arXiv subjects

Guotong Xie

Publications and source records attributed to Guotong Xie.

30 records · Page 2Linked to original sources

arXiv2021

SAME: Deformable Image Registration based on Self-supervised Anatomical Embeddings

In this work, we introduce a fast and accurate method for unsupervised 3D medical image registration. This work is built on top of a recent algorithm SAM, which is capable of computing dense anatomical/semantic correspondences between two images at the pixel level. Our method is named SAME, which breaks down image registration into three steps: affine transformation, coarse deformation, and deep deformable registration. Using SAM embeddings, we enhance these steps by finding more coherent correspondences, and providing features and a loss function with better semantic guidance. We collect a multi-phase chest computed tomography dataset with 35 annotated organs for each patient and conduct inter-subject registration for quantitative evaluation. Results show that SAME outperforms widely-used traditional registration techniques (Elastix FFD, ANTs SyN) and learning based VoxelMorph method by at least 4.7% and 2.7% in Dice scores for two separate tasks of within-contrast-phase and across-contrast-phase registration, respectively. SAME achieves the comparable performance to the best traditional registration method, DEEDS (from our evaluation), while being orders of magnitude faster (from 45 seconds to 1.2 seconds).

eess.IV↗

arXiv2021

DeepStationing: Thoracic Lymph Node Station Parsing in CT Scans using Anatomical Context Encoding and Key Organ Auto-Search

Lymph node station (LNS) delineation from computed tomography (CT) scans is an indispensable step in radiation oncology workflow. High inter-user variabilities across oncologists and prohibitive laboring costs motivated the automated approach. Previous works exploit anatomical priors to infer LNS based on predefined ad-hoc margins. However, without voxel-level supervision, the performance is severely limited. LNS is highly context-dependent - LNS boundaries are constrained by anatomical organs - we formulate it as a deep spatial and contextual parsing problem via encoded anatomical organs. This permits the deep network to better learn from both CT appearance and organ context. We develop a stratified referencing organ segmentation protocol that divides the organs into anchor and non-anchor categories and uses the former's predictions to guide the later segmentation. We further develop an auto-search module to identify the key organs that opt for the optimal LNS parsing performance. Extensive four-fold cross-validation experiments on a dataset of 98 esophageal cancer patients (with the most comprehensive set of 12 LNSs + 22 organs in thoracic region to date) are conducted. Our LNS parsing model produces significant performance improvements, with an average Dice score of 81.1% +/- 6.1%, which is 5.0% and 19.2% higher over the pure CT-based deep model and the previous representative approach, respectively.

eess.IV↗

arXiv2021

AutoTrans: Automating Transformer Design via Reinforced Architecture Search

Though the transformer architectures have shown dominance in many natural language understanding tasks, there are still unsolved issues for the training of transformer models, especially the need for a principled way of warm-up which has shown importance for stable training of a transformer, as well as whether the task at hand prefer to scale the attention product or not. In this paper, we empirically explore automating the design choices in the transformer model, i.e., how to set layer-norm, whether to scale, number of layers, number of heads, activation function, etc, so that one can obtain a transformer architecture that better suits the tasks at hand. RL is employed to navigate along search space, and special parameter sharing strategies are designed to accelerate the search. It is shown that sampling a proportion of training data per epoch during search help to improve the search quality. Experiments on the CoNLL03, Multi-30k, IWSLT14 and WMT-14 shows that the searched transformer model can outperform the standard transformers. In particular, we show that our learned model can be trained more robustly with large learning rates without warm-up.

cs.CL↗

arXiv2021

Semi-Supervised Learning for Bone Mineral Density Estimation in Hip X-ray Images

Bone mineral density (BMD) is a clinically critical indicator of osteoporosis, usually measured by dual-energy X-ray absorptiometry (DEXA). Due to the limited accessibility of DEXA machines and examinations, osteoporosis is often under-diagnosed and under-treated, leading to increased fragility fracture risks. Thus it is highly desirable to obtain BMDs with alternative cost-effective and more accessible medical imaging examinations such as X-ray plain films. In this work, we formulate the BMD estimation from plain hip X-ray images as a regression problem. Specifically, we propose a new semi-supervised self-training algorithm to train the BMD regression model using images coupled with DEXA measured BMDs and unlabeled images with pseudo BMDs. Pseudo BMDs are generated and refined iteratively for unlabeled images during self-training. We also present a novel adaptive triplet loss to improve the model's regression accuracy. On an in-house dataset of 1,090 images (819 unique patients), our BMD estimation method achieves a high Pearson correlation coefficient of 0.8805 to ground-truth BMDs. It offers good feasibility to use the more accessible and cheaper X-ray imaging for opportunistic osteoporosis screening.

eess.IV↗

arXiv2021

Lesion Segmentation and RECIST Diameter Prediction via Click-driven Attention and Dual-path Connection

Measuring lesion size is an important step to assess tumor growth and monitor disease progression and therapy response in oncology image analysis. Although it is tedious and highly time-consuming, radiologists have to work on this task by using RECIST criteria (Response Evaluation Criteria In Solid Tumors) routinely and manually. Even though lesion segmentation may be the more accurate and clinically more valuable means, physicians can not manually segment lesions as now since much more heavy laboring will be required. In this paper, we present a prior-guided dual-path network (PDNet) to segment common types of lesions throughout the whole body and predict their RECIST diameters accurately and automatically. Similar to [1], a click guidance from radiologists is the only requirement. There are two key characteristics in PDNet: 1) Learning lesion-specific attention matrices in parallel from the click prior information by the proposed prior encoder, named click-driven attention; 2) Aggregating the extracted multi-scale features comprehensively by introducing top-down and bottom-up connections in the proposed decoder, named dual-path connection. Experiments show the superiority of our proposed PDNet in lesion segmentation and RECIST diameter prediction using the DeepLesion dataset and an external test set. PDNet learns comprehensive and representative deep image features for our tasks and produces more accurate results on both lesion segmentation and RECIST diameter prediction.

eess.IV↗

arXiv2021

Weakly-Supervised Universal Lesion Segmentation with Regional Level Set Loss

Accurately segmenting a variety of clinically significant lesions from whole body computed tomography (CT) scans is a critical task on precision oncology imaging, denoted as universal lesion segmentation (ULS). Manual annotation is the current clinical practice, being highly time-consuming and inconsistent on tumor's longitudinal assessment. Effectively training an automatic segmentation model is desirable but relies heavily on a large number of pixel-wise labelled data. Existing weakly-supervised segmentation approaches often struggle with regions nearby the lesion boundaries. In this paper, we present a novel weakly-supervised universal lesion segmentation method by building an attention enhanced model based on the High-Resolution Network (HRNet), named AHRNet, and propose a regional level set (RLS) loss for optimizing lesion boundary delineation. AHRNet provides advanced high-resolution deep image features by involving a decoder, dual-attention and scale attention mechanisms, which are crucial to performing accurate lesion segmentation. RLS can optimize the model reliably and effectively in a weakly-supervised fashion, forcing the segmentation close to lesion boundary. Extensive experimental results demonstrate that our method achieves the best performance on the publicly large-scale DeepLesion dataset and a hold-out test set.

eess.IV↗

arXiv2021

Scalable Semi-supervised Landmark Localization for X-ray Images using Few-shot Deep Adaptive Graph

Landmark localization plays an important role in medical image analysis. Learning based methods, including CNN and GCN, have demonstrated the state-of-the-art performance. However, most of these methods are fully-supervised and heavily rely on manual labeling of a large training dataset. In this paper, based on a fully-supervised graph-based method, DAG, we proposed a semi-supervised extension of it, termed few-shot DAG, \ie five-shot DAG. It first trains a DAG model on the labeled data and then fine-tunes the pre-trained model on the unlabeled data with a teacher-student SSL mechanism. In addition to the semi-supervised loss, we propose another loss using JS divergence to regulate the consistency of the intermediate feature maps. We extensively evaluated our method on pelvis, hand and chest landmark detection tasks. Our experiment results demonstrate consistent and significant improvements over previous methods.

cs.CV↗

arXiv2020

Learn molecular representations from large-scale unlabeled molecules for drug discovery

How to produce expressive molecular representations is a fundamental challenge in AI-driven drug discovery. Graph neural network (GNN) has emerged as a powerful technique for modeling molecular data. However, previous supervised approaches usually suffer from the scarcity of labeled data and have poor generalization capability. Here, we proposed a novel Molecular Pre-training Graph-based deep learning framework, named MPG, that leans molecular representations from large-scale unlabeled molecules. In MPG, we proposed a powerful MolGNet model and an effective self-supervised strategy for pre-training the model at both the node and graph-level. After pre-training on 11 million unlabeled molecules, we revealed that MolGNet can capture valuable chemistry insights to produce interpretable representation. The pre-trained MolGNet can be fine-tuned with just one additional output layer to create state-of-the-art models for a wide range of drug discovery tasks, including molecular properties prediction, drug-drug interaction, and drug-target interaction, involving 13 benchmark datasets. Our work demonstrates that MPG is promising to become a novel approach in the drug discovery pipeline.

cs.LG↗

arXiv2020

Semi-supervised Active Learning for Instance Segmentation via Scoring Predictions

Active learning generally involves querying the most representative samples for human labeling, which has been widely studied in many fields such as image classification and object detection. However, its potential has not been explored in the more complex instance segmentation task that usually has relatively higher annotation cost. In this paper, we propose a novel and principled semi-supervised active learning framework for instance segmentation. Specifically, we present an uncertainty sampling strategy named Triplet Scoring Predictions (TSP) to explicitly incorporate samples ranking clues from classes, bounding boxes and masks. Moreover, we devise a progressive pseudo labeling regime using the above TSP in semi-supervised manner, it can leverage both the labeled and unlabeled data to minimize labeling effort while maximize performance of instance segmentation. Results on medical images datasets demonstrate that the proposed method results in the embodiment of knowledge from available data in a meaningful way. The extensive quantitatively and qualitatively experiments show that, our method can yield the best-performing model with notable less annotation costs, compared with state-of-the-arts.

cs.CV↗

arXiv2020

AutoRC: Improving BERT Based Relation Classification Models via Architecture Search

Although BERT based relation classification (RC) models have achieved significant improvements over the traditional deep learning models, it seems that no consensus can be reached on what is the optimal architecture. Firstly, there are multiple alternatives for entity span identification. Second, there are a collection of pooling operations to aggregate the representations of entities and contexts into fixed length vectors. Third, it is difficult to manually decide which feature vectors, including their interactions, are beneficial for classifying the relation types. In this work, we design a comprehensive search space for BERT based RC models and employ neural architecture search (NAS) method to automatically discover the design choices mentioned above. Experiments on seven benchmark RC tasks show that our method is efficient and effective in finding better architectures than the baseline BERT based RC model. Ablation study demonstrates the necessity of our search space design and the effectiveness of our search method.

cs.CL↗

arXiv2019

Inpatient2Vec: Medical Representation Learning for Inpatients

Representation learning (RL) plays an important role in extracting proper representations from complex medical data for various analyzing tasks, such as patient grouping, clinical endpoint prediction and medication recommendation. Medical data can be divided into two typical categories, outpatient and inpatient, that have different data characteristics. However, few of existing RL methods are specially designed for inpatients data, which have strong temporal relations and consistent diagnosis. In addition, for unordered medical activity set, existing medical RL methods utilize a simple pooling strategy, which would result in indistinguishable contributions among the activities for learning. In this work, weproposeInpatient2Vec, anovelmodel for learning three kinds of representations for inpatient, including medical activity, hospital day and diagnosis. A multi-layer self-attention mechanism with two training tasks is designed to capture the inpatient data characteristics and process the unordered set. Using a real-world dataset, we demonstrate that the proposed approach outperforms the competitive baselines on semantic similarity measurement and clinical events prediction tasks.

cs.LG↗

arXiv2017

Developing Knowledge-enhanced Chronic Disease Risk Prediction Models from Regional EHR Repositories

Precision medicine requires the precision disease risk prediction models. In literature, there have been a lot well-established (inter-)national risk models, but when applying them into the local population, the prediction performance becomes unsatisfactory. To address the localization issue, this paper exploits the way to develop knowledge-enhanced localized risk models. On the one hand, we tune models by learning from regional Electronic Health Record (EHR) repositories, and on the other hand, we propose knowledge injection into the EHR data learning process. For experiments, we leverage the Pooled Cohort Equations (PCE, as recommended in ACC/AHA guidelines to estimate the risk of ASCVD) to develop a localized ASCVD risk prediction model in diabetes. The experimental results show that, if directly using the PCE algorithm on our cohort, the AUC is only 0.653, while our knowledge-enhanced localized risk model can achieve higher prediction performance with AUC of 0.723 (improved by 10.7%).

cs.AI↗