the human eye. We show that interpretability can reveal connections between the microscopic appearance of cancer tissue and its gene expression profiling. While exhaustive profiling of all genes from the histology images is still challenging, we estimate the expression values of a well-known subset of genes that is indicative of cancer molecular subtype, survival, and treatment response in colorectal cancer. Our approach successfully identifies meaningful information from the image slides, highlighting hotspots of high gene expression. Our method can help characterise how gene expression shapes tissue morphology and this may be beneficial for patient stratification in the pathology unit. The code is available on GitHub.

Causality-inspired Single-source Domain Generalization for Medical Image Segmentation

Deep learning models usually suffer from domain shift issues, where models trained on one source domain do not generalize well to other unseen domains. In this work, we investigate the single-source domain generalization problem: training a deep network that is robust to unseen domains, under the condition that training data is only available from one source domain, which is common in medical imaging applications. We tackle this problem in the context of cross-domain medical image segmentation. Under this scenario, domain shifts are mainly caused by different acquisition processes. We propose a simple causality-inspired data augmentation approach to expose a segmentation model to synthesized domain-shifted training examples. Specifically, 1) to make the deep model robust to discrepancies in image intensities and textures, we employ a family of randomly-weighted shallow networks. They augment training images using diverse appearance transformations. 2) Further we show that spurious correlations among objects in an image are detrimental to domain robustness. These correlations might be taken by the network as domain-specific clues for making predictions, and they may break on unseen domains. We remove these spurious correlations via causal intervention. This is achieved by resampling the appearances of potentially correlated objects independently. The proposed approach is validated on three cross-domain segmentation tasks: cross-modality (CT-MRI) abdominal image segmentation, cross-sequence (bSSFP-LGE) cardiac MRI segmentation, and cross-center prostate MRI segmentation. The proposed approach yields consistent performance gains compared with competitive methods when tested on unseen domains.

A new face swap method for image and video domains: a technical report

Deep fake technology became a hot field of research in the last few years. Researchers investigate sophisticated Generative Adversarial Networks (GAN), autoencoders, and other approaches to establish precise and robust algorithms for face swapping. Achieved results show that the deep fake unsupervised synthesis task has problems in terms of the visual quality of generated data. These problems usually lead to high fake detection accuracy when an expert analyzes them. The first problem is that existing image-to-image approaches do not consider video domain specificity and frame-by-frame processing leads to face jittering and other clearly visible distortions. Another problem is the generated data resolution, which is low for many existing methods due to high computational complexity. The third problem appears when the source face has larger proportions (like bigger cheeks), and after replacement it becomes visible on the face border. Our main goal was to develop such an approach that could solve these problems and outperform existing solutions on a number of clue metrics. We introduce a new face swap pipeline that is based on FaceShifter architecture and fixes the problems stated above. With a new eye loss function, super-resolution block, and Gaussian-based face mask generation leads to improvements in quality which is confirmed during evaluation.

Unsupervised Image Denoising with Frequency Domain Knowledge

Supervised learning-based methods yield robust denoising results, yet they are inherently limited by the need for large-scale clean/noisy paired datasets. The use of unsupervised denoisers, on the other hand, necessitates a more detailed understanding of the underlying image statistics. In particular, it is well known that apparent differences between clean and noisy images are most prominent on high-frequency bands, justifying the use of low-pass filters as part of conventional image preprocessing steps. However, most learning-based denoising methods utilize only one-sided information from the spatial domain without considering frequency domain information. To address this limitation, in this study we propose a frequency-sensitive unsupervised denoising method. To this end, a generative adversarial network (GAN) is used as a base structure. Subsequently, we include spectral discriminator and frequency reconstruction loss to transfer frequency knowledge into the generator. Results using natural and synthetic datasets indicate that our unsupervised learning method augmented with frequency information achieves state-of-the-art denoising performance, suggesting that frequency domain information could be a viable factor in improving the overall performance of unsupervised learning-based methods.

The Curious Layperson: Fine-Grained Image Recognition without Expert Labels

Most of us are not experts in specific fields, such as ornithology. Nonetheless, we do have general image and language understanding capabilities that we use to match what we see to expert resources. This allows us to expand our knowledge and perform novel tasks without ad-hoc external supervision. On the contrary, machines have a much harder time consulting expert-curated knowledge bases unless trained specifically with that knowledge in mind. Thus, in this paper we consider a new problem: fine-grained image recognition without expert annotations, which we address by leveraging the vast knowledge available in web encyclopedias. First, we learn a model to describe the visual appearance of objects using non-expert image descriptions. We then train a fine-grained textual similarity model that matches image descriptions with documents on a sentence-level basis. We evaluate the method on two datasets and compare with several strong baselines and the state of the art in cross-modal retrieval. Code is available at: https://github.com/subhc/clever

SGBANet: Semantic GAN and Balanced Attention Network for Arbitrarily Oriented Scene Text Recognition

Scene text recognition is a challenging task due to the complex backgrounds and diverse variations of text instances. In this paper, we propose a novel Semantic GAN and Balanced Attention Network (SGBANet) to recognize the texts in scene images. The proposed method first generates the simple semantic feature using Semantic GAN and then recognizes the scene text with the Balanced Attention Module. The Semantic GAN aims to align the semantic feature distribution between the support domain and target domain. Different from the conventional image-to-image translation methods that perform at the image level, the Semantic GAN performs the generation and discrimination on the semantic level with the Semantic Generator Module (SGM) and Semantic Discriminator Module (SDM). For target images (scene text images), the Semantic Generator Module generates simple semantic features that share the same feature distribution with support images (clear text images). The Semantic Discriminator Module is used to distinguish the semantic features between the support domain and target domain. In addition, a Balanced Attention Module is designed to alleviate the problem of attention drift. The Balanced Attention Module first learns a balancing parameter based on the visual glimpse vector and semantic glimpse vector, and then performs the balancing operation for obtaining a balanced glimpse vector. Experiments on six benchmarks, including regular datasets, i.e., IIIT5K, SVT, ICDAR2013, and irregular datasets, i.e., ICDAR2015, SVTP, CUTE80, validate the effectiveness of our proposed method.

Self-supervised motion descriptor for cardiac phase detection in 4D CMR based on discrete vector field estimations

Cardiac magnetic resonance (CMR) sequences visualise the cardiac function voxel-wise over time. Simultaneously, deep learning-based deformable image registration is able to estimate discrete vector fields which warp one time step of a CMR sequence to the following in a self-supervised manner. However, despite the rich source of information included in these 3D+t vector fields, a standardised interpretation is challenging and the clinical applications remain limited so far. In this work, we show how to efficiently use a deformable vector field to describe the underlying dynamic process of a cardiac cycle in form of a derived 1D motion descriptor. Additionally, based on the expected cardiovascular physiological properties of a contracting or relaxing ventricle, we define a set of rules that enables the identification of five cardiovascular phases including the end-systole (ES) and end-diastole (ED) without the usage of labels. We evaluate the plausibility of the motion descriptor on two challenging multi-disease, -center, -scanner short-axis CMR datasets. First, by reporting quantitative measures such as the periodic frame difference for the extracted phases. Second, by comparing qualitatively the general pattern when we temporally resample and align the motion descriptors of all instances across both datasets. The average periodic frame difference for the ED, ES key phases of our approach is $0.80\pm{0.85}$, $0.69\pm{0.79}$ which is slightly better than the inter-observer variability ($1.07\pm{0.86}$, $0.91\pm{1.6}$) and the supervised baseline method ($1.18\pm{1.91}$, $1.21\pm{1.78}$). Code and labels will be made available on our GitHub repository. https://github.com/Cardio-AI/cmr-phase-detection

A constrained Shannon-Fano entropy coder for image storage in synthetic DNA

The exponentially increasing demand for data storage has been facing more and more challenges during the past years. The energy costs that it represents are also increasing, and the availability of the storage hardware is not able to follow the storage demand's trend. The short lifespan of conventional storage media -- 10 to 20 years - forces the duplication of the hardware and worsens the situation. The majority of this storage demand concerns "cold" data, data very rarely accessed but that has to be kept for long periods of time. The coding abilities of synthetic DNA, and its long durability (several hundred years), make it a serious candidate as an alternative storage media for "cold" data. In this paper, we propose a variable-length coding algorithm adapted to DNA data storage with improved performance. The proposed algorithm is based on a modified Shannon-Fano code that respects some biochemichal constraints imposed by the synthesis chemistry. We have inserted this code in a JPEG compression algorithm adapted to DNA image storage and we highlighted an improvement of the compression ratio ranging from 0.5 up to 2 bits per nucleotide compared to the state-of-the-art solution, without affecting the reconstruction quality.

Monocular Human Shape and Pose with Dense Mesh-borne Local Image Features

We propose to improve on graph convolution based approaches for human shape and pose estimation from monocular input, using pixel-aligned local image features. Given a single input color image, existing graph convolutional network (GCN) based techniques for human shape and pose estimation use a single convolutional neural network (CNN) generated global image feature appended to all mesh vertices equally to initialize the GCN stage, which transforms a template T-posed mesh into the target pose. In contrast, we propose for the first time the idea of using local image features per vertex. These features are sampled from the CNN image feature maps by utilizing pixel-to-mesh correspondences generated with DensePose. Our quantitative and qualitative results on standard benchmarks show that using local features improves on global ones and leads to competitive performances with respect to the state-of-the-art.

Wound Segmentation with Dynamic Illumination Correction and Dual-view Semantic Fusion

Wound image segmentation is a critical component for the clinical diagnosis and in-time treatment of wounds. Recently, deep learning has become the mainstream methodology for wound image segmentation. However, the pre-processing of the wound image, such as the illumination correction, is required before the training phase as the performance can be greatly improved. The correction procedure and the training of deep models are independent of each other, which leads to sub-optimal segmentation performance as the fixed illumination correction may not be suitable for all images. To address aforementioned issues, an end-to-end dual-view segmentation approach was proposed in this paper, by incorporating a learn-able illumination correction module into the deep segmentation models. The parameters of the module can be learned and updated during the training stage automatically, while the dual-view fusion can fully employ the features from both the raw images and the enhanced ones. To demonstrate the effectiveness and robustness of the proposed framework, the extensive experiments are conducted on the benchmark datasets. The encouraging results suggest that our framework can significantly improve the segmentation performance, compared to the state-of-the-art methods.