arXiv subjects

Junlin Yang

Publications and source records attributed to Junlin Yang.

25 records · Page 2Linked to original sources

arXiv2020

2018 Robotic Scene Segmentation Challenge

In 2015 we began a sub-challenge at the EndoVis workshop at MICCAI in Munich using endoscope images of ex-vivo tissue with automatically generated annotations from robot forward kinematics and instrument CAD models. However, the limited background variation and simple motion rendered the dataset uninformative in learning about which techniques would be suitable for segmentation in real surgery. In 2017, at the same workshop in Quebec we introduced the robotic instrument segmentation dataset with 10 teams participating in the challenge to perform binary, articulating parts and type segmentation of da Vinci instruments. This challenge included realistic instrument motion and more complex porcine tissue as background and was widely addressed with modifications on U-Nets and other popular CNN architectures. In 2018 we added to the complexity by introducing a set of anatomical objects and medical devices to the segmented classes. To avoid over-complicating the challenge, we continued with porcine data which is dramatically simpler than human tissue due to the lack of fatty tissue occluding many organs.

cs.CV↗

arXiv2019

Hepatocellular Carcinoma Intra-arterial Treatment Response Prediction for Improved Therapeutic Decision-Making

This work proposes a pipeline to predict treatment response to intra-arterial therapy of patients with Hepatocellular Carcinoma (HCC) for improved therapeutic decision-making. Our graph neural network model seamlessly combines heterogeneous inputs of baseline MR scans, pre-treatment clinical information, and planned treatment characteristics and has been validated on patients with HCC treated by transarterial chemoembolization (TACE). It achieves Accuracy of $0.713 \pm 0.075$, F1 of $0.702 \pm 0.082$ and AUC of $0.710 \pm 0.108$. In addition, the pipeline incorporates uncertainty estimation to select hard cases and most align with the misclassified cases. The proposed pipeline arrives at more informed intra-arterial therapeutic decisions for patients with HCC via improving model accuracy and incorporating uncertainty estimation.

eess.IV↗

arXiv2019

Decision Explanation and Feature Importance for Invertible Networks

Deep neural networks are vulnerable to adversarial attacks and hard to interpret because of their black-box nature. The recently proposed invertible network is able to accurately reconstruct the inputs to a layer from its outputs, thus has the potential to unravel the black-box model. An invertible network classifier can be viewed as a two-stage model: (1) invertible transformation from input space to the feature space; (2) a linear classifier in the feature space. We can determine the decision boundary of a linear classifier in the feature space; since the transform is invertible, we can invert the decision boundary from the feature space to the input space. Furthermore, we propose to determine the projection of a data point onto the decision boundary, and define explanation as the difference between data and its projection. Finally, we propose to locally approximate a neural network with its first-order Taylor expansion, and define feature importance using a local linear model. We provide the implementation of our method: \url{https://github.com/juntang-zhuang/explain_invertible}.

cs.LG↗

arXiv2019

ShelfNet for Fast Semantic Segmentation

In this paper, we present ShelfNet, a novel architecture for accurate fast semantic segmentation. Different from the single encoder-decoder structure, ShelfNet has multiple encoder-decoder branch pairs with skip connections at each spatial level, which looks like a shelf with multiple columns. The shelf-shaped structure can be viewed as an ensemble of multiple deep and shallow paths, thus improving accuracy. We significantly reduce computation burden by reducing channel number, at the same time achieving high accuracy with this unique structure. In addition, we propose a shared-weight strategy in the residual block which reduces parameter number without sacrificing performance. Compared with popular non real-time methods such as PSPNet, our ShelfNet achieves 4$\times$ faster inference speed with similar accuracy on PASCAL VOC dataset. Compared with real-time segmentation models such as BiSeNet, our model achieves higher accuracy at comparable speed on the Cityscapes Dataset, enabling the application in speed-demanding tasks such as street-scene understanding for autonomous driving. Furthermore, our ShelfNet achieves 79.0\% mIoU on Cityscapes Dataset with ResNet34 backbone, outperforming PSPNet and BiSeNet with large backbones such as ResNet101. Through extensive experiments, we validated the superior performance of ShelfNet. We provide link to the implementation \url{https://github.com/juntang-zhuang/ShelfNet-lw-cityscapes}.

cs.CV↗

arXiv2019

Unsupervised Domain Adaptation via Disentangled Representations: Application to Cross-Modality Liver Segmentation

A deep learning model trained on some labeled data from a certain source domain generally performs poorly on data from different target domains due to domain shifts. Unsupervised domain adaptation methods address this problem by alleviating the domain shift between the labeled source data and the unlabeled target data. In this work, we achieve cross-modality domain adaptation, i.e. between CT and MRI images, via disentangled representations. Compared to learning a one-to-one mapping as the state-of-art CycleGAN, our model recovers a many-to-many mapping between domains to capture the complex cross-domain relations. It preserves semantic feature-level information by finding a shared content space instead of a direct pixelwise style transfer. Domain adaptation is achieved in two steps. First, images from each domain are embedded into two spaces, a shared domain-invariant content space and a domain-specific style space. Next, the representation in the content space is extracted to perform a task. We validated our method on a cross-modality liver segmentation task, to train a liver segmentation model on CT images that also performs well on MRI. Our method achieved Dice Similarity Coefficient (DSC) of 0.81, outperforming a CycleGAN-based method of 0.72. Moreover, our model achieved good generalization to joint-domain learning, in which unpaired data from different modalities are jointly learned to improve the segmentation performance on each individual modality. Lastly, under a multi-modal target domain with significant diversity, our approach exhibited the potential for diverse image generation and remained effective with DSC of 0.74 on multi-phasic MRI while the CycleGAN-based method performed poorly with a DSC of only 0.52.

eess.IV↗

arXiv2019

Domain-Agnostic Learning with Anatomy-Consistent Embedding for Cross-Modality Liver Segmentation

Domain Adaptation (DA) has the potential to greatly help the generalization of deep learning models. However, the current literature usually assumes to transfer the knowledge from the source domain to a specific known target domain. Domain Agnostic Learning (DAL) proposes a new task of transferring knowledge from the source domain to data from multiple heterogeneous target domains. In this work, we propose the Domain-Agnostic Learning framework with Anatomy-Consistent Embedding (DALACE) that works on both domain-transfer and task-transfer to learn a disentangled representation, aiming to not only be invariant to different modalities but also preserve anatomical structures for the DA and DAL tasks in cross-modality liver segmentation. We validated and compared our model with state-of-the-art methods, including CycleGAN, Task Driven Generative Adversarial Network (TD-GAN), and Domain Adaptation via Disentangled Representations (DADR). For the DA task, our DALACE model outperformed CycleGAN, TD-GAN ,and DADR with DSC of 0.847 compared to 0.721, 0.793 and 0.806. For the DAL task, our model improved the performance with DSC of 0.794 from 0.522, 0.719 and 0.742 by CycleGAN, TD-GAN, and DADR. Further, we visualized the success of disentanglement, which added human interpretability of the learned meaningful representations. Through ablation analysis, we specifically showed the concrete benefits of disentanglement for downstream tasks and the role of supervision for better disentangled representation with segmentation consistency to be invariant to domains with the proposed Domain-Agnostic Module (DAM) and to preserve anatomical information with the proposed Anatomy-Preserving Module (APM).

eess.IV↗

arXiv2019

Look Again at the Syntax: Relational Graph Convolutional Network for Gendered Ambiguous Pronoun Resolution

Gender bias has been found in existing coreference resolvers. In order to eliminate gender bias, a gender-balanced dataset Gendered Ambiguous Pronouns (GAP) has been released and the best baseline model achieves only 66.9% F1. Bidirectional Encoder Representations from Transformers (BERT) has broken several NLP task records and can be used on GAP dataset. However, fine-tune BERT on a specific task is computationally expensive. In this paper, we propose an end-to-end resolver by combining pre-trained BERT with Relational Graph Convolutional Network (R-GCN). R-GCN is used for digesting structural syntactic information and learning better task-specific embeddings. Empirical results demonstrate that, under explicit syntactic supervision and without the need to fine tune BERT, R-GCN's embeddings outperform the original BERT embeddings on the coreference task. Our work significantly improves the snippet-context baseline F1 score on GAP dataset from 66.9% to 80.3%. We participated in the 2019 GAP Coreference Shared Task, and our codes are available online.

cs.CL↗