GRAtt-VIS: Gated Residual Attention for Auto Rectifying Video Instance Segmentation

Recent trends in Video Instance Segmentation (VIS) have seen a growing reliance on online methods to model complex and lengthy video sequences. However, the degradation of representation and noise accumulation of the online methods, especially during occlusion and abrupt changes, pose substantial challenges. Transformer-based query propagation provides promising directions at the cost of quadratic memory attention. However, they are susceptible to the degradation of instance features due to the above-mentioned challenges and suffer from cascading effects. The detection and rectification of such errors remain largely underexplored. To this end, we introduce \textbf{GRAtt-VIS}, \textbf{G}ated \textbf{R}esidual \textbf{Att}ention for \textbf{V}ideo \textbf{I}nstance \textbf{S}egmentation. Firstly, we leverage a Gumbel-Softmax-based gate to detect possible errors in the current frame. Next, based on the gate activation, we rectify degraded features from its past representation. Such a residual configuration alleviates the need for dedicated memory and provides a continuous stream of relevant instance features. Secondly, we propose a novel inter-instance interaction using gate activation as a mask for self-attention. This masking strategy dynamically restricts the unrepresentative instance queries in the self-attention and preserves vital information for long-term tracking. We refer to this novel combination of Gated Residual Connection and Masked Self-Attention as \textbf{GRAtt} block, which can easily be integrated into the existing propagation-based framework. Further, GRAtt blocks significantly reduce the attention overhead and simplify dynamic temporal modeling. GRAtt-VIS achieves state-of-the-art performance on YouTube-VIS and the highly challenging OVIS dataset, significantly improving over previous methods. Code is available at \url{https://github.com/Tanveer81/GRAttVIS}.

FedPIDAvg: A PID controller inspired aggregation method for Federated Learning

This paper presents FedPIDAvg, the winning submission to the Federated Tumor Segmentation Challenge 2022 (FETS22). Inspired by FedCostWAvg, our winning contribution to FETS21, we contribute an improved aggregation strategy for federated and collaborative learning. FedCostWAvg is a weighted averaging method that not only considers the number of training samples of each cluster but also the size of the drop of the respective cost function in the last federated round. This can be interpreted as the derivative part of a PID controller (proportional-integral-derivative controller). In FedPIDAvg, we further add the missing integral term. Another key challenge was the vastly varying size of data samples per center. We addressed this by modeling the data center sizes as following a Poisson distribution and choosing the training iterations per center accordingly. Our method outperformed all other submissions.

Multi-contrast MRI Super-resolution via Implicit Neural Representations

Clinical routine and retrospective cohorts commonly include multi-parametric Magnetic Resonance Imaging; however, they are mostly acquired in different anisotropic 2D views due to signal-to-noise-ratio and scan-time constraints. Thus acquired views suffer from poor out-of-plane resolution and affect downstream volumetric image analysis that typically requires isotropic 3D scans. Combining different views of multi-contrast scans into high-resolution isotropic 3D scans is challenging due to the lack of a large training cohort, which calls for a subject-specific framework.This work proposes a novel solution to this problem leveraging Implicit Neural Representations (INR). Our proposed INR jointly learns two different contrasts of complementary views in a continuous spatial function and benefits from exchanging anatomical information between them. Trained within minutes on a single commodity GPU, our model provides realistic super-resolution across different pairs of contrasts in our experiments with three datasets. Using Mutual Information (MI) as a metric, we find that our model converges to an optimum MI amongst sequences, achieving anatomically faithful reconstruction. Code is available at: https://github.com/jqmcginnis/multi_contrast_inr.

A Domain-specific Perceptual Metric via Contrastive Self-supervised Representation: Applications on Natural and Medical Images

Quantifying the perceptual similarity of two images is a long-standing problem in low-level computer vision. The natural image domain commonly relies on supervised learning, e.g., a pre-trained VGG, to obtain a latent representation. However, due to domain shift, pre-trained models from the natural image domain might not apply to other image domains, such as medical imaging. Notably, in medical imaging, evaluating the perceptual similarity is exclusively performed by specialists trained extensively in diverse medical fields. Thus, medical imaging remains devoid of task-specific, objective perceptual measures. This work answers the question: Is it necessary to rely on supervised learning to obtain an effective representation that could measure perceptual similarity, or is self-supervision sufficient? To understand whether recent contrastive self-supervised representation (CSR) may come to the rescue, we start with natural images and systematically evaluate CSR as a metric across numerous contemporary architectures and tasks and compare them with existing methods. We find that in the natural image domain, CSR behaves on par with the supervised one on several perceptual tests as a metric, and in the medical domain, CSR better quantifies perceptual similarity concerning the experts' ratings. We also demonstrate that CSR can significantly improve image quality in two image synthesis tasks. Finally, our extensive results suggest that perceptuality is an emergent property of CSR, which can be adapted to many image domains without requiring annotations.

Topologically faithful image segmentation via induced matching of persistence barcodes

Image segmentation is a largely researched field where neural networks find vast applications in many facets of technology. Some of the most popular approaches to train segmentation networks employ loss functions optimizing pixel-overlap, an objective that is insufficient for many segmentation tasks. In recent years, their limitations fueled a growing interest in topology-aware methods, which aim to recover the correct topology of the segmented structures. However, so far, none of the existing approaches achieve a spatially correct matching between the topological features of ground truth and prediction. In this work, we propose the first topologically and feature-wise accurate metric and loss function for supervised image segmentation, which we term Betti matching. We show how induced matchings guarantee the spatially correct matching between barcodes in a segmentation setting. Furthermore, we propose an efficient algorithm to compute the Betti matching of images. We show that the Betti matching error is an interpretable metric to evaluate the topological correctness of segmentations, which is more sensitive than the well-established Betti number error. Moreover, the differentiability of the Betti matching loss enables its use as a loss function. It improves the topological performance of segmentation networks across six diverse datasets while preserving the volumetric performance. Our code is available in https://github.com/nstucki/Betti-matching.

InstanceFormer: An Online Video Instance Segmentation Framework

Recent transformer-based offline video instance segmentation (VIS) approaches achieve encouraging results and significantly outperform online approaches. However, their reliance on the whole video and the immense computational complexity caused by full Spatio-temporal attention limit them in real-life applications such as processing lengthy videos. In this paper, we propose a single-stage transformer-based efficient online VIS framework named InstanceFormer, which is especially suitable for long and challenging videos. We propose three novel components to model short-term and long-term dependency and temporal coherence. First, we propagate the representation, location, and semantic information of prior instances to model short-term changes. Second, we propose a novel memory cross-attention in the decoder, which allows the network to look into earlier instances within a certain temporal window. Finally, we employ a temporal contrastive loss to impose coherence in the representation of an instance across all frames. Memory attention and temporal coherence are particularly beneficial to long-range dependency modeling, including challenging scenarios like occlusion. The proposed InstanceFormer outperforms previous online benchmark methods by a large margin across multiple datasets. Most importantly, InstanceFormer surpasses offline approaches for challenging and long datasets such as YouTube-VIS-2021 and OVIS. Code is available at https://github.com/rajatkoner08/InstanceFormer.

Focused Decoding Enables 3D Anatomical Detection by Transformers

Detection Transformers represent end-to-end object detection approaches based on a Transformer encoder-decoder architecture, exploiting the attention mechanism for global relation modeling. Although Detection Transformers deliver results on par with or even superior to their highly optimized CNN-based counterparts operating on 2D natural images, their success is closely coupled to access to a vast amount of training data. This, however, restricts the feasibility of employing Detection Transformers in the medical domain, as access to annotated data is typically limited. To tackle this issue and facilitate the advent of medical Detection Transformers, we propose a novel Detection Transformer for 3D anatomical structure detection, dubbed Focused Decoder. Focused Decoder leverages information from an anatomical region atlas to simultaneously deploy query anchors and restrict the cross-attention's field of view to regions of interest, which allows for a precise focus on relevant anatomical structures. We evaluate our proposed approach on two publicly available CT datasets and demonstrate that Focused Decoder not only provides strong detection results and thus alleviates the need for a vast amount of annotated data but also exhibits exceptional and highly intuitive explainability of results via attention weights. Code for Focused Decoder is available in our medical Vision Transformer library github.com/bwittmann/transoar.

Deep Quality Estimation: Creating Surrogate Models for Human Quality Ratings

Human ratings are abstract representations of segmentation quality. To approximate human quality ratings on scarce expert data, we train surrogate quality estimation models. We evaluate on a complex multi-class segmentation problem, specifically glioma segmentation following the BraTS annotation protocol. The training data features quality ratings from 15 expert neuroradiologists on a scale ranging from 1 to 6 stars for various computer-generated and manual 3D annotations. Even though the networks operate on 2D images and with scarce training data, we can approximate segmentation quality within a margin of error comparable to human intra-rater reliability. Segmentation quality prediction has broad applications. While an understanding of segmentation quality is imperative for successful clinical translation of automatic segmentation quality algorithms, it can play an essential role in training new segmentation models. Due to the split-second inference times, it can be directly applied within a loss function or as a fully-automatic dataset curation mechanism in a federated learning setting.

blob loss: instance imbalance aware loss functions for semantic segmentation

Deep convolutional neural networks have proven to be remarkably effective in semantic segmentation tasks. Most popular loss functions were introduced targeting improved volumetric scores, such as the Sorensen Dice coefficient. By design, DSC can tackle class imbalance; however, it does not recognize instance imbalance within a class. As a result, a large foreground instance can dominate minor instances and still produce a satisfactory Sorensen Dice coefficient. Nevertheless, missing out on instances will lead to poor detection performance. This represents a critical issue in applications such as disease progression monitoring. For example, it is imperative to locate and surveil small-scale lesions in the follow-up of multiple sclerosis patients. We propose a novel family of loss functions, nicknamed blob loss, primarily aimed at maximizing instance-level detection metrics, such as F1 score and sensitivity. Blob loss is designed for semantic segmentation problems in which the instances are the connected components within a class. We extensively evaluate a DSC-based blob loss in five complex 3D semantic segmentation tasks featuring pronounced instance heterogeneity in terms of texture and morphology. Compared to soft Dice loss, we achieve 5 percent improvement for MS lesions, 3 percent improvement for liver tumor, and an average 2 percent improvement for Microscopy segmentation tasks considering F1 score.

Relationformer: A Unified Framework for Image-to-Graph Generation

A comprehensive representation of an image requires understanding objects and their mutual relationship, especially in image-to-graph generation, e.g., road network extraction, blood-vessel network extraction, or scene graph generation. Traditionally, image-to-graph generation is addressed with a two-stage approach consisting of object detection followed by a separate relation prediction, which prevents simultaneous object-relation interaction. This work proposes a unified one-stage transformer-based framework, namely Relationformer, that jointly predicts objects and their relations. We leverage direct set-based object prediction and incorporate the interaction among the objects to learn an object-relation representation jointly. In addition to existing [obj]-tokens, we propose a novel learnable token, namely [rln]-token. Together with [obj]-tokens, [rln]-token exploits local and global semantic reasoning in an image through a series of mutual associations. In combination with the pair-wise [obj]-token, the [rln]-token contributes to a computationally efficient relation prediction. We achieve state-of-the-art performance on multiple, diverse and multi-domain datasets that demonstrate our approach's effectiveness and generalizability.