arXiv subjects

Wei Shen

Publications and source records attributed to Wei Shen.

At least 181 records · Page 10Linked to original sources

arXiv2021

The Medical Segmentation Decathlon

International challenges have become the de facto standard for comparative assessment of image analysis algorithms given a specific task. Segmentation is so far the most widely investigated medical image processing task, but the various segmentation challenges have typically been organized in isolation, such that algorithm development was driven by the need to tackle a single specific clinical problem. We hypothesized that a method capable of performing well on multiple tasks will generalize well to a previously unseen task and potentially outperform a custom-designed solution. To investigate the hypothesis, we organized the Medical Segmentation Decathlon (MSD) - a biomedical image analysis challenge, in which algorithms compete in a multitude of both tasks and modalities. The underlying data set was designed to explore the axis of difficulties typically encountered when dealing with medical images, such as small data sets, unbalanced labels, multi-site data and small objects. The MSD challenge confirmed that algorithms with a consistent good performance on a set of tasks preserved their good average performance on a different set of previously unseen tasks. Moreover, by monitoring the MSD winner for two years, we found that this algorithm continued generalizing well to a wide range of other clinical problems, further confirming our hypothesis. Three main conclusions can be drawn from this study: (1) state-of-the-art image segmentation algorithms are mature, accurate, and generalize well when retrained on unseen tasks; (2) consistent algorithmic performance across multiple tasks is a strong surrogate of algorithmic generalizability; (3) the training of accurate AI segmentation models is now commoditized to non AI experts.

eess.IV↗

arXiv2021

Making CNNs Interpretable by Building Dynamic Sequential Decision Forests with Top-down Hierarchy Learning

In this paper, we propose a generic model transfer scheme to make Convlutional Neural Networks (CNNs) interpretable, while maintaining their high classification accuracy. We achieve this by building a differentiable decision forest on top of CNNs, which enjoys two characteristics: 1) During training, the tree hierarchies of the forest are learned in a top-down manner under the guidance from the category semantics embedded in the pre-trained CNN weights; 2) During inference, a single decision tree is dynamically selected from the forest for each input sample, enabling the transferred model to make sequential decisions corresponding to the attributes shared by semantically-similar categories, rather than directly performing flat classification. We name the transferred model deep Dynamic Sequential Decision Forest (dDSDF). Experimental results show that dDSDF not only achieves higher classification accuracy than its conuterpart, i.e., the original CNN, but has much better interpretability, as qualitatively it has plausible hierarchies and quantitatively it leads to more precise saliency maps.

cs.CV↗

arXiv2021

Glance-and-Gaze Vision Transformer

Recently, there emerges a series of vision Transformers, which show superior performance with a more compact model size than conventional convolutional neural networks, thanks to the strong ability of Transformers to model long-range dependencies. However, the advantages of vision Transformers also come with a price: Self-attention, the core part of Transformer, has a quadratic complexity to the input sequence length. This leads to a dramatic increase of computation and memory cost with the increase of sequence length, thus introducing difficulties when applying Transformers to the vision tasks that require dense predictions based on high-resolution feature maps. In this paper, we propose a new vision Transformer, named Glance-and-Gaze Transformer (GG-Transformer), to address the aforementioned issues. It is motivated by the Glance and Gaze behavior of human beings when recognizing objects in natural scenes, with the ability to efficiently model both long-range dependencies and local context. In GG-Transformer, the Glance and Gaze behavior is realized by two parallel branches: The Glance branch is achieved by performing self-attention on the adaptively-dilated partitions of the input, which leads to a linear complexity while still enjoying a global receptive field; The Gaze branch is implemented by a simple depth-wise convolutional layer, which compensates local image context to the features obtained by the Glance mechanism. We empirically demonstrate our method achieves consistently superior performance over previous state-of-the-art Transformers on various vision tasks and benchmarks. The codes and models will be made available at https://github.com/yucornetto/GG-Transformer.

cs.CV↗

arXiv2021

Learning Inductive Attention Guidance for Partially Supervised Pancreatic Ductal Adenocarcinoma Prediction

Pancreatic ductal adenocarcinoma (PDAC) is the third most common cause of cancer death in the United States. Predicting tumors like PDACs (including both classification and segmentation) from medical images by deep learning is becoming a growing trend, but usually a large number of annotated data are required for training, which is very labor-intensive and time-consuming. In this paper, we consider a partially supervised setting, where cheap image-level annotations are provided for all the training data, and the costly per-voxel annotations are only available for a subset of them. We propose an Inductive Attention Guidance Network (IAG-Net) to jointly learn a global image-level classifier for normal/PDAC classification and a local voxel-level classifier for semi-supervised PDAC segmentation. We instantiate both the global and the local classifiers by multiple instance learning (MIL), where the attention guidance, indicating roughly where the PDAC regions are, is the key to bridging them: For global MIL based normal/PDAC classification, attention serves as a weight for each instance (voxel) during MIL pooling, which eliminates the distraction from the background; For local MIL based semi-supervised PDAC segmentation, the attention guidance is inductive, which not only provides bag-level pseudo-labels to training data without per-voxel annotations for MIL training, but also acts as a proxy of an instance-level classifier. Experimental results show that our IAG-Net boosts PDAC segmentation accuracy by more than 5% compared with the state-of-the-arts.

cs.CV↗

arXiv2021

Shape-Texture Debiased Neural Network Training

Shape and texture are two prominent and complementary cues for recognizing objects. Nonetheless, Convolutional Neural Networks are often biased towards either texture or shape, depending on the training dataset. Our ablation shows that such bias degenerates model performance. Motivated by this observation, we develop a simple algorithm for shape-texture debiased learning. To prevent models from exclusively attending on a single cue in representation learning, we augment training data with images with conflicting shape and texture information (eg, an image of chimpanzee shape but with lemon texture) and, most importantly, provide the corresponding supervisions from shape and texture simultaneously. Experiments show that our method successfully improves model performance on several image recognition benchmarks and adversarial robustness. For example, by training on ImageNet, it helps ResNet-152 achieve substantial improvements on ImageNet (+1.2%), ImageNet-A (+5.2%), ImageNet-C (+8.3%) and Stylized-ImageNet (+11.1%), and on defending against FGSM adversarial attacker on ImageNet (+14.4%). Our method also claims to be compatible with other advanced data augmentation strategies, eg, Mixup, and CutMix. The code is available here: https://github.com/LiYingwei/ShapeTextureDebiasedTraining.

cs.CV↗

arXiv2021

Deeply Shape-guided Cascade for Instance Segmentation

The key to a successful cascade architecture for precise instance segmentation is to fully leverage the relationship between bounding box detection and mask segmentation across multiple stages. Although modern instance segmentation cascades achieve leading performance, they mainly make use of a unidirectional relationship, i.e., mask segmentation can benefit from iteratively refined bounding box detection. In this paper, we investigate an alternative direction, i.e., how to take the advantage of precise mask segmentation for bounding box detection in a cascade architecture. We propose a Deeply Shape-guided Cascade (DSC) for instance segmentation, which iteratively imposes the shape guidances extracted from mask prediction at the previous stage on bounding box detection at current stage. It forms a bi-directional relationship between the two tasks by introducing three key components: (1) Initial shape guidance: A mask-supervised Region Proposal Network (mPRN) with the ability to generate class-agnostic masks; (2) Explicit shape guidance: A mask-guided region-of-interest (RoI) feature extractor, which employs mask segmentation at previous stage to focus feature extraction at current stage within a region aligned well with the shape of the instance-of-interest rather than a rectangular RoI; (3) Implicit shape guidance: A feature fusion operation which feeds intermediate mask features at previous stage to the bounding box head at current stage. Experimental results show that DSC outperforms the state-of-the-art instance segmentation cascade, Hybrid Task Cascade (HTC), by a large margin and achieves 51.8 box AP and 45.5 mask AP on COCO test-dev. The code is released at: https://github.com/hding2455/DSC.

cs.CV↗

arXiv2021

SpecTr: Spectral Transformer for Hyperspectral Pathology Image Segmentation

Hyperspectral imaging (HSI) unlocks the huge potential to a wide variety of applications relied on high-precision pathology image segmentation, such as computational pathology and precision medicine. Since hyperspectral pathology images benefit from the rich and detailed spectral information even beyond the visible spectrum, the key to achieve high-precision hyperspectral pathology image segmentation is to felicitously model the context along high-dimensional spectral bands. Inspired by the strong context modeling ability of transformers, we hereby, for the first time, formulate the contextual feature learning across spectral bands for hyperspectral pathology image segmentation as a sequence-to-sequence prediction procedure by transformers. To assist spectral context learning procedure, we introduce two important strategies: (1) a sparsity scheme enforces the learned contextual relationship to be sparse, so as to eliminates the distraction from the redundant bands; (2) a spectral normalization, a separate group normalization for each spectral band, mitigates the nuisance caused by heterogeneous underlying distributions of bands. We name our method Spectral Transformer (SpecTr), which enjoys two benefits: (1) it has a strong ability to model long-range dependency among spectral bands, and (2) it jointly explores the spatial-spectral features of HSI. Experiments show that SpecTr outperforms other competing methods in a hyperspectral pathology image segmentation benchmark without the need of pre-training. Code is available at https://github.com/hfut-xc-yun/SpecTr.

eess.IV↗

arXiv2021

The Mu3e Data Acquisition

The Mu3e experiment aims to find or exclude the lepton flavour violating decay $μ^+\to e^+e^-e^+$ with a sensitivity of one in 10$^{16}$ muon decays. The first phase of the experiment is currently under construction at the Paul Scherrer Institute (PSI, Switzerland), where beams with up to 10$^8$ muons per second are available. The detector will consist of an ultra-thin pixel tracker made from High-Voltage Monolithic Active Pixel Sensors (HV-MAPS), complemented by scintillating tiles and fibres for precise timing measurements. The experiment produces about 100 Gbit/s of zero-suppressed data which are transported to a filter farm using a network of FPGAs and fast optical links. On the filter farm, tracks and three-particle vertices are reconstructed using highly parallel algorithms running on graphics processing units, leading to a reduction of the data to 100 Mbyte/s for mass storage and offline analysis. The paper introduces the system design and hardware implementation of the Mu3e data acquisition and filter farm.

physics.ins-det↗

arXiv2020

Batch Normalization with Enhanced Linear Transformation

Batch normalization (BN) is a fundamental unit in modern deep networks, in which a linear transformation module was designed for improving BN's flexibility of fitting complex data distributions. In this paper, we demonstrate properly enhancing this linear transformation module can effectively improve the ability of BN. Specifically, rather than using a single neuron, we propose to additionally consider each neuron's neighborhood for calculating the outputs of the linear transformation. Our method, named BNET, can be implemented with 2-3 lines of code in most deep learning libraries. Despite the simplicity, BNET brings consistent performance gains over a wide range of backbones and visual benchmarks. Moreover, we verify that BNET accelerates the convergence of network training and enhances spatial information by assigning the important neurons with larger weights accordingly. The code is available at https://github.com/yuhuixu1993/BNET.

cs.CV↗

arXiv2020

Evaluation of the KLauS ASIC at low temperature

The Taishan Antineutrino Observatory (TAO) is proposed to first use a cold liquid scintillator detector (-50~$^\circ$C) equipped with large-area silicon photomultipliers (SiPMs) ($\sim$10~m$^2$) to precisely measure the reactor antineutrino spectrum with a record energy resolution of < 2\% at 1 MeV. The KLauS ASIC shows excellent performance at room temperature and is a potential readout solution for TAO. In this work, we report evaluations of the fifth version of the KLauS ASIC (KLauS5) from room temperature to -50~$^\circ$C with inputs of injected charge or SiPMs. Our results show that KLauS5 has good performance at the tested temperatures with no significant degradation of the charge noise, charge linearity, gain uniformity or recovery time. Meanwhile, we also observe that several key parameters degrade when the chip operates in cold conditions, including the dynamic range and power consumption. However, even with this degradation, a good signal-to-noise ratio and good resolution of a single photoelectron can still be achieved for the tested SiPM with a gain of greater than 1.5$\times$10$^6$ and even an area of SiPM up to 1~cm$^2$ in one channel, corresponding to an input capacitance of approximately 5~nF. Thus, we conclude that KLauS5 can fulfill the TAO requirements for precise charge measurement.

physics.ins-det↗

arXiv2020

Volumetric Medical Image Segmentation: A 3D Deep Coarse-to-fine Framework and Its Adversarial Examples

Although deep neural networks have been a dominant method for many 2D vision tasks, it is still challenging to apply them to 3D tasks, such as medical image segmentation, due to the limited amount of annotated 3D data and limited computational resources. In this chapter, by rethinking the strategy to apply 3D Convolutional Neural Networks to segment medical images, we propose a novel 3D-based coarse-to-fine framework to efficiently tackle these challenges. The proposed 3D-based framework outperforms their 2D counterparts by a large margin since it can leverage the rich spatial information along all three axes. We further analyze the threat of adversarial attacks on the proposed framework and show how to defense against the attack. We conduct experiments on three datasets, the NIH pancreas dataset, the JHMI pancreas dataset and the JHMI pathological cyst dataset, where the first two and the last one contain healthy and pathological pancreases respectively, and achieve the current state-of-the-art in terms of Dice-Sorensen Coefficient (DSC) on all of them. Especially, on the NIH pancreas segmentation dataset, we outperform the previous best by an average of over $2\%$, and the worst case is improved by $7\%$ to reach almost $70\%$, which indicates the reliability of our framework in clinical applications.

cs.CV↗

arXiv2020

AutoADR: Automatic Model Design for Ad Relevance

Large-scale pre-trained models have attracted extensive attention in the research community and shown promising results on various tasks of natural language processing. However, these pre-trained models are memory and computation intensive, hindering their deployment into industrial online systems like Ad Relevance. Meanwhile, how to design an effective yet efficient model architecture is another challenging problem in online Ad Relevance. Recently, AutoML shed new lights on architecture design, but how to integrate it with pre-trained language models remains unsettled. In this paper, we propose AutoADR (Automatic model design for AD Relevance) -- a novel end-to-end framework to address this challenge, and share our experience to ship these cutting-edge techniques into online Ad Relevance system at Microsoft Bing. Specifically, AutoADR leverages a one-shot neural architecture search algorithm to find a tailored network architecture for Ad Relevance. The search process is simultaneously guided by knowledge distillation from a large pre-trained teacher model (e.g. BERT), while taking the online serving constraints (e.g. memory and latency) into consideration. We add the model designed by AutoADR as a sub-model into the production Ad Relevance model. This additional sub-model improves the Precision-Recall AUC (PR AUC) on top of the original Ad Relevance model by 2.65X of the normalized shipping bar. More importantly, adding this automatically designed sub-model leads to a statistically significant 4.6% Bad-Ad ratio reduction in online A/B testing. This model has been shipped into Microsoft Bing Ad Relevance Production model.

cs.CL↗

arXiv2020

CO2: Consistent Contrast for Unsupervised Visual Representation Learning

Contrastive learning has been adopted as a core method for unsupervised visual representation learning. Without human annotation, the common practice is to perform an instance discrimination task: Given a query image crop, this task labels crops from the same image as positives, and crops from other randomly sampled images as negatives. An important limitation of this label assignment strategy is that it can not reflect the heterogeneous similarity between the query crop and each crop from other images, taking them as equally negative, while some of them may even belong to the same semantic class as the query. To address this issue, inspired by consistency regularization in semi-supervised learning on unlabeled data, we propose Consistent Contrast (CO2), which introduces a consistency regularization term into the current contrastive learning framework. Regarding the similarity of the query crop to each crop from other images as "unlabeled", the consistency term takes the corresponding similarity of a positive crop as a pseudo label, and encourages consistency between these two similarities. Empirically, CO2 improves Momentum Contrast (MoCo) by 2.9% top-1 accuracy on ImageNet linear protocol, 3.8% and 1.1% top-5 accuracy on 1% and 10% labeled semi-supervised settings. It also transfers to image classification, object detection, and semantic segmentation on PASCAL VOC. This shows that CO2 learns better visual representations for these downstream tasks.

cs.CV↗

arXiv2020

Synthesize then Compare: Detecting Failures and Anomalies for Semantic Segmentation

The ability to detect failures and anomalies are fundamental requirements for building reliable systems for computer vision applications, especially safety-critical applications of semantic segmentation, such as autonomous driving and medical image analysis. In this paper, we systematically study failure and anomaly detection for semantic segmentation and propose a unified framework, consisting of two modules, to address these two related problems. The first module is an image synthesis module, which generates a synthesized image from a segmentation layout map, and the second is a comparison module, which computes the difference between the synthesized image and the input image. We validate our framework on three challenging datasets and improve the state-of-the-arts by large margins, \emph{i.e.}, 6% AUPR-Error on Cityscapes, 7% Pearson correlation on pancreatic tumor segmentation in MSD and 20% AUPR on StreetHazards anomaly segmentation.

cs.CV↗

arXiv2020

Auxiliary-task Based Deep Reinforcement Learning for Participant Selection Problem in Mobile Crowdsourcing

In mobile crowdsourcing (MCS), the platform selects participants to complete location-aware tasks from the recruiters aiming to achieve multiple goals (e.g., profit maximization, energy efficiency, and fairness). However, different MCS systems have different goals and there are possibly conflicting goals even in one MCS system. Therefore, it is crucial to design a participant selection algorithm that applies to different MCS systems to achieve multiple goals. To deal with this issue, we formulate the participant selection problem as a reinforcement learning problem and propose to solve it with a novel method, which we call auxiliary-task based deep reinforcement learning (ADRL). We use transformers to extract representations from the context of the MCS system and a pointer network to deal with the combinatorial optimization problem. To improve the sample efficiency, we adopt an auxiliary-task training process that trains the network to predict the imminent tasks from the recruiters, which facilitates the embedding learning of the deep learning model. Additionally, we release a simulated environment on a specific MCS task, the ride-sharing task, and conduct extensive performance evaluations in this environment. The experimental results demonstrate that ADRL outperforms and improves sample efficiency over other well-recognized baselines in various settings.

cs.LG↗

arXiv2020

Micro-Batch Training with Batch-Channel Normalization and Weight Standardization

Batch Normalization (BN) has become an out-of-box technique to improve deep network training. However, its effectiveness is limited for micro-batch training, i.e., each GPU typically has only 1-2 images for training, which is inevitable for many computer vision tasks, e.g., object detection and semantic segmentation, constrained by memory consumption. To address this issue, we propose Weight Standardization (WS) and Batch-Channel Normalization (BCN) to bring two success factors of BN into micro-batch training: 1) the smoothing effects on the loss landscape and 2) the ability to avoid harmful elimination singularities along the training trajectory. WS standardizes the weights in convolutional layers to smooth the loss landscape by reducing the Lipschitz constants of the loss and the gradients; BCN combines batch and channel normalizations and leverages estimated statistics of the activations in convolutional layers to keep networks away from elimination singularities. We validate WS and BCN on comprehensive computer vision tasks, including image classification, object detection, instance segmentation, video recognition and semantic segmentation. All experimental results consistently show that WS and BCN improve micro-batch training significantly. Moreover, using WS and BCN with micro-batch training is even able to match or outperform the performances of BN with large-batch training.

cs.CV↗

arXiv2020

Domain Adaptive Relational Reasoning for 3D Multi-Organ Segmentation

In this paper, we present a novel unsupervised domain adaptation (UDA) method, named Domain Adaptive Relational Reasoning (DARR), to generalize 3D multi-organ segmentation models to medical data collected from different scanners and/or protocols (domains). Our method is inspired by the fact that the spatial relationship between internal structures in medical images is relatively fixed, e.g., a spleen is always located at the tail of a pancreas, which serves as a latent variable to transfer the knowledge shared across multiple domains. We formulate the spatial relationship by solving a jigsaw puzzle task, i.e., recovering a CT scan from its shuffled patches, and jointly train it with the organ segmentation task. To guarantee the transferability of the learned spatial relationship to multiple domains, we additionally introduce two schemes: 1) Employing a super-resolution network also jointly trained with the segmentation model to standardize medical images from different domain to a certain spatial resolution; 2) Adapting the spatial relationship for a test image by test-time jigsaw puzzle training. Experimental results show that our method improves the performance by 29.60% DSC on target datasets on average without using any data from the target domain during training.

cs.CV↗

arXiv2020

Towards Unsupervised Learning for Instrument Segmentation in Robotic Surgery with Cycle-Consistent Adversarial Networks

Surgical tool segmentation in endoscopic images is an important problem: it is a crucial step towards full instrument pose estimation and it is used for integration of pre- and intra-operative images into the endoscopic view. While many recent approaches based on convolutional neural networks have shown great results, a key barrier to progress lies in the acquisition of a large number of manually-annotated images which is necessary for an algorithm to generalize and work well in diverse surgical scenarios. Unlike the surgical image data itself, annotations are difficult to acquire and may be of variable quality. On the other hand, synthetic annotations can be automatically generated by using forward kinematic model of the robot and CAD models of tools by projecting them onto an image plane. Unfortunately, this model is very inaccurate and cannot be used for supervised learning of image segmentation models. Since generated annotations will not directly correspond to endoscopic images due to errors, we formulate the problem as an unpaired image-to-image translation where the goal is to learn the mapping between an input endoscopic image and a corresponding annotation using an adversarial model. Our approach allows to train image segmentation models without the need to acquire expensive annotations and can potentially exploit large unlabeled endoscopic image collection outside the annotated distributions of image/annotation data. We test our proposed method on Endovis 2017 challenge dataset and show that it is competitive with supervised segmentation methods.

cs.CV↗