GLFNET: Global-Local (frequency) Filter Networks for efficient medical image segmentation

We propose a novel transformer-style architecture called Global-Local Filter Network (GLFNet) for medical image segmentation and demonstrate its state-of-the-art performance. We replace the self-attention mechanism with a combination of global-local filter blocks to optimize model efficiency. The global filters extract features from the whole feature map whereas the local filters are being adaptively created as 4x4 patches of the same feature map and add restricted scale information. In particular, the feature extraction takes place in the frequency domain rather than the commonly used spatial (image) domain to facilitate faster computations. The fusion of information from both spatial and frequency spaces creates an efficient model with regards to complexity, required data and performance. We test GLFNet on three benchmark datasets achieving state-of-the-art performance on all of them while being almost twice as efficient in terms of GFLOP operations.

Generative Fractional Diffusion Models

We generalize the continuous time framework for score-based generative models from an underlying Brownian motion (BM) to an approximation of fractional Brownian motion (FBM). We derive a continuous reparameterization trick and the reverse time model by representing FBM as a stochastic integral over a family of Ornstein-Uhlenbeck processes to define generative fractional diffusion models (GFDM) with driving noise converging to a non-Markovian process of infinite quadratic variation. The Hurst index $H\in(0,1)$ of FBM enables control of the roughness of the distribution transforming path. To the best of our knowledge, this is the first attempt to build a generative model upon a stochastic process with infinite quadratic variation.

DiffInfinite: Large Mask-Image Synthesis via Parallel Random Patch Diffusion in Histopathology

We present DiffInfinite, a hierarchical diffusion model that generates arbitrarily large histological images while preserving long-range correlation structural information. Our approach first generates synthetic segmentation masks, subsequently used as conditions for the high-fidelity generative diffusion process. The proposed sampling method can be scaled up to any desired image size while only requiring small patches for fast training. Moreover, it can be parallelized more efficiently than previous large-content generation methods while avoiding tiling artefacts. The training leverages classifier-free guidance to augment a small, sparsely annotated dataset with unlabelled data. Our method alleviates unique challenges in histopathological imaging practice: large-scale information, costly manual annotation, and protective data handling. The biological plausibility of DiffInfinite data is validated in a survey by ten experienced pathologists as well as a downstream segmentation task. Furthermore, the model scores strongly on anti-copying metrics which is beneficial for the protection of patient data.

mmSense: Detecting Concealed Weapons with a Miniature Radar Sensor

For widespread adoption, public security and surveillance systems must be accurate, portable, compact, and real-time, without impeding the privacy of the individuals being observed. Current systems broadly fall into two categories -- image-based which are accurate, but lack privacy, and RF signal-based, which preserve privacy but lack portability, compactness and accuracy. Our paper proposes mmSense, an end-to-end portable miniaturised real-time system that can accurately detect the presence of concealed metallic objects on persons in a discrete, privacy-preserving modality. mmSense features millimeter wave radar technology, provided by Google's Soli sensor for its data acquisition, and TransDope, our real-time neural network, capable of processing a single radar data frame in 19 ms. mmSense achieves high recognition rates on a diverse set of challenging scenes while running on standard laptop hardware, demonstrating a significant advancement towards creating portable, cost-effective real-time radar based surveillance systems.

Data Models for Dataset Drift Controls in Machine Learning With Images

Camera images are ubiquitous in machine learning research. They also play a central role in the delivery of important services spanning medicine and environmental surveying. However, the application of machine learning models in these domains has been limited because of robustness concerns. A primary failure mode are performance drops due to differences between the training and deployment data. While there are methods to prospectively validate the robustness of machine learning models to such dataset drifts, existing approaches do not account for explicit models of the primary object of interest: the data. This makes it difficult to create physically faithful drift test cases or to provide specifications of data models that should be avoided when deploying a machine learning model. In this study, we demonstrate how these shortcomings can be overcome by pairing machine learning robustness validation with physical optics. We examine the role raw sensor data and differentiable data models can play in controlling performance risks related to image dataset drift. The findings are distilled into three applications. First, drift synthesis enables the controlled generation of physically faithful drift test cases. The experiments presented here show that the average decrease in model performance is ten to four times less severe than under post-hoc augmentation testing. Second, the gradient connection between task and data models allows for drift forensics that can be used to specify performance-sensitive data models which should be avoided during deployment of a machine learning model. Third, drift adjustment opens up the possibility for processing adjustments in the face of drift. This can lead to speed up and stabilization of classifier training at a margin of up to 20% in validation accuracy. A guide to access the open code and datasets is available at https://github.com/aiaudit-org/raw2logit.

Optimizing Vision Transformers for Medical Image Segmentation and Few-Shot Domain Adaptation

The adaptation of transformers to computer vision is not straightforward because the modelling of image contextual information results in quadratic computational complexity with relation to the input features. Most of existing methods require extensive pre-training on massive datasets such as ImageNet and therefore their application to fields such as healthcare is less effective. CNNs are the dominant architecture in computer vision tasks because convolutional filters can effectively model local dependencies and reduce drastically the parameters required. However, convolutional filters cannot handle more complex interactions, which are beyond a small neighbour of pixels. Furthermore, their weights are fixed after training and thus they do not take into consideration changes in the visual input. Inspired by recent work on hybrid visual transformers with convolutions and hierarchical transformers, we propose Convolutional Swin-Unet (CS-Unet) transformer blocks and optimise their settings with relation to patch embedding, projection, the feed-forward network, up sampling and skip connections. CS-Unet can be trained from scratch and inherits the superiority of convolutions in each feature process phase. It helps to encode precise spatial information and produce hierarchical representations that contribute to object concepts at various scales. Experiments show that CS-Unet without pre-training surpasses other state-of-the-art counterparts by large margins on two medical CT and MRI datasets with fewer parameters. In addition, two domain-adaptation experiments on optic disc and polyp image segmentation further prove that our method is highly generalizable and effectively bridges the domain gap between images from different sources.

Bessel Equivariant Networks for Inversion of Transmission Effects in Multi-Mode Optical Fibres

We develop a new type of model for solving the task of inverting the transmission effects of multi-mode optical fibres through the construction of an $\mathrm{SO}^{+}(2,1)$-equivariant neural network. This model takes advantage of the of the azimuthal correlations known to exist in fibre speckle patterns and naturally accounts for the difference in spatial arrangement between input and speckle patterns. In addition, we use a second post-processing network to remove circular artifacts, fill gaps, and sharpen the images, which is required due to the nature of optical fibre transmission. This two stage approach allows for the inspection of the predicted images produced by the more robust physically motivated equivariant model, which could be useful in a safety-critical application, or by the output of both models, which produces high quality images. Further, this model can scale to previously unachievable resolutions of imaging with multi-mode optical fibres and is demonstrated on $256 \times 256$ pixel images. This is a result of improving the trainable parameter requirement from $\mathcal{O}(N^4)$ to $\mathcal{O}(m)$, where $N$ is pixel size and $m$ is number of fibre modes. Finally, this model generalises to new images, outside of the set of training data classes, better than previous models.

The Fully Convolutional Transformer for Medical Image Segmentation

We propose a novel transformer model, capable of segmenting medical images of varying modalities. Challenges posed by the fine grained nature of medical image analysis mean that the adaptation of the transformer for their analysis is still at nascent stages. The overwhelming success of the UNet lay in its ability to appreciate the fine-grained nature of the segmentation task, an ability which existing transformer based models do not currently posses. To address this shortcoming, we propose The Fully Convolutional Transformer (FCT), which builds on the proven ability of Convolutional Neural Networks to learn effective image representations, and combines them with the ability of Transformers to effectively capture long-term dependencies in its inputs. The FCT is the first fully convolutional Transformer model in medical imaging literature. It processes its input in two stages, where first, it learns to extract long range semantic dependencies from the input image, and then learns to capture hierarchical global attributes from the features. FCT is compact, accurate and robust. Our results show that it outperforms all existing transformer architectures by large margins across multiple medical image segmentation datasets of varying data modalities without the need for any pre-training. FCT outperforms its immediate competitor on the ACDC dataset by 1.3%, on the Synapse dataset by 4.4%, on the Spleen dataset by 1.2% and on ISIC 2017 dataset by 1.1% on the dice metric, with up to five times fewer parameters. Our code, environments and models will be available via GitHub.

Improving Sequential Query Recommendation with Immediate User Feedback

We propose an algorithm for next query recommendation in interactive data exploration settings, like knowledge discovery for information gathering. The state-of-the-art query recommendation algorithms are based on sequence-to-sequence learning approaches that exploit historical interaction data. We propose to augment the transformer-based causal language models for query recommendations to adapt to the immediate user feedback using multi-armed bandit (MAB) framework. We conduct a large-scale experimental study using log files from a popular online literature discovery service and demonstrate that our algorithm improves the cumulative regret substantially, with respect to the state-of-the-art transformer-based query recommendation models, which do not make use of the immediate user feedback. Our data model and source code are available at ~\url{https://anonymous.4open.science/r/exp3_ss-9985/}.

Rotation Equivariant 3D Hand Mesh Generation from a Single RGB Image

We develop a rotation equivariant model for generating 3D hand meshes from 2D RGB images. This guarantees that as the input image of a hand is rotated the generated mesh undergoes a corresponding rotation. Furthermore, this removes undesirable deformations in the meshes often generated by methods without rotation equivariance. By building a rotation equivariant model, through considering symmetries in the problem, we reduce the need for training on very large datasets to achieve good mesh reconstruction. The encoder takes images defined on $\mathbb{Z}^{2}$ and maps these to latent functions defined on the group $C_{8}$. We introduce a novel vector mapping function to map the function defined on $C_{8}$ to a latent point cloud space defined on the group $\mathrm{SO}(2)$. Further, we introduce a 3D projection function that learns a 3D function from the $\mathrm{SO}(2)$ latent space. Finally, we use an $\mathrm{SO}(3)$ equivariant decoder to ensure rotation equivariance. Our rotation equivariant model outperforms state-of-the-art methods on a real-world dataset and we demonstrate that it accurately captures the shape and pose in the generated meshes under rotation of the input hand.