arXiv subjects

Shizhong Han

Publications and source records attributed to Shizhong Han.

29 records · Page 2Linked to original sources

arXiv2020

Validating uncertainty in medical image translation

Medical images are increasingly used as input to deep neural networks to produce quantitative values that aid researchers and clinicians. However, standard deep neural networks do not provide a reliable measure of uncertainty in those quantitative values. Recent work has shown that using dropout during training and testing can provide estimates of uncertainty. In this work, we investigate using dropout to estimate epistemic and aleatoric uncertainty in a CT-to-MR image translation task. We show that both types of uncertainty are captured, as defined, providing confidence in the output uncertainty estimates.

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arXiv2020

Outlier Guided Optimization of Abdominal Segmentation

Abdominal multi-organ segmentation of computed tomography (CT) images has been the subject of extensive research interest. It presents a substantial challenge in medical image processing, as the shape and distribution of abdominal organs can vary greatly among the population and within an individual over time. While continuous integration of novel datasets into the training set provides potential for better segmentation performance, collection of data at scale is not only costly, but also impractical in some contexts. Moreover, it remains unclear what marginal value additional data have to offer. Herein, we propose a single-pass active learning method through human quality assurance (QA). We built on a pre-trained 3D U-Net model for abdominal multi-organ segmentation and augmented the dataset either with outlier data (e.g., exemplars for which the baseline algorithm failed) or inliers (e.g., exemplars for which the baseline algorithm worked). The new models were trained using the augmented datasets with 5-fold cross-validation (for outlier data) and withheld outlier samples (for inlier data). Manual labeling of outliers increased Dice scores with outliers by 0.130, compared to an increase of 0.067 with inliers (p<0.001, two-tailed paired t-test). By adding 5 to 37 inliers or outliers to training, we find that the marginal value of adding outliers is higher than that of adding inliers. In summary, improvement on single-organ performance was obtained without diminishing multi-organ performance or significantly increasing training time. Hence, identification and correction of baseline failure cases present an effective and efficient method of selecting training data to improve algorithm performance.

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arXiv2020

Validation and Optimization of Multi-Organ Segmentation on Clinical Imaging Archives

Segmentation of abdominal computed tomography(CT) provides spatial context, morphological properties, and a framework for tissue-specific radiomics to guide quantitative Radiological assessment. A 2015 MICCAI challenge spurred substantial innovation in multi-organ abdominal CT segmentation with both traditional and deep learning methods. Recent innovations in deep methods have driven performance toward levels for which clinical translation is appealing. However, continued cross-validation on open datasets presents the risk of indirect knowledge contamination and could result in circular reasoning. Moreover, 'real world' segmentations can be challenging due to the wide variability of abdomen physiology within patients. Herein, we perform two data retrievals to capture clinically acquired deidentified abdominal CT cohorts with respect to a recently published variation on 3D U-Net (baseline algorithm). First, we retrieved 2004 deidentified studies on 476 patients with diagnosis codes involving spleen abnormalities (cohort A). Second, we retrieved 4313 deidentified studies on 1754 patients without diagnosis codes involving spleen abnormalities (cohort B). We perform prospective evaluation of the existing algorithm on both cohorts, yielding 13% and 8% failure rate, respectively. Then, we identified 51 subjects in cohort A with segmentation failures and manually corrected the liver and gallbladder labels. We re-trained the model adding the manual labels, resulting in performance improvement of 9% and 6% failure rate for the A and B cohorts, respectively. In summary, the performance of the baseline on the prospective cohorts was similar to that on previously published datasets. Moreover, adding data from the first cohort substantively improved performance when evaluated on the second withheld validation cohort.

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arXiv2019

Stochastic tissue window normalization of deep learning on computed tomography

Tissue window filtering has been widely used in deep learning for computed tomography (CT) image analyses to improve training performance (e.g., soft tissue windows for abdominal CT). However, the effectiveness of tissue window normalization is questionable since the generalizability of the trained model might be further harmed, especially when such models are applied to new cohorts with different CT reconstruction kernels, contrast mechanisms, dynamic variations in the acquisition, and physiological changes. We evaluate the effectiveness of both with and without using soft tissue window normalization on multisite CT cohorts. Moreover, we propose a stochastic tissue window normalization (SWN) method to improve the generalizability of tissue window normalization. Different from the random sampling, the SWN method centers the randomization around the soft tissue window to maintain the specificity for abdominal organs. To evaluate the performance of different strategies, 80 training and 453 validation and testing scans from six datasets are employed to perform multi-organ segmentation using standard 2D U-Net. The six datasets cover the scenarios, where the training and testing scans are from (1) same scanner and same population, (2) same CT contrast but different pathology, and (3) different CT contrast and pathology. The traditional soft tissue window and nonwindowed approaches achieved better performance on (1). The proposed SWN achieved general superior performance on (2) and (3) with statistical analyses, which offers better generalizability for a trained model.

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arXiv2019

Contrast Phase Classification with a Generative Adversarial Network

Dynamic contrast enhanced computed tomography (CT) is an imaging technique that provides critical information on the relationship of vascular structure and dynamics in the context of underlying anatomy. A key challenge for image processing with contrast enhanced CT is that phase discrepancies are latent in different tissues due to contrast protocols, vascular dynamics, and metabolism variance. Previous studies with deep learning frameworks have been proposed for classifying contrast enhancement with networks inspired by computer vision. Here, we revisit the challenge in the context of whole abdomen contrast enhanced CTs. To capture and compensate for the complex contrast changes, we propose a novel discriminator in the form of a multi-domain disentangled representation learning network. The goal of this network is to learn an intermediate representation that separates contrast enhancement from anatomy and enables classification of images with varying contrast time. Briefly, our unpaired contrast disentangling GAN(CD-GAN) Discriminator follows the ResNet architecture to classify a CT scan from different enhancement phases. To evaluate the approach, we trained the enhancement phase classifier on 21060 slices from two clinical cohorts of 230 subjects. Testing was performed on 9100 slices from 30 independent subjects who had been imaged with CT scans from all contrast phases. Performance was quantified in terms of the multi-class normalized confusion matrix. The proposed network significantly improved correspondence over baseline UNet, ResNet50 and StarGAN performance of accuracy scores 0.54. 0.55, 0.62 and 0.91, respectively. The proposed discriminator from the disentangled network presents a promising technique that may allow deeper modeling of dynamic imaging against patient specific anatomies.

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arXiv2019

Semi-Supervised Multi-Organ Segmentation through Quality Assurance Supervision

Human in-the-loop quality assurance (QA) is typically performed after medical image segmentation to ensure that the systems are performing as intended, as well as identifying and excluding outliers. By performing QA on large-scale, previously unlabeled testing data, categorical QA scores can be generatedIn this paper, we propose a semi-supervised multi-organ segmentation deep neural network consisting of a traditional segmentation model generator and a QA involved discriminator. A large-scale dataset of 2027 volumes are used to train the generator, whose 2-D montage images and segmentation mask with QA scores are used to train the discriminator. To generate the QA scores, the 2-D montage images were reviewed manually and coded 0 (success), 1 (errors consistent with published performance), and 2 (gross failure). Then, the ResNet-18 network was trained with 1623 montage images in equal distribution of all three code labels and achieved an accuracy 94% for classification predictions with 404 montage images withheld for the test cohort. To assess the performance of using the QA supervision, the discriminator was used as a loss function in a multi-organ segmentation pipeline. The inclusion of QA-loss function boosted performance on the unlabeled test dataset from 714 patients to 951 patients over the baseline model. Additionally, the number of failures decreased from 606 (29.90%) to 402 (19.83%). The contributions of the proposed method are threefold: We show that (1) the QA scores can be used as a loss function to perform semi-supervised learning for unlabeled data, (2) the well trained discriminator is learnt by QA score rather than traditional true/false, and (3) the performance of multi-organ segmentation on unlabeled datasets can be fine-tuned with more robust and higher accuracy than the original baseline method.

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arXiv2019

Feature-level and Model-level Audiovisual Fusion for Emotion Recognition in the Wild

Emotion recognition plays an important role in human-computer interaction (HCI) and has been extensively studied for decades. Although tremendous improvements have been achieved for posed expressions, recognizing human emotions in "close-to-real-world" environments remains a challenge. In this paper, we proposed two strategies to fuse information extracted from different modalities, i.e., audio and visual. Specifically, we utilized LBP-TOP, an ensemble of CNNs, and a bi-directional LSTM (BLSTM) to extract features from the visual channel, and the OpenSmile toolkit to extract features from the audio channel. Two kinds of fusion methods, i,e., feature-level fusion and model-level fusion, were developed to utilize the information extracted from the two channels. Experimental results on the EmotiW2018 AFEW dataset have shown that the proposed fusion methods outperform the baseline methods significantly and achieve better or at least comparable performance compared with the state-of-the-art methods, where the model-level fusion performs better when one of the channels totally fails.

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arXiv2017

Optimizing Filter Size in Convolutional Neural Networks for Facial Action Unit Recognition

Recognizing facial action units (AUs) during spontaneous facial displays is a challenging problem. Most recently, Convolutional Neural Networks (CNNs) have shown promise for facial AU recognition, where predefined and fixed convolution filter sizes are employed. In order to achieve the best performance, the optimal filter size is often empirically found by conducting extensive experimental validation. Such a training process suffers from expensive training cost, especially as the network becomes deeper. This paper proposes a novel Optimized Filter Size CNN (OFS-CNN), where the filter sizes and weights of all convolutional layers are learned simultaneously from the training data along with learning convolution filters. Specifically, the filter size is defined as a continuous variable, which is optimized by minimizing the training loss. Experimental results on two AU-coded spontaneous databases have shown that the proposed OFS-CNN is capable of estimating optimal filter size for varying image resolution and outperforms traditional CNNs with the best filter size obtained by exhaustive search. The OFS-CNN also beats the CNN using multiple filter sizes and more importantly, is much more efficient during testing with the proposed forward-backward propagation algorithm.

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arXiv2017

Listen to Your Face: Inferring Facial Action Units from Audio Channel

Extensive efforts have been devoted to recognizing facial action units (AUs). However, it is still challenging to recognize AUs from spontaneous facial displays especially when they are accompanied with speech. Different from all prior work that utilized visual observations for facial AU recognition, this paper presents a novel approach that recognizes speech-related AUs exclusively from audio signals based on the fact that facial activities are highly correlated with voice during speech. Specifically, dynamic and physiological relationships between AUs and phonemes are modeled through a continuous time Bayesian network (CTBN); then AU recognition is performed by probabilistic inference via the CTBN model. A pilot audiovisual AU-coded database has been constructed to evaluate the proposed audio-based AU recognition framework. The database consists of a "clean" subset with frontal and neutral faces and a challenging subset collected with large head movements and occlusions. Experimental results on this database show that the proposed CTBN model achieves promising recognition performance for 7 speech-related AUs and outperforms the state-of-the-art visual-based methods especially for those AUs that are activated at low intensities or "hardly visible" in the visual channel. Furthermore, the CTBN model yields more impressive recognition performance on the challenging subset, where the visual-based approaches suffer significantly.

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arXiv2017

Incremental Boosting Convolutional Neural Network for Facial Action Unit Recognition

Recognizing facial action units (AUs) from spontaneous facial expressions is still a challenging problem. Most recently, CNNs have shown promise on facial AU recognition. However, the learned CNNs are often overfitted and do not generalize well to unseen subjects due to limited AU-coded training images. We proposed a novel Incremental Boosting CNN (IB-CNN) to integrate boosting into the CNN via an incremental boosting layer that selects discriminative neurons from the lower layer and is incrementally updated on successive mini-batches. In addition, a novel loss function that accounts for errors from both the incremental boosted classifier and individual weak classifiers was proposed to fine-tune the IB-CNN. Experimental results on four benchmark AU databases have demonstrated that the IB-CNN yields significant improvement over the traditional CNN and the boosting CNN without incremental learning, as well as outperforming the state-of-the-art CNN-based methods in AU recognition. The improvement is more impressive for the AUs that have the lowest frequencies in the databases.

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arXiv2017

Improving Speech Related Facial Action Unit Recognition by Audiovisual Information Fusion

It is challenging to recognize facial action unit (AU) from spontaneous facial displays, especially when they are accompanied by speech. The major reason is that the information is extracted from a single source, i.e., the visual channel, in the current practice. However, facial activity is highly correlated with voice in natural human communications. Instead of solely improving visual observations, this paper presents a novel audiovisual fusion framework, which makes the best use of visual and acoustic cues in recognizing speech-related facial AUs. In particular, a dynamic Bayesian network (DBN) is employed to explicitly model the semantic and dynamic physiological relationships between AUs and phonemes as well as measurement uncertainty. A pilot audiovisual AU-coded database has been collected to evaluate the proposed framework, which consists of a "clean" subset containing frontal faces under well controlled circumstances and a challenging subset with large head movements and occlusions. Experiments on this database have demonstrated that the proposed framework yields significant improvement in recognizing speech-related AUs compared to the state-of-the-art visual-based methods especially for those AUs whose visual observations are impaired during speech, and more importantly also outperforms feature-level fusion methods by explicitly modeling and exploiting physiological relationships between AUs and phonemes.

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