pwc-archive/papers-with-abstracts huggingface dataset:
Learning to Exploit Temporal Structure for Biomedical Vision-Language Processing
Authors: Shruthi Bannur, Stephanie Hyland, Qianchu Liu, Fernando Pérez-García, Maximilian Ilse, Daniel C. Castro, Benedikt Boecking, Harshita Sharma, Kenza Bouzid, Anja Thieme, Anton Schwaighofer, Maria Wetscherek, Matthew P. Lungren, Aditya Nori, Javier Alvarez-Valle, Ozan Oktay
Date: 2023-01-11 00:00:00
Proceeding: CVPR 2023 1
Tasks: Phrase Grounding, Self-Supervised Learning, Sentence, Sentence Similarity

Self-supervised learning in vision-language processing exploits semantic alignment between imaging and text modalities. Prior work in biomedical VLP has mostly relied on the alignment of single image and report pairs even though clinical notes commonly refer to prior images. This does not only introduce poor alignment between the modalities but also a missed opportunity to exploit rich self-supervision through existing temporal content in the data. In this work, we explicitly account for prior images and reports when available during both training and fine-tuning. Our approach, named BioViL-T, uses a CNN-Transformer hybrid multi-image encoder trained jointly with a text model. It is designed to be versatile to arising challenges such as pose variations and missing input images across time. The resulting model excels on downstream tasks both in single- and multi-image setups, achieving state-of-the-art performance on (I) progression classification, (II) phrase grounding, and (III) report generation, whilst offering consistent improvements on disease classification and sentence-similarity tasks. We release a novel multi-modal temporal benchmark dataset, MS-CXR-T, to quantify the quality of vision-language representations in terms of temporal semantics. Our experimental results show the advantages of incorporating prior images and reports to make most use of the data.
Clustering disease trajectories in contrastive feature space for biomarker discovery in age-related macular degeneration
Authors: Robbie Holland, Oliver Leingang, Christopher Holmes, Philipp Anders, Rebecca Kaye, Sophie Riedl, Johannes C. Paetzold, Ivan Ezhov, Hrvoje Bogunović, Ursula Schmidt-Erfurth, Lars Fritsche, Hendrik P. N. Scholl, Sobha Sivaprasad, Andrew J. Lotery, Daniel Rueckert, Martin J. Menten
Date: 2023-01-11 00:00:00
Tasks: Contrastive Learning, Management, Time Series, Time Series Analysis

Age-related macular degeneration (AMD) is the leading cause of blindness in the elderly. Current grading systems based on imaging biomarkers only coarsely group disease stages into broad categories and are unable to predict future disease progression. It is widely believed that this is due to their focus on a single point in time, disregarding the dynamic nature of the disease. In this work, we present the first method to automatically discover biomarkers that capture temporal dynamics of disease progression. Our method represents patient time series as trajectories in a latent feature space built with contrastive learning. Then, individual trajectories are partitioned into atomic sub-sequences that encode transitions between disease states. These are clustered using a newly introduced distance metric. In quantitative experiments we found our method yields temporal biomarkers that are predictive of conversion to late AMD. Furthermore, these clusters were highly interpretable to ophthalmologists who confirmed that many of the clusters represent dynamics that have previously been linked to the progression of AMD, even though they are currently not included in any clinical grading system.
A new dataset for measuring the performance of blood vessel segmentation methods under distribution shifts
Authors: Matheus Viana da Silva, Natália de Carvalho Santos, Julie Ouellette, Baptiste Lacoste, Cesar Henrique Comin
Date: 2023-01-11 00:00:00
Tasks: Image Segmentation, Medical Image Segmentation, Segmentation, Semantic Segmentation

Creating a dataset for training supervised machine learning algorithms can be a demanding task. This is especially true for medical image segmentation since one or more specialists are usually required for image annotation, and creating ground truth labels for just a single image can take up to several hours. In addition, it is paramount that the annotated samples represent well the different conditions that might affect the imaged tissues as well as possible changes in the image acquisition process. This can only be achieved by considering samples that are typical in the dataset as well as atypical, or even outlier, samples. We introduce VessMAP, a heterogeneous blood vessel segmentation dataset acquired by carefully sampling relevant images from a larger non-annotated dataset. A methodology was developed to select both prototypical and atypical samples from the base dataset, thus defining an assorted set of images that can be used for measuring the performance of segmentation algorithms on samples that are highly distinct from each other. To demonstrate the potential of the new dataset, we show that the validation performance of a neural network changes significantly depending on the splits used for training the network.
A Distinct Unsupervised Reference Model From The Environment Helps Continual Learning
Authors: Seyyed AmirHossein Ameli Kalkhoran, Mohammadamin Banayeeanzade, Mahdi Samiei, Mahdieh Soleymani Baghshah
Date: 2023-01-11 00:00:00
Tasks: Continual Learning

The existing continual learning methods are mainly focused on fully-supervised scenarios and are still not able to take advantage of unlabeled data available in the environment. Some recent works tried to investigate semi-supervised continual learning (SSCL) settings in which the unlabeled data are available, but it is only from the same distribution as the labeled data. This assumption is still not general enough for real-world applications and restricts the utilization of unsupervised data. In this work, we introduce Open-Set Semi-Supervised Continual Learning (OSSCL), a more realistic semi-supervised continual learning setting in which out-of-distribution (OoD) unlabeled samples in the environment are assumed to coexist with the in-distribution ones. Under this configuration, we present a model with two distinct parts: (i) the reference network captures general-purpose and task-agnostic knowledge in the environment by using a broad spectrum of unlabeled samples, (ii) the learner network is designed to learn task-specific representations by exploiting supervised samples. The reference model both provides a pivotal representation space and also segregates unlabeled data to exploit them more efficiently. By performing a diverse range of experiments, we show the superior performance of our model compared with other competitors and prove the effectiveness of each component of the proposed model.
Pruning Compact ConvNets for Efficient Inference
Authors: Sayan Ghosh, Karthik Prasad, Xiaoliang Dai, Peizhao Zhang, Bichen Wu, Graham Cormode, Peter Vajda
Date: 2023-01-11 00:00:00
Tasks: GPU, Network Pruning, Neural Architecture Search

Neural network pruning is frequently used to compress over-parameterized networks by large amounts, while incurring only marginal drops in generalization performance. However, the impact of pruning on networks that have been highly optimized for efficient inference has not received the same level of attention. In this paper, we analyze the effect of pruning for computer vision, and study state-of-the-art ConvNets, such as the FBNetV3 family of models. We show that model pruning approaches can be used to further optimize networks trained through NAS (Neural Architecture Search). The resulting family of pruned models can consistently obtain better performance than existing FBNetV3 models at the same level of computation, and thus provide state-of-the-art results when trading off between computational complexity and generalization performance on the ImageNet benchmark. In addition to better generalization performance, we also demonstrate that when limited computation resources are available, pruning FBNetV3 models incur only a fraction of GPU-hours involved in running a full-scale NAS.
Dynamic Background Reconstruction via MAE for Infrared Small Target Detection
Authors: Jingchao Peng, Haitao Zhao, Kaijie Zhao, Zhongze Wang, Lujian Yao
Date: 2023-01-11 00:00:00

Infrared small target detection (ISTD) under complex backgrounds is a difficult problem, for the differences between targets and backgrounds are not easy to distinguish. Background reconstruction is one of the methods to deal with this problem. This paper proposes an ISTD method based on background reconstruction called Dynamic Background Reconstruction (DBR). DBR consists of three modules: a dynamic shift window module (DSW), a background reconstruction module (BR), and a detection head (DH). BR takes advantage of Vision Transformers in reconstructing missing patches and adopts a grid masking strategy with a masking ratio of 50\% to reconstruct clean backgrounds without targets. To avoid dividing one target into two neighboring patches, resulting in reconstructing failure, DSW is performed before input embedding. DSW calculates offsets, according to which infrared images dynamically shift. To reduce False Positive (FP) cases caused by regarding reconstruction errors as targets, DH utilizes a structure of densely connected Transformer to further improve the detection performance. Experimental results show that DBR achieves the best F1-score on the two ISTD datasets, MFIRST (64.10\%) and SIRST (75.01\%).
Multi-label Image Classification using Adaptive Graph Convolutional Networks: from a Single Domain to Multiple Domains
Authors: Indel Pal Singh, Enjie Ghorbel, Oyebade Oyedotun, Djamila Aouada
Date: 2023-01-11 00:00:00
Tasks: image-classification, Image Classification, Multi-Label Classification, MUlTI-LABEL-ClASSIFICATION, Multi-Label Image Classification

This paper proposes an adaptive graph-based approach for multi-label image classification. Graph-based methods have been largely exploited in the field of multi-label classification, given their ability to model label correlations. Specifically, their effectiveness has been proven not only when considering a single domain but also when taking into account multiple domains. However, the topology of the used graph is not optimal as it is pre-defined heuristically. In addition, consecutive Graph Convolutional Network (GCN) aggregations tend to destroy the feature similarity. To overcome these issues, an architecture for learning the graph connectivity in an end-to-end fashion is introduced. This is done by integrating an attention-based mechanism and a similarity-preserving strategy. The proposed framework is then extended to multiple domains using an adversarial training scheme. Numerous experiments are reported on well-known single-domain and multi-domain benchmarks. The results demonstrate that our approach achieves competitive results in terms of mean Average Precision (mAP) and model size as compared to the state-of-the-art. The code will be made publicly available.
Co-training with High-Confidence Pseudo Labels for Semi-supervised Medical Image Segmentation
Authors: Zhiqiang Shen, Peng Cao, Hua Yang, Xiaoli Liu, Jinzhu Yang, Osmar R. Zaiane
Date: 2023-01-11 00:00:00
Tasks: Image Segmentation, Left Atrium Segmentation, Medical Image Segmentation, Segmentation, Semantic Segmentation, Semi-supervised Medical Image Segmentation, Semi-Supervised Semantic Segmentation

Consistency regularization and pseudo labeling-based semi-supervised methods perform co-training using the pseudo labels from multi-view inputs. However, such co-training models tend to converge early to a consensus, degenerating to the self-training ones, and produce low-confidence pseudo labels from the perturbed inputs during training. To address these issues, we propose an Uncertainty-guided Collaborative Mean-Teacher (UCMT) for semi-supervised semantic segmentation with the high-confidence pseudo labels. Concretely, UCMT consists of two main components: 1) collaborative mean-teacher (CMT) for encouraging model disagreement and performing co-training between the sub-networks, and 2) uncertainty-guided region mix (UMIX) for manipulating the input images according to the uncertainty maps of CMT and facilitating CMT to produce high-confidence pseudo labels. Combining the strengths of UMIX with CMT, UCMT can retain model disagreement and enhance the quality of pseudo labels for the co-training segmentation. Extensive experiments on four public medical image datasets including 2D and 3D modalities demonstrate the superiority of UCMT over the state-of-the-art. Code is available at: https://github.com/Senyh/UCMT.
Fast spline detection in high density microscopy data
Authors: Albert Alonso, Julius B. Kirkegaard
Date: 2023-01-11 00:00:00
Tasks: Body Detection, Overlapping Pose Estimation

Computer-aided analysis of biological microscopy data has seen a massive improvement with the utilization of general-purpose deep learning techniques. Yet, in microscopy studies of multi-organism systems, the problem of collision and overlap remains challenging. This is particularly true for systems composed of slender bodies such as crawling nematodes, swimming spermatozoa, or the beating of eukaryotic or prokaryotic flagella. Here, we develop a novel end-to-end deep learning approach to extract precise shape trajectories of generally motile and overlapping splines. Our method works in low resolution settings where feature keypoints are hard to define and detect. Detection is fast and we demonstrate the ability to track thousands of overlapping organisms simultaneously. While our approach is agnostic to area of application, we present it in the setting of and exemplify its usability on dense experiments of crawling Caenorhabditis elegans. The model training is achieved purely on synthetic data, utilizing a physics-based model for nematode motility, and we demonstrate the model's ability to generalize from simulations to experimental videos.
Heterogeneous Tri-stream Clustering Network
Authors: Xiaozhi Deng, Dong Huang, Chang-Dong Wang
Date: 2023-01-11 00:00:00
Tasks: Clustering, Contrastive Learning, Deep Clustering

Contrastive deep clustering has recently gained significant attention with its ability of joint contrastive learning and clustering via deep neural networks. Despite the rapid progress, previous works mostly require both positive and negative sample pairs for contrastive clustering, which rely on a relative large batch-size. Moreover, they typically adopt a two-stream architecture with two augmented views, which overlook the possibility and potential benefits of multi-stream architectures (especially with heterogeneous or hybrid networks). In light of this, this paper presents a new end-to-end deep clustering approach termed Heterogeneous Tri-stream Clustering Network (HTCN). The tri-stream architecture in HTCN consists of three main components, including two weight-sharing online networks and a target network, where the parameters of the target network are the exponential moving average of that of the online networks. Notably, the two online networks are trained by simultaneously (i) predicting the instance representations of the target network and (ii) enforcing the consistency between the cluster representations of the target network and that of the two online networks. Experimental results on four challenging image datasets demonstrate the superiority of HTCN over the state-of-the-art deep clustering approaches. The code is available at https://github.com/dengxiaozhi/HTCN.
VS-Net: Multiscale Spatiotemporal Features for Lightweight Video Salient Document Detection
Authors: Hemraj Singh, Mridula Verma, Ramalingaswamy Cheruku
Date: 2023-01-11 00:00:00

Video Salient Document Detection (VSDD) is an essential task of practical computer vision, which aims to highlight visually salient document regions in video frames. Previous techniques for VSDD focus on learning features without considering the cooperation among and across the appearance and motion cues and thus fail to perform in practical scenarios. Moreover, most of the previous techniques demand high computational resources, which limits the usage of such systems in resource-constrained settings. To handle these issues, we propose VS-Net, which captures multi-scale spatiotemporal information with the help of dilated depth-wise separable convolution and Approximation Rank Pooling. VS-Net extracts the key features locally from each frame across embedding sub-spaces and forwards the features between adjacent and parallel nodes, enhancing model performance globally. Our model generates saliency maps considering both the background and foreground simultaneously, making it perform better in challenging scenarios. The immense experiments regulated on the benchmark MIDV-500 dataset show that the VS-Net model outperforms state-of-the-art approaches in both time and robustness measures.
Multi-Scanner Canine Cutaneous Squamous Cell Carcinoma Histopathology Dataset
Authors: Frauke Wilm, Marco Fragoso, Christof A. Bertram, Nikolas Stathonikos, Mathias Öttl, Jingna Qiu, Robert Klopfleisch, Andreas Maier, Katharina Breininger, Marc Aubreville
Date: 2023-01-11 00:00:00
Tasks: Domain Generalization, Tumor Segmentation

In histopathology, scanner-induced domain shifts are known to impede the performance of trained neural networks when tested on unseen data. Multi-domain pre-training or dedicated domain-generalization techniques can help to develop domain-agnostic algorithms. For this, multi-scanner datasets with a high variety of slide scanning systems are highly desirable. We present a publicly available multi-scanner dataset of canine cutaneous squamous cell carcinoma histopathology images, composed of 44 samples digitized with five slide scanners. This dataset provides local correspondences between images and thereby isolates the scanner-induced domain shift from other inherent, e.g. morphology-induced domain shifts. To highlight scanner differences, we present a detailed evaluation of color distributions, sharpness, and contrast of the individual scanner subsets. Additionally, to quantify the inherent scanner-induced domain shift, we train a tumor segmentation network on each scanner subset and evaluate the performance both in- and cross-domain. We achieve a class-averaged in-domain intersection over union coefficient of up to 0.86 and observe a cross-domain performance decrease of up to 0.38, which confirms the inherent domain shift of the presented dataset and its negative impact on the performance of deep neural networks.
Optical Flow for Autonomous Driving: Applications, Challenges and Improvements
Authors: Shihao Shen, Louis Kerofsky, Senthil Yogamani
Date: 2023-01-11 00:00:00
Tasks: Autonomous Driving, Optical Flow Estimation

Optical flow estimation is a well-studied topic for automated driving applications. Many outstanding optical flow estimation methods have been proposed, but they become erroneous when tested in challenging scenarios that are commonly encountered. Despite the increasing use of fisheye cameras for near-field sensing in automated driving, there is very limited literature on optical flow estimation with strong lens distortion. Thus we propose and evaluate training strategies to improve a learning-based optical flow algorithm by leveraging the only existing fisheye dataset with optical flow ground truth. While trained with synthetic data, the model demonstrates strong capabilities to generalize to real world fisheye data. The other challenge neglected by existing state-of-the-art algorithms is low light. We propose a novel, generic semi-supervised framework that significantly boosts performances of existing methods in such conditions. To the best of our knowledge, this is the first approach that explicitly handles optical flow estimation in low light.
Failure Detection for Motion Prediction of Autonomous Driving: An Uncertainty Perspective
Authors: Wenbo Shao, Yanchao Xu, Liang Peng, Jun Li, Hong Wang
Date: 2023-01-11 00:00:00
Tasks: Autonomous Driving, motion prediction, Prediction

Motion prediction is essential for safe and efficient autonomous driving. However, the inexplicability and uncertainty of complex artificial intelligence models may lead to unpredictable failures of the motion prediction module, which may mislead the system to make unsafe decisions. Therefore, it is necessary to develop methods to guarantee reliable autonomous driving, where failure detection is a potential direction. Uncertainty estimates can be used to quantify the degree of confidence a model has in its predictions and may be valuable for failure detection. We propose a framework of failure detection for motion prediction from the uncertainty perspective, considering both motion uncertainty and model uncertainty, and formulate various uncertainty scores according to different prediction stages. The proposed approach is evaluated based on different motion prediction algorithms, uncertainty estimation methods, uncertainty scores, etc., and the results show that uncertainty is promising for failure detection for motion prediction but should be used with caution.
pyssam -- a Python library for statistical modelling of biomedical shape and appearance
Authors: Josh Williams, Ali Ozel, Uwe Wolfram
Date: 2023-01-11 00:00:00
Tasks: Image Segmentation, Medical Image Segmentation, Semantic Segmentation

pyssam is a Python library for creating statistical shape and appearance models (SSAMs) for biological (and other) shapes such as bones, lungs or other organs. A point cloud best describing the anatomical 'landmarks' of the organ are required from each sample in a small population as an input. Additional information such as landmark gray-value can be included to incorporate joint correlations of shape and 'appearance' into the model. Our library performs alignment and scaling of the input data and creates a SSAM based on covariance across the population. The output SSAM can be used to parameterise and quantify shape change across a population. pyssam is a small and low dependency codebase with examples included as Jupyter notebooks for several common SSAM computations. The given examples can easily be extended to alternative datasets, and also alternative tasks such as medical image segmentation by incorporating a SSAM as a constraint for segmented organs.