Search

Protein-protein interactions (PPIs) play key roles in a broad range of biological processes. Numerous strategies have been proposed for predicting PPIs, and among them, graph-based methods have demonstrated promising outcomes owing to the inherent graph structure of PPI networks. This paper reviews various graph-based methodologies, and discusses their applications in PPI prediction. We classify these approaches into two primary groups based on their model structures. The first category employs Graph Neural Networks (GNN) or Graph Convolutional Networks (GCN), while the second category utilizes Graph Attention Networks (GAT), Graph Auto-Encoders and Graph-BERT. We highlight the distinctive methodologies of each approach in managing the graph-structured data inherent in PPI networks and anticipate future research directions in this domain.

A popular track of network compression approach is Quantization aware Training (QAT), which accelerates the forward pass during the neural network training and inference. However, not much prior efforts have been made to quantize and accelerate the backward pass during training, even though that contributes around half of the training time. This can be partly attributed to the fact that errors of low-precision gradients during backward cannot be amortized by the training objective as in the QAT setting. In this work, we propose to solve this problem by incorporating the gradients into the computation graph of the next training iteration via a hypernetwork. Various experiments on CIFAR-10 dataset with different CNN network architectures demonstrate that our hypernetwork-based approach can effectively reduce the negative effect of gradient quantization noise and successfully quantizes the gradients to INT4 with only 0.64 accuracy drop for VGG-16 on CIFAR-10.

Protein-protein interactions (PPIs) are crucial in various biological processes and their study has significant implications for drug development and disease diagnosis. Existing deep learning methods suffer from significant performance degradation under complex real-world scenarios due to various factors, e.g., label scarcity and domain shift. In this paper, we propose a self-ensembling multigraph neural network (SemiGNN-PPI) that can effectively predict PPIs while being both efficient and generalizable. In SemiGNN-PPI, we not only model the protein correlations but explore the label dependencies by constructing and processing multiple graphs from the perspectives of both features and labels in the graph learning process. We further marry GNN with Mean Teacher to effectively leverage unlabeled graph-structured PPI data for self-ensemble graph learning. We also design multiple graph consistency constraints to align the student and teacher graphs in the feature embedding space, enabling the student model to better learn from the teacher model by incorporating more relationships. Extensive experiments on PPI datasets of different scales with different evaluation settings demonstrate that SemiGNN-PPI outperforms state-of-the-art PPI prediction methods, particularly in challenging scenarios such as training with limited annotations and testing on unseen data., Comment: Accepted by IJCAI 2023

Domain shift and label scarcity heavily limit deep learning applications to various medical image analysis tasks. Unsupervised domain adaptation (UDA) techniques have recently achieved promising cross-modality medical image segmentation by transferring knowledge from a label-rich source domain to an unlabeled target domain. However, it is also difficult to collect annotations from the source domain in many clinical applications, rendering most prior works suboptimal with the label-scarce source domain, particularly for few-shot scenarios, where only a few source labels are accessible. To achieve efficient few-shot cross-modality segmentation, we propose a novel transformation-consistent meta-hallucination framework, meta-hallucinator, with the goal of learning to diversify data distributions and generate useful examples for enhancing cross-modality performance. In our framework, hallucination and segmentation models are jointly trained with the gradient-based meta-learning strategy to synthesize examples that lead to good segmentation performance on the target domain. To further facilitate data hallucination and cross-domain knowledge transfer, we develop a self-ensembling model with a hallucination-consistent property. Our meta-hallucinator can seamlessly collaborate with the meta-segmenter for learning to hallucinate with mutual benefits from a combined view of meta-learning and self-ensembling learning. Extensive studies on MM-WHS 2017 dataset for cross-modality cardiac segmentation demonstrate that our method performs favorably against various approaches by a lot in the few-shot UDA scenario., Comment: Accepted by MICCAI 2022 (top 13% paper; early accept)

Domain shift has been a long-standing issue for medical image segmentation. Recently, unsupervised domain adaptation (UDA) methods have achieved promising cross-modality segmentation performance by distilling knowledge from a label-rich source domain to a target domain without labels. In this work, we propose a multi-scale self-ensembling based UDA framework for automatic segmentation of two key brain structures i.e., Vestibular Schwannoma (VS) and Cochlea on high-resolution T2 images. First, a segmentation-enhanced contrastive unpaired image translation module is designed for image-level domain adaptation from source T1 to target T2. Next, multi-scale deep supervision and consistency regularization are introduced to a mean teacher network for self-ensemble learning to further close the domain gap. Furthermore, self-training and intensity augmentation techniques are utilized to mitigate label scarcity and boost cross-modality segmentation performance. Our method demonstrates promising segmentation performance with a mean Dice score of 83.8% and 81.4% and an average asymmetric surface distance (ASSD) of 0.55 mm and 0.26 mm for the VS and Cochlea, respectively in the validation phase of the crossMoDA 2022 challenge., Comment: Accepted by BrainLes MICCAI proceedings (5th solution for MICCAI 2022 Cross-Modality Domain Adaptation (crossMoDA) Challenge)

We used two multimodal models for continuous valence-arousal recognition using visual, audio, and linguistic information. The first model is the same as we used in ABAW2 and ABAW3, which employs the leader-follower attention. The second model has the same architecture for spatial and temporal encoding. As for the fusion block, it employs a compact and straightforward channel attention, borrowed from the End2You toolkit. Unlike our previous attempts that use Vggish feature directly as the audio feature, this time we feed the pre-trained VGG model using logmel-spectrogram and finetune it during the training. To make full use of the data and alleviate over-fitting, cross-validation is carried out. The code is available at https://github.com/sucv/ABAW3., Comment: 6 pages. 1 figure. arXiv admin note: substantial text overlap with arXiv:2203.13031

Deep learning has achieved notable success in 3D object detection with the advent of large-scale point cloud datasets. However, severe performance degradation in the past trained classes, i.e., catastrophic forgetting, still remains a critical issue for real-world deployment when the number of classes is unknown or may vary. Moreover, existing 3D class-incremental detection methods are developed for the single-domain scenario, which fail when encountering domain shift caused by different datasets, varying environments, etc. In this paper, we identify the unexplored yet valuable scenario, i.e., class-incremental learning under domain shift, and propose a novel 3D domain adaptive class-incremental object detection framework, DA-CIL, in which we design a novel dual-domain copy-paste augmentation method to construct multiple augmented domains for diversifying training distributions, thereby facilitating gradual domain adaptation. Then, multi-level consistency is explored to facilitate dual-teacher knowledge distillation from different domains for domain adaptive class-incremental learning. Extensive experiments on various datasets demonstrate the effectiveness of the proposed method over baselines in the domain adaptive class-incremental learning scenario., Comment: Accepted by the 33rd British Machine Vision Conference (BMVC 2022)

While deep learning methods hitherto have achieved considerable success in medical image segmentation, they are still hampered by two limitations: (i) reliance on large-scale well-labeled datasets, which are difficult to curate due to the expert-driven and time-consuming nature of pixel-level annotations in clinical practices, and (ii) failure to generalize from one domain to another, especially when the target domain is a different modality with severe domain shifts. Recent unsupervised domain adaptation~(UDA) techniques leverage abundant labeled source data together with unlabeled target data to reduce the domain gap, but these methods degrade significantly with limited source annotations. In this study, we address this underexplored UDA problem, investigating a challenging but valuable realistic scenario, where the source domain not only exhibits domain shift~w.r.t. the target domain but also suffers from label scarcity. In this regard, we propose a novel and generic framework called ``Label-Efficient Unsupervised Domain Adaptation"~(LE-UDA). In LE-UDA, we construct self-ensembling consistency for knowledge transfer between both domains, as well as a self-ensembling adversarial learning module to achieve better feature alignment for UDA. To assess the effectiveness of our method, we conduct extensive experiments on two different tasks for cross-modality segmentation between MRI and CT images. Experimental results demonstrate that the proposed LE-UDA can efficiently leverage limited source labels to improve cross-domain segmentation performance, outperforming state-of-the-art UDA approaches in the literature. Code is available at: https://github.com/jacobzhaoziyuan/LE-UDA., Comment: Accepted by IEEE Transactions on Medical Imaging, 2022

With large-scale well-labeled datasets, deep learning has shown significant success in medical image segmentation. However, it is challenging to acquire abundant annotations in clinical practice due to extensive expertise requirements and costly labeling efforts. Recently, contrastive learning has shown a strong capacity for visual representation learning on unlabeled data, achieving impressive performance rivaling supervised learning in many domains. In this work, we propose a novel multi-scale multi-view global-local contrastive learning (MMGL) framework to thoroughly explore global and local features from different scales and views for robust contrastive learning performance, thereby improving segmentation performance with limited annotations. Extensive experiments on the MM-WHS dataset demonstrate the effectiveness of MMGL framework on semi-supervised cardiac image segmentation, outperforming the state-of-the-art contrastive learning methods by a large margin., Comment: Accepted by IEEE International Conference on Image Processing (ICIP 2022)

While deep models have shown promising performance in medical image segmentation, they heavily rely on a large amount of well-annotated data, which is difficult to access, especially in clinical practice. On the other hand, high-accuracy deep models usually come in large model sizes, limiting their employment in real scenarios. In this work, we propose a novel asymmetric co-teacher framework, ACT-Net, to alleviate the burden on both expensive annotations and computational costs for semi-supervised knowledge distillation. We advance teacher-student learning with a co-teacher network to facilitate asymmetric knowledge distillation from large models to small ones by alternating student and teacher roles, obtaining tiny but accurate models for clinical employment. To verify the effectiveness of our ACT-Net, we employ the ACDC dataset for cardiac substructure segmentation in our experiments. Extensive experimental results demonstrate that ACT-Net outperforms other knowledge distillation methods and achieves lossless segmentation performance with 250x fewer parameters.

Intracranial arteries are critical blood vessels that supply the brain with oxygenated blood. Intracranial artery labels provide valuable guidance and navigation to numerous clinical applications and disease diagnoses. Various machine learning algorithms have been carried out for automation in the anatomical labeling of cerebral arteries. However, the task remains challenging because of the high complexity and variations of intracranial arteries. This study investigates a novel graph convolutional neural network with deep feature fusion for cerebral artery labeling. We introduce stacked graph convolutions in an encoder-core-decoder architecture, extracting high-level representations from graph nodes and their neighbors. Furthermore, we efficiently aggregate intermediate features from different hierarchies to enhance the proposed model's representation capability and labeling performance. We perform extensive experiments on public datasets, in which the results prove the superiority of our approach over baselines by a clear margin., Comment: Accepted by the 44th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC 2022)

A glioma is a malignant brain tumor that seriously affects cognitive functions and lowers patients' life quality. Segmentation of brain glioma is challenging because of interclass ambiguities in tumor regions. Recently, deep learning approaches have achieved outstanding performance in the automatic segmentation of brain glioma. However, existing algorithms fail to exploit channel-wise feature interdependence to select semantic attributes for glioma segmentation. In this study, we implement a novel deep neural network that integrates residual channel attention modules to calibrate intermediate features for glioma segmentation. The proposed channel attention mechanism adaptively weights feature channel-wise to optimize the latent representation of gliomas. We evaluate our method on the established dataset BraTS2017. Experimental results indicate the superiority of our method., Comment: Accepted by the 44th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC 2022)

Label scarcity has been a long-standing issue for biomedical image segmentation, due to high annotation costs and professional requirements. Recently, active learning (AL) strategies strive to reduce annotation costs by querying a small portion of data for annotation, receiving much traction in the field of medical imaging. However, most of the existing AL methods have to initialize models with some randomly selected samples followed by active selection based on various criteria, such as uncertainty and diversity. Such random-start initialization methods inevitably introduce under-value redundant samples and unnecessary annotation costs. For the purpose of addressing the issue, we propose a novel self-supervised assisted active learning framework in the cold-start setting, in which the segmentation model is first warmed up with self-supervised learning (SSL), and then SSL features are used for sample selection via latent feature clustering without accessing labels. We assess our proposed methodology on skin lesions segmentation task. Extensive experiments demonstrate that our approach is capable of achieving promising performance with substantial improvements over existing baselines., Comment: Accepted by the 44th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC 2022)

Automated facial age estimation has diverse real-world applications in multimedia analysis, e.g., video surveillance, and human-computer interaction. However, due to the randomness and ambiguity of the aging process, age assessment is challenging. Most research work over the topic regards the task as one of age regression, classification, and ranking problems, and cannot well leverage age distribution in representing labels with age ambiguity. In this work, we propose a simple yet effective loss function for robust facial age estimation via distribution learning, i.e., adaptive mean-residue loss, in which, the mean loss penalizes the difference between the estimated age distribution's mean and the ground-truth age, whereas the residue loss penalizes the entropy of age probability out of dynamic top-K in the distribution. Experimental results in the datasets FG-NET and CLAP2016 have validated the effectiveness of the proposed loss. Our code is available at https://github.com/jacobzhaoziyuan/AMR-Loss., Comment: Accepted by IEEE International Conference on Multimedia and Expo (ICME 2022)

The success of deep convolutional neural networks (DCNNs) benefits from high volumes of annotated data. However, annotating medical images is laborious, expensive, and requires human expertise, which induces the label scarcity problem. Especially when encountering the domain shift, the problem becomes more serious. Although deep unsupervised domain adaptation (UDA) can leverage well-established source domain annotations and abundant target domain data to facilitate cross-modality image segmentation and also mitigate the label paucity problem on the target domain, the conventional UDA methods suffer from severe performance degradation when source domain annotations are scarce. In this paper, we explore a challenging UDA setting - limited source domain annotations. We aim to investigate how to efficiently leverage unlabeled data from the source and target domains with limited source annotations for cross-modality image segmentation. To achieve this, we propose a new label-efficient UDA framework, termed MT-UDA, in which the student model trained with limited source labels learns from unlabeled data of both domains by two teacher models respectively in a semi-supervised manner. More specifically, the student model not only distills the intra-domain semantic knowledge by encouraging prediction consistency but also exploits the inter-domain anatomical information by enforcing structural consistency. Consequently, the student model can effectively integrate the underlying knowledge beneath available data resources to mitigate the impact of source label scarcity and yield improved cross-modality segmentation performance. We evaluate our method on MM-WHS 2017 dataset and demonstrate that our approach outperforms the state-of-the-art methods by a large margin under the source-label scarcity scenario., Comment: Accept by MICCAI 2021, code at: https://github.com/jacobzhaoziyuan/MT-UDA

Pre-training on time series poses a unique challenge due to the potential mismatch between pre-training and target domains, such as shifts in temporal dynamics, fast-evolving trends, and long-range and short-cyclic effects, which can lead to poor downstream performance. While domain adaptation methods can mitigate these shifts, most methods need examples directly from the target domain, making them suboptimal for pre-training. To address this challenge, methods need to accommodate target domains with different temporal dynamics and be capable of doing so without seeing any target examples during pre-training. Relative to other modalities, in time series, we expect that time-based and frequency-based representations of the same example are located close together in the time-frequency space. To this end, we posit that time-frequency consistency (TF-C) -- embedding a time-based neighborhood of an example close to its frequency-based neighborhood -- is desirable for pre-training. Motivated by TF-C, we define a decomposable pre-training model, where the self-supervised signal is provided by the distance between time and frequency components, each individually trained by contrastive estimation. We evaluate the new method on eight datasets, including electrodiagnostic testing, human activity recognition, mechanical fault detection, and physical status monitoring. Experiments against eight state-of-the-art methods show that TF-C outperforms baselines by 15.4% (F1 score) on average in one-to-one settings (e.g., fine-tuning an EEG-pretrained model on EMG data) and by 8.4% (precision) in challenging one-to-many settings (e.g., fine-tuning an EEG-pretrained model for either hand-gesture recognition or mechanical fault prediction), reflecting the breadth of scenarios that arise in real-world applications. Code and datasets: https://github.com/mims-harvard/TFC-pretraining., Comment: Accepted by NeruIPS 2022; 32pages (14 pages main paper + 18 pages supplementary materials). Code: https://github.com/mims-harvard/TFC-pretraining

Heterogeneous information networks (HINs) are usually used to model information systems with multi-type objects and relations. In contrast, graphs that have a single type of nodes and edges, are often called homogeneous graphs. Measuring similarities among objects is an important task in data mining applications, such as web search, link prediction, and clustering. Currently, several similarity measures are defined for HINs. Most of these measures are based on meta-paths, which show sequences of node classes and edge types along the paths between two nodes. However, meta-paths, which are often designed by domain experts, are hard to enumerate and choose w.r.t. the quality of similarity scores. This makes using existing similarity measures in real applications difficult. To address this problem, we extend SimRank, a well-known similarity measure on homogeneous graphs, to HINs, by introducing the concept of the decay graph. The newly proposed similarity measure is called HowSim, which has the property of being meta-path free, and capturing the structural and semantic similarity simultaneously. The generality and effectiveness of HowSim, and the efficiency of our proposed algorithms for computing HowSim scores, are demonstrated by extensive experiments. IEEE

Diabetic retinopathy (DR) is one of the most common eye conditions among diabetic patients. However, vision loss occurs primarily in the late stages of DR, and the symptoms of visual impairment, ranging from mild to severe, can vary greatly, adding to the burden of diagnosis and treatment in clinical practice. Deep learning methods based on retinal images have achieved remarkable success in automatic DR grading, but most of them neglect that the presence of diabetes usually affects both eyes, and ophthalmologists usually compare both eyes concurrently for DR diagnosis, leaving correlations between left and right eyes unexploited. In this study, simulating the diagnostic process, we propose a two-stream binocular network to capture the subtle correlations between left and right eyes, in which, paired images of eyes are fed into two identical subnetworks separately during training. We design a contrastive grading loss to learn binocular correlation for five-class DR detection, which maximizes inter-class dissimilarity while minimizing the intra-class difference. Experimental results on the EyePACS dataset show the superiority of the proposed binocular model, outperforming monocular methods by a large margin., Comment: Accepted in 43rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society, IEEE EMBC 2021

Accurate automatic liver and tumor segmentation plays a vital role in treatment planning and disease monitoring. Recently, deep convolutional neural network (DCNNs) has obtained tremendous success in 2D and 3D medical image segmentation. However, 2D DCNNs cannot fully leverage the inter-slice information, while 3D DCNNs are computationally expensive and memory intensive. To address these issues, we first propose a novel dense-sparse training flow from a data perspective, in which, densely adjacent slices and sparsely adjacent slices are extracted as inputs for regularizing DCNNs, thereby improving the model performance. Moreover, we design a 2.5D light-weight nnU-Net from a network perspective, in which, depthwise separable convolutions are adopted to improve the efficiency. Extensive experiments on the LiTS dataset have demonstrated the superiority of the proposed method., Comment: Accepted in 43rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society, IEEE EMBC 2021

Deep learning has achieved promising segmentation performance on 3D left atrium MR images. However, annotations for segmentation tasks are expensive, costly and difficult to obtain. In this paper, we introduce a novel hierarchical consistency regularized mean teacher framework for 3D left atrium segmentation. In each iteration, the student model is optimized by multi-scale deep supervision and hierarchical consistency regularization, concurrently. Extensive experiments have shown that our method achieves competitive performance as compared with full annotation, outperforming other state-of-the-art semi-supervised segmentation methods., Comment: Accepted in 43rd Annual International Conference of the IEEE Engineering in Medicine and Biology Society, IEEE EMBC 2021

Image segmentation is one of the most essential biomedical image processing problems for different imaging modalities, including microscopy and X-ray in the Internet-of-Medical-Things (IoMT) domain. However, annotating biomedical images is knowledge-driven, time-consuming, and labor-intensive, making it difficult to obtain abundant labels with limited costs. Active learning strategies come into ease the burden of human annotation, which queries only a subset of training data for annotation. Despite receiving attention, most of active learning methods generally still require huge computational costs and utilize unlabeled data inefficiently. They also tend to ignore the intermediate knowledge within networks. In this work, we propose a deep active semi-supervised learning framework, DSAL, combining active learning and semi-supervised learning strategies. In DSAL, a new criterion based on deep supervision mechanism is proposed to select informative samples with high uncertainties and low uncertainties for strong labelers and weak labelers respectively. The internal criterion leverages the disagreement of intermediate features within the deep learning network for active sample selection, which subsequently reduces the computational costs. We use the proposed criteria to select samples for strong and weak labelers to produce oracle labels and pseudo labels simultaneously at each active learning iteration in an ensemble learning manner, which can be examined with IoMT Platform. Extensive experiments on multiple medical image datasets demonstrate the superiority of the proposed method over state-of-the-art active learning methods., Comment: Published as a journal paper at IEEE J-BHI

Heterogeneous information networks (HINs) are usually used to model information systems with multi-type objects and relations. In contrast, graphs that have a single type of nodes and edges, are often called homogeneous graphs. Measuring similarities among objects is an important task in data mining applications, such as web search, link prediction, and clustering. Currently, several similarity measures are defined for HINs. Most of these measures are based on meta-paths, which show sequences of node classes and edge types along the paths between two nodes. However, meta-paths, which are often designed by domain experts, are hard to enumerate and choose w.r.t. the quality of similarity scores. This makes using existing similarity measures in real applications difficult. To address this problem, we extend SimRank, a well-known similarity measure on homogeneous graphs, to HINs, by introducing the concept of the decay graph. The newly proposed similarity measure is called HowSim, which has the property of being meta-path free, and capturing the structural and semantic similarity simultaneously. The generality and effectiveness of HowSim, and the efficiency of our proposed algorithms for computing HowSim scores, are demonstrated by extensive experiments. IEEE

Learning network embeddings has attracted growing attention in recent years. However, most of the existing methods focus on homogeneous networks, which cannot capture the important type information in heterogeneous networks. To address this problem, in this paper, we propose TransN, a novel multi-view network embedding framework for heterogeneous networks. Compared with the existing methods, TransN is an unsupervised framework which does not require node labels or user-specified meta-paths as inputs. In addition, TransN is capable of handling more general types of heterogeneous networks than the previous works. Specifically, in our framework TransN, we propose a novel algorithm to capture the proximity information inside each single view. Moreover, to transfer the learned information across views, we propose an algorithm to translate the node embeddings between different views based on the dual-learning mechanism, which can both capture the complex relations between node embeddings in different views, and preserve the proximity information inside each view during the translation. We conduct extensive experiments on real-world heterogeneous networks, whose results demonstrate that the node embeddings generated by TransN outperform those of competitors in various network mining tasks. © 2020 IEEE.

Learning network embeddings has attracted growing attention in recent years. However, most of the existing methods focus on homogeneous networks, which cannot capture the important type information in heterogeneous networks. To address this problem, in this paper, we propose TransN, a novel multi-view network embedding framework for heterogeneous networks. Compared with the existing methods, TransN is an unsupervised framework which does not require node labels or user-specified meta-paths as inputs. In addition, TransN is capable of handling more general types of heterogeneous networks than the previous works. Specifically, in our framework TransN, we propose a novel algorithm to capture the proximity information inside each single view. Moreover, to transfer the learned information across views, we propose an algorithm to translate the node embeddings between different views based on the dual-learning mechanism, which can both capture the complex relations between node embeddings in different views, and preserve the proximity information inside each view during the translation. We conduct extensive experiments on real-world heterogeneous networks, whose results demonstrate that the node embeddings generated by TransN outperform those of competitors in various network mining tasks. © 2020 IEEE.

Learning network embeddings has attracted growing attention in recent years. However, most of the existing methods focus on homogeneous networks, which cannot capture the important type information in heterogeneous networks. To address this problem, in this paper, we propose TransN, a novel multi-view network embedding framework for heterogeneous networks. Compared with the existing methods, TransN is an unsupervised framework which does not require node labels or user-specified meta-paths as inputs. In addition, TransN is capable of handling more general types of heterogeneous networks than the previous works. Specifically, in our framework TransN, we propose a novel algorithm to capture the proximity information inside each single view. Moreover, to transfer the learned information across views, we propose an algorithm to translate the node embeddings between different views based on the dual-learning mechanism, which can both capture the complex relations between node embeddings in different views, and preserve the proximity information inside each view during the translation. We conduct extensive experiments on real-world heterogeneous networks, whose results demonstrate that the node embeddings generated by TransN outperform those of competitors in various network mining tasks. © 2020 IEEE.

Gene mutation prediction in hepatocellular carcinoma (HCC) is of great diagnostic and prognostic value for personalized treatments and precision medicine. In this paper, we tackle this problem with multi-instance multi-label learning to address the difficulties on label correlations, label representations, etc. Furthermore, an effective oversampling strategy is applied for data imbalance. Experimental results have shown the superiority of the proposed approach., Comment: Accepted version to be published in the 42nd IEEE Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2020, Montreal, Canada

Hepatocellular carcinoma (HCC) is the most common type of primary liver cancer and the fourth most common cause of cancer-related death worldwide. Understanding the underlying gene mutations in HCC provides great prognostic value for treatment planning and targeted therapy. Radiogenomics has revealed an association between non-invasive imaging features and molecular genomics. However, imaging feature identification is laborious and error-prone. In this paper, we propose an end-to-end deep learning framework for mutation prediction in APOB, COL11A1 and ATRX genes using multiphasic CT scans. Considering intra-tumour heterogeneity (ITH) in HCC, multi-region sampling technology is implemented to generate the dataset for experiments. Experimental results demonstrate the effectiveness of the proposed model., Comment: Accepted version to be published in the 42nd IEEE Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2020, Montreal, Canada

Segmentation is a prerequisite yet challenging task for medical image analysis. In this paper, we introduce a novel deeply supervised active learning approach for finger bones segmentation. The proposed architecture is fine-tuned in an iterative and incremental learning manner. In each step, the deep supervision mechanism guides the learning process of hidden layers and selects samples to be labeled. Extensive experiments demonstrated that our method achieves competitive segmentation results using less labeled samples as compared with full annotation., Comment: Accepted version to be published in the 42nd IEEE Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2020, Montreal, Canada

Water quality has a direct impact on industry, agriculture, and public health. Algae species are common indicators of water quality. It is because algal communities are sensitive to changes in their habitats, giving valuable knowledge on variations in water quality. However, water quality analysis requires professional inspection of algal detection and classification under microscopes, which is very time-consuming and tedious. In this paper, we propose a novel multi-target deep learning framework for algal detection and classification. Extensive experiments were carried out on a large-scale colored microscopic algal dataset. Experimental results demonstrate that the proposed method leads to the promising performance on algal detection, class identification and genus identification., Comment: Accepted version to be published in the 42nd IEEE Annual International Conference of the IEEE Engineering in Medicine and Biology Society, EMBC 2020, Montreal, Canada

Diabetes is one of the most common disease in individuals. \textit{Diabetic retinopathy} (DR) is a complication of diabetes, which could lead to blindness. Automatic DR grading based on retinal images provides a great diagnostic and prognostic value for treatment planning. However, the subtle differences among severity levels make it difficult to capture important features using conventional methods. To alleviate the problems, a new deep learning architecture for robust DR grading is proposed, referred to as SEA-Net, in which, spatial attention and channel attention are alternatively carried out and boosted with each other, improving the classification performance. In addition, a hybrid loss function is proposed to further maximize the inter-class distance and reduce the intra-class variability. Experimental results have shown the effectiveness of the proposed architecture., Comment: Accepted to ICIP 2020

Electrides are unique compounds where most of the electrons reside at interstitial regions of the crystal behaving as anions, which strongly determines its physical properties. Interestingly, the magnitude and distribution of interstitial electrons can be effectively modified either by modulating its chemical composition or external conditions (e.g., pressure). Most of the electrides under high pressure are nonmetallic, and superconducting electrides are very rare. Here we report that a pressure-induced stable Li6P electride, identified by first-principles swarm structure calculations, becomes a superconductor with a predicted superconducting transition temperature Tc of 39.3 K, which is the highest among the already known electrides. The interstitial electrons in Li6P, with dumbbell-like connected electride states, play a dominant role in the superconducting transition. Other Li-rich phosphides, Li5P, Li11P2, Li15P2, and Li8P, are also predicted to be superconducting electrides, but with a lower Tc. Superconductivity in all these compounds can be attributed to a combination of a weak electronegativity of phosphorus (P) with a strong electropositivity of lithium (Li), and opens up the interest to explore high-temperature superconductivity in similar binary compounds.

Graphene and phosphorene are two major types of atomically thin two-dimensional materials under extensive investigation. However, the zero band gap of graphene and the instability of phosphorene greatly restrict their applications. Here, we make first-principle unbiased structure search calculations to identify a new buckled graphene-like PC6 monolayer with a number of desirable functional properties. The PC6 monolayer is a direct-gap semiconductor with a band gap of 0.84 eV, and it has an extremely high intrinsic conductivity with anisotropic character (i.e., its electron mobility is 2.94 × 105 cm2 V-1 s-1 along the armchair direction, whereas the hole mobility reaches 1.64 × 105 cm2 V-1 s-1 along the zigzag direction), which is comparable to that of graphene. On the other hand, PC6 shows a high absorption coefficient (105 cm-1) in a broad band, from 300 to 2000 nm. Additionally, its direct band gap character can remain within a biaxial strain of 5%. All these appealing properties make the predicted PC6 monolayer a promising candidate for applications in electronic and photovoltaic devices.

Bone age assessment is an important clinical trial to measure skeletal child maturity and diagnose of growth disorders. Conventional approaches such as the Tanner-Whitehouse (TW) and Greulich and Pyle (GP) may not perform well due to their large inter-observer and intra-observer variations. In this paper, we propose a finger joint localization strategy to filter out most non-informative parts of images. When combining with the conventional full image-based deep network, we observe a much-improved performance. % Our approach utilizes full hand and specific joints images for skeletal maturity prediction. In this study, we applied powerful deep neural network and explored a process in the forecast of skeletal bone age with the specifically combine joints images to increase the performance accuracy compared with the whole hand images., Comment: Some changes will be made

Diabetic retinopathy (DR) is a common retinal disease that leads to blindness. For diagnosis purposes, DR image grading aims to provide automatic DR grade classification, which is not addressed in conventional research methods of binary DR image classification. Small objects in the eye images, like lesions and microaneurysms, are essential to DR grading in medical imaging, but they could easily be influenced by other objects. To address these challenges, we propose a new deep learning architecture, called BiRA-Net, which combines the attention model for feature extraction and bilinear model for fine-grained classification. Furthermore, in considering the distance between different grades of different DR categories, we propose a new loss function, called grading loss, which leads to improved training convergence of the proposed approach. Experimental results are provided to demonstrate the superior performance of the proposed approach., Comment: Accepted at ICIP 2019

Segmentation stands at the forefront of many high-level vision tasks. In this study, we focus on segmenting finger bones within a newly introduced semi-supervised self-taught deep learning framework which consists of a student network and a stand-alone teacher module. The whole system is boosted in a life-long learning manner wherein each step the teacher module provides a refinement for the student network to learn with newly unlabeled data. Experimental results demonstrate the superiority of the proposed method over conventional supervised deep learning methods., Comment: IEEE BHI 2019 accepted

Black phosphorus, the result of white P under high pressure, has received much attention as a promising anode material for Li-ion batteries (LIBs). However, the final product of lithiation, P6/mmc LiP, is not satisfactory due to its poor conductivity. In this article we explore the highpressure phase diagram of the Li-P system through firstprinciples swarm-intelligence structural search and present two hitherto unknown stable Li-rich compounds, Fm-3m LiP at 4.2 GPa and P6/mmm LiP at 10.3 GPa. Metallic LiP exhibits interesting structural features, including graphene-like Li layers and P-centered octadecahedrons, where P is 14-fold coordinated with Li. Interestingly, both compounds exhibit good dynamical and thermal stability properties at ambient pressure, and the theoretical capacity of P6/mmm LiP reaches 4326 mAhg, the highest among the already known Li-P compounds. Additionally, their mechanical properties are also favorable for electrode materials. Our work represents a significant step toward the performance improvement of Li-P batteries and understanding Li-P compounds.

The ubiquity of mobile devices has brought the popularity of a new problem solving mechanism - spatial crowdsourcing, which utilizes the power of crowds to accomplish location-specific tasks. Many spatial-crowdsourcing-based applications have emerged and deeply influenced our daily life, such as taxi taking, package dispatching and food delivering. Many unified and standardized crowdsourcing services adopt the server assigned tasks(SAT) mode, in which the system proactively assigns tasks to workers in proximity of requested locations. Under this task assignment mode, the travel cost between workers and tasks becomes of vital importance, less travel cost means less response time and higher task acceptance ratio. In this thesis, we formally define the minimum travel cost assignment (MTCA) problem in spatial crowdsourcing. Since we consider the total travel cost during a period of time, we explore the possible locations of future tasks to assist task assignment planning. By adopting various task-distribution prediction algorithms, we propose several effective and scalable approaches for task assignment. We conduct comprehensive experiments on real-world data to compare the effectiveness and efficiency of our proposed solutions.

The ubiquity of mobile devices has brought the popularity of a new problem solving mechanism - spatial crowdsourcing, which utilizes the power of crowds to accomplish location-specific tasks. Many spatial-crowdsourcing-based applications have emerged and deeply influenced our daily life, such as taxi taking, package dispatching and food delivering. Many unified and standardized crowdsourcing services adopt the server assigned tasks(SAT) mode, in which the system proactively assigns tasks to workers in proximity of requested locations. Under this task assignment mode, the travel cost between workers and tasks becomes of vital importance, less travel cost means less response time and higher task acceptance ratio. In this thesis, we formally define the minimum travel cost assignment (MTCA) problem in spatial crowdsourcing. Since we consider the total travel cost during a period of time, we explore the possible locations of future tasks to assist task assignment planning. By adopting various task-distribution prediction algorithms, we propose several effective and scalable approaches for task assignment. We conduct comprehensive experiments on real-world data to compare the effectiveness and efficiency of our proposed solutions.

The ubiquity of mobile devices has brought the popularity of a new problem solving mechanism - spatial crowdsourcing, which utilizes the power of crowds to accomplish location-specific tasks. Many spatial-crowdsourcing-based applications have emerged and deeply influenced our daily life, such as taxi taking, package dispatching and food delivering. Many unified and standardized crowdsourcing services adopt the server assigned tasks(SAT) mode, in which the system proactively assigns tasks to workers in proximity of requested locations. Under this task assignment mode, the travel cost between workers and tasks becomes of vital importance, less travel cost means less response time and higher task acceptance ratio. In this thesis, we formally define the minimum travel cost assignment (MTCA) problem in spatial crowdsourcing. Since we consider the total travel cost during a period of time, we explore the possible locations of future tasks to assist task assignment planning. By adopting various task-distribution prediction algorithms, we propose several effective and scalable approaches for task assignment. We conduct comprehensive experiments on real-world data to compare the effectiveness and efficiency of our proposed solutions.

As one of the successful forms of using Wisdom of Crowd, crowdsourcing, has been widely used for many human intrinsic tasks, such as image labeling, natural language understanding, market predication and opinion mining. Meanwhile, with advances in pervasive technology, mobile devices, such as mobile phones and tablets, have become extremely popular. These mobile devices can work as sensors to collect multimedia data(audios, images and videos) and location information. This power makes it possible to implement the new crowdsourcing mode: spatial crowdsourcing. In spatial crowdsourcing, a requester can ask for resources related a specific location, the mobile users who would like to take the task will travel to that place and get the data. Due to the rapid growth of mobile device uses, spatial crowdsourcing is likely to become more popular than general crowdsourcing, such as Amazon Turk and Crowd ower. However, to implement such a platform, effective and efficient solutions for worker incentives, task assignment, result aggregation and data quality control must be developed. In this demo, we will introduce gMission, a general spatial crowdsourcing platform, which features with a collection of novel techniques, including geographic sensing, worker detection, and task recommendation. We introduce the sketch of system architecture and illustrate scenarios via several case analysis. © 2014 VLDB Endowment 2150-8097/14/08.

Schema matching is a central challenge for data integration systems. Due to the inherent uncertainty arose from the inability of schema in fully capturing the semantics of the represented data, automatic tools are often uncertain about suggested matching results. However, human is good at understanding data represented in various forms and crowdsourcing platforms are making the human annotation process more affordable. Thus in this demo, we will show how to utilize the crowd to find the right matching. In order to do that, we need to make the tasks posted on the crowdsouricng platforms extremely simple, to be performed by non-expert people, and reduce the number of tasks as less as possible to save the cost. We demonstrate CrowdMatcher, a hybrid machine-crowd system for schema matching. The machine-generated matchings are verified by correspondence correctness queries (CCQs), which is to ask the crowd to determine whether a given correspondence is correct or not. CrowdMatcher includes several original features: it integrates different matchings generated from classical schema matching tools; in order to minimize the cost of crowdsourcing, it automatically selects the most informative set of CCQs from the possible matchings; it is able to manage inaccurate answers provided by the workers; the crowdsourced answers are used to improve matching results. © 2014 ACM.

Schema matching is a central challenge for data integration systems. Due to the inherent uncertainty arose from the inability of schema in fully capturing the semantics of the represented data, automatic tools are often uncertain about suggested matching results. However, human is good at understanding data represented in various forms and crowdsourcing platforms are making the human annotation process more affordable. Thus in this demo, we will show how to utilize the crowd to find the right matching. In order to do that, we need to make the tasks posted on the crowdsouricng platforms extremely simple, to be performed by non-expert people, and reduce the number of tasks as less as possible to save the cost. We demonstrate CrowdMatcher, a hybrid machine-crowd system for schema matching. The machine-generated matchings are verified by correspondence correctness queries (CCQs), which is to ask the crowd to determine whether a given correspondence is correct or not. CrowdMatcher includes several original features: it integrates different matchings generated from classical schema matching tools; in order to minimize the cost of crowdsourcing, it automatically selects the most informative set of CCQs from the possible matchings; it is able to manage inaccurate answers provided by the workers; the crowdsourced answers are used to improve matching results. © 2014 ACM.

As one of the successful forms of using Wisdom of Crowd, crowdsourcing, has been widely used for many human intrinsic tasks, such as image labeling, natural language understanding, market predication and opinion mining. Meanwhile, with advances in pervasive technology, mobile devices, such as mobile phones and tablets, have become extremely popular. These mobile devices can work as sensors to collect multimedia data(audios, images and videos) and location information. This power makes it possible to implement the new crowdsourcing mode: spatial crowdsourcing. In spatial crowdsourcing, a requester can ask for resources related a specific location, the mobile users who would like to take the task will travel to that place and get the data. Due to the rapid growth of mobile device uses, spatial crowdsourcing is likely to become more popular than general crowdsourcing, such as Amazon Turk and Crowd ower. However, to implement such a platform, effective and efficient solutions for worker incentives, task assignment, result aggregation and data quality control must be developed. In this demo, we will introduce gMission, a general spatial crowdsourcing platform, which features with a collection of novel techniques, including geographic sensing, worker detection, and task recommendation. We introduce the sketch of system architecture and illustrate scenarios via several case analysis. © 2014 VLDB Endowment 2150-8097/14/08.

Schema matching is a central challenge for data integration systems. Due to the inherent uncertainty arose from the inability of schema in fully capturing the semantics of the represented data, automatic tools are often uncertain about suggested matching results. However, human is good at understanding data represented in various forms and crowdsourcing platforms are making the human annotation process more affordable. Thus in this demo, we will show how to utilize the crowd to find the right matching. In order to do that, we need to make the tasks posted on the crowdsouricng platforms extremely simple, to be performed by non-expert people, and reduce the number of tasks as less as possible to save the cost. We demonstrate CrowdMatcher, a hybrid machine-crowd system for schema matching. The machine-generated matchings are verified by correspondence correctness queries (CCQs), which is to ask the crowd to determine whether a given correspondence is correct or not. CrowdMatcher includes several original features: it integrates different matchings generated from classical schema matching tools; in order to minimize the cost of crowdsourcing, it automatically selects the most informative set of CCQs from the possible matchings; it is able to manage inaccurate answers provided by the workers; the crowdsourced answers are used to improve matching results. © 2014 ACM.

As one of the successful forms of using Wisdom of Crowd, crowdsourcing, has been widely used for many human intrinsic tasks, such as image labeling, natural language understanding, market predication and opinion mining. Meanwhile, with advances in pervasive technology, mobile devices, such as mobile phones and tablets, have become extremely popular. These mobile devices can work as sensors to collect multimedia data(audios, images and videos) and location information. This power makes it possible to implement the new crowdsourcing mode: spatial crowdsourcing. In spatial crowdsourcing, a requester can ask for resources related a specific location, the mobile users who would like to take the task will travel to that place and get the data. Due to the rapid growth of mobile device uses, spatial crowdsourcing is likely to become more popular than general crowdsourcing, such as Amazon Turk and Crowd ower. However, to implement such a platform, effective and efficient solutions for worker incentives, task assignment, result aggregation and data quality control must be developed. In this demo, we will introduce gMission, a general spatial crowdsourcing platform, which features with a collection of novel techniques, including geographic sensing, worker detection, and task recommendation. We introduce the sketch of system architecture and illustrate scenarios via several case analysis. © 2014 VLDB Endowment 2150-8097/14/08.