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In the field of Computer-Aided Detection (CADx), the use of AI-based algorithms for disease detection in endoscopy images, especially colonoscopy images, is on the rise. However, these algorithms often encounter performance issues due to obstructions like specular reflection, resulting in false positives. This paper presents a novel algorithm specifically designed to tackle the challenges posed by high specular reflection regions in colonoscopy images. The proposed algorithm identifies these regions and applies precise inpainting for restoration. The process entails converting the input image from RGB to HSV color space and focusing on the Saturation (S) component in convex regions detected using a Hessian-based method. This step creates a binary mask that pinpoints areas of specular reflection. The inpainting function then uses this mask to guide the restoration of these identified regions and their borders. To ensure a seamless blend of the restored regions with the background and adjacent pixels, a feathering process is applied to the repaired regions. This enhances both the accuracy and aesthetic coherence of the inpainted images. The performance of our algorithm was rigorously tested on five unique colonoscopy datasets and various endoscopy images from the Kvasir dataset, using an extensive set of evaluation metrics and a comparative analysis with existing methods consistently highlighted the superior performance of our algorithm.

Thoracic computed tomography (CT) currently plays the primary role in pulmonary nodule detection, where the reconstruction kernel significantly impacts performance in computer-aided pulmonary nodule detectors. The issue of kernel selection affecting performance has been overlooked in pulmonary nodule detection. This paper first introduces a novel pulmonary nodule detection dataset named Reconstruction Kernel Imaging for Pulmonary Nodule Detection (RKPN) for quantifying algorithm differences between the two imaging types. The dataset contains pairs of images taken from the same patient on the same date, featuring both smooth (B31f) and sharp kernel (B60f) reconstructions. All other imaging parameters and pulmonary nodule labels remain entirely consistent across these pairs. Extensive quantification reveals mainstream detectors perform better on smooth kernel imaging than on sharp kernel imaging. To address suboptimal detection on the sharp kernel imaging, we further propose an image conversion-based pulmonary nodule detector called ICNoduleNet. A lightweight 3D slice-channel converter (LSCC) module is introduced to convert sharp kernel images into smooth kernel images, which can sufficiently learn inter-slice and inter-channel feature information while avoiding introducing excessive parameters. We conduct thorough experiments that validate the effectiveness of ICNoduleNet, it takes sharp kernel images as input and can achieve comparable or even superior detection performance to the baseline that uses the smooth kernel images. The evaluation shows promising results and proves the effectiveness of ICNoduleNet.

Accurate polyp detection is critical for early colorectal cancer diagnosis. Although remarkable progress has been achieved in recent years, the complex colon environment and concealed polyps with unclear boundaries still pose severe challenges in this area. Existing methods either involve computationally expensive context aggregation or lack prior modeling of polyps, resulting in poor performance in challenging cases. In this paper, we propose the Enhanced CenterNet with Contrastive Learning (ECC-PolypDet), a two-stage training & end-to-end inference framework that leverages images and bounding box annotations to train a general model and fine-tune it based on the inference score to obtain a final robust model. Specifically, we conduct Box-assisted Contrastive Learning (BCL) during training to minimize the intra-class difference and maximize the inter-class difference between foreground polyps and backgrounds, enabling our model to capture concealed polyps. Moreover, to enhance the recognition of small polyps, we design the Semantic Flow-guided Feature Pyramid Network (SFFPN) to aggregate multi-scale features and the Heatmap Propagation (HP) module to boost the model's attention on polyp targets. In the fine-tuning stage, we introduce the IoU-guided Sample Re-weighting (ISR) mechanism to prioritize hard samples by adaptively adjusting the loss weight for each sample during fine-tuning. Extensive experiments on six large-scale colonoscopy datasets demonstrate the superiority of our model compared with previous state-of-the-art detectors.

Chronic ankle instability (CAI) is a major public health concern and adversely affects people's mobility and quality of life. Traditional assessment methods are subjective and qualitative by means of clinician observation and patient self-reporting, which may lead to inaccurate assessment and reduce the effectiveness of treatment in clinical practice. Gait analysis becomes a commonly used approach for monitoring human motion behaviors, which can be applied to specific diagnosis and assessment of CAI. However, it is still challenging to recognize the pathological gait pattern for CAI subjects. In this paper, we propose an integrated deep learning framework to solve the CAI recognition problem using kinematic data. Specifically, inspired by the biomechanics of human body system, we create a simple graph neural network (GNN), termed GaitNet, that operates on a spatial domain and exploits interactions among 3-D joint coordinates. We also develop an attention reinforcement learning (ARL) model that determines attention weights of frames on a temporal domain, which is combined with GaitNet for prediction. The effectiveness of our method is validated on the kinematic NEU-CAI dataset which is collected in our institution using a stereophotogrammetric system. According to extensive experiments, we demonstrate that the selected key phases (i.e., sequences of frames with high attentions) significantly increase the predictability of the proposed biomechanics-based GNN model to differentiate between CAI cohort and control cohort. Moreover, we show a significant prediction accuracy improvement (20%-25%) by our approach compared to state-of-the-art machine learning and deep learning methods.

Applying affective computing techniques to recognize fear and combining them with portable signal monitors makes it possible to create real-time detection systems that could act as bodyguards when users are in danger. With this aim, this paper presents a fear recognition method based on physiological signals obtained from wearable devices. The procedure involves creating two-dimensional feature maps from the raw signals, using data augmentation and feature selection algorithms, followed by deep learning-based classification models, taking inspiration from those used in image processing. This proposal has been validated with two different datasets, achieving, in WEMAC, WESAD 3-classes, and WESAD 2-classes, F1-score results of 78.13%, 88.07%, and 99.60%, respectively, and 79.90%, 89.12%, and 99.60% in accuracy. Furthermore, the paper demonstrates the feasibility of implementing the proposed method on the Coral Edge TPU device, prepared to make inferences on the edge.

Multi-Object tracking in real world environments is a tough problem, especially for cell morphogenesis with division. Most cell tracking methods are hard to achieve reliable mitosis detection, efficient inter-frame matching, and accurate state estimation simultaneously within a unified tracking framework. In this paper, we propose a novel unified framework that leverages a spatio-temporal ant colony evolutionary algorithm to track cells amidst mitosis under measurement uncertainty. Each Bernoulli ant colony representing a migrating cell is able to capture the occurrence of mitosis through the proposed Isolation Random Forest (IRF)-assisted temporal mitosis detection algorithm with the assumption that mitotic cells exhibit unique spatio-temporal features different from non-mitotic ones. Guided by prediction of a division event, multiple ant colonies evolve between consecutive frames according to an augmented assignment matrix solved by the extended Hungarian method. To handle dense cell populations, an efficient group partition between cells and measurements is exploited, which enables multiple assignment tasks to be executed in parallel with a reduction in matrix dimension. After inter-frame traversing, the ant colony transitions to a foraging stage in which it begins approximating the Bernoulli parameter to estimate cell state by iteratively updating its pheromone field. Experiments on multi-cell tracking in the presence of cell mitosis and morphological changes are conducted, and the results demonstrate that the proposed method outperforms state-of-the-art approaches, striking a balance between accuracy and computational efficiency.

Magnetic Resonance Imaging (MRI) reconstruction has made significant progress with the introduction of Deep Learning (DL) technology combined with Compressed Sensing (CS). However, most existing methods require large fully sampled training datasets to supervise the training process, which may be unavailable in many applications. Current unsupervised models also show limitations in performance or speed and may face unaligned distributions during testing. This paper proposes an unsupervised method to train competitive reconstruction models that can generate high-quality samples in an end-to-end style. Firstly teacher models are trained by filling the re-undersampled images and compared with the undersampled images in a self-supervised manner. The teacher models are then distilled to train another cascade model that can leverage the entire undersampled k-space during its training and testing. Additionally, we propose an adaptive distillation method to re-weight the samples based on the variance of teachers, which represents the confidence of the reconstruction results, to improve the quality of distillation. Experimental results on multiple datasets demonstrate that our method significantly accelerates the inference process while preserving or even improving the performance compared to the teacher model. In our tests, the distilled models show 5%-10% improvements in PSNR and SSIM compared with no distillation and are 10 times faster than the teacher.

Health disparities among marginalized populations with lower socioeconomic status significantly impact the fairness and effectiveness of healthcare delivery. The increasing integration of artificial intelligence (AI) into healthcare presents an opportunity to address these inequalities, provided that AI models are free from bias. This paper aims to address the bias challenges by population disparities within healthcare systems, existing in the presentation of and development of algorithms, leading to inequitable medical implementation for conditions such as pulmonary embolism (PE) prognosis. In this study, we explore the diverse bias in healthcare systems, which highlights the demand for a holistic framework to reducing bias by complementary aggregation. By leveraging de-biasing deep survival prediction models, we propose a framework that disentangles identifiable information from images, text reports, and clinical variables to mitigate potential biases within multimodal datasets. Our study offers several advantages over traditional clinical-based survival prediction methods, including richer survival-related characteristics and bias-complementary predicted results. By improving the robustness of survival analysis through this framework, we aim to benefit patients, clinicians, and researchers by enhancing fairness and accuracy in healthcare AI systems.

Accuratedetection and segmentation of brain tumors is critical for medical diagnosis. However, current supervised learning methods require extensively annotated images and the state-of-the-art generative models used in unsupervised methods often have limitations in covering the whole data distribution. In this paper, we propose a novel framework Two-Stage Generative Model (TSGM) that combines Cycle Generative Adversarial Network (CycleGAN) and Variance Exploding stochastic differential equation using joint probability (VE-JP) to improve brain tumor detection and segmentation. The CycleGAN is trained on unpaired data to generate abnormal images from healthy images as data prior. Then VE-JP is implemented to reconstruct healthy images using synthetic paired abnormal images as a guide, which alters only pathological regions but not regions of healthy. Notably, our method directly learned the joint probability distribution for conditional generation. The residual between input and reconstructed images suggests the abnormalities and a thresholding method is subsequently applied to obtain segmentation results. Furthermore, the multimodal results are weighted with different weights to improve the segmentation accuracy further. We validated our method on three datasets, and compared with other unsupervised methods for anomaly detection and segmentation. The DSC score of 0.8590 in BraTs2020 dataset, 0.6226 in ITCS dataset and 0.7403 in In-house dataset show that our method achieves better segmentation performance and has better generalization.

Medical image registration is crucial in medical image analysis applications. Recently, U-Net-style networks have been commonly used for unsupervised image registration, predicting dense displacement fields in full-resolution space. However, this process is resource-intensive and time-consuming for high-resolution volumetric image data. To address this challenge, this paper proposes a novel model named RegFSC-Net, which utilizes Fourier transform with spatial reorganization (SR) and channel refinement (CR) network for registration. We embed efficient feature extraction modules SR and CR modules into the encoder, and adopt a parameter-free model to drive the decoder to improve the U-shaped network. Precisely, RegFSC-Net does not directly predict the full-resolution displacement field in space but learns the low-dimensional representation of the displacement field in the bandlimited Fourier domain, which is beneficial in reducing network parameters, memory usage, and computational costs. Experimental results show that RegFSC-Net outperforms various state-of-the-art methods. Specifically, in comparison to the widely recognized Transformer-based method TransMorph, RegFSC-Net utilizes only around 8.2% of its parameters, resulting in a 1.95% higher Dice score and significantly faster inference speeds of 126.67% and 419.99% on GPU and CPU, respectively. Furthermore, we also designed three variants of RegFSC-Net and demonstrated their potential applications in computer-aided diagnosis.

CircRNA has been proved to play an important role in the diseases diagnosis and treatment. Considering that the wet-lab is time-consuming and expensive, computational methods are viable alternative in these years. However, the number of circRNA-disease associations (CDAs) that can be verified is relatively few, and some methods do not take full advantage of dependencies between attributes. To solve these problems, this paper proposes a novel method based on Kernel Fusion and Deep Auto-encoder (KFDAE) to predict the potential associations between circRNAs and diseases. Firstly, KFDAE uses a non-linear method to fuse the circRNA similarity kernels and disease similarity kernels. Then the vectors are connected to make the positive and negative sample sets, and these data are send to deep auto-encoder to reduce dimension and extract features. Finally, three-layer deep feedforward neural network is used to learn features and gain the prediction score. The experimental results show that compared with existing methods, KFDAE achieves the best performance. In addition, the results of case studies prove the effectiveness and practical significance of KFDAE, which means KFDAE is able to capture more comprehensive information and generate credible candidate for subsequent wet-lab.

Ultrasound-guided percutaneous interventions have numerous advantages over traditional techniques. Accurate needle placement in the target anatomy is crucial for successful intervention, and reliable visual information is essential to achieve this. However, previous studies have revealed several challenges, such as the variability in needle echogenicity and the common misalignment of the ultrasound beam and the needle. Advanced techniques have been developed to optimize needle visualization, including hardware-based and image-processing-based methods. This paper proposes a novel strategy of integrating ultrasound-based deep learning approaches into an optical navigation system to enhance needle visualization and improve tip positioning accuracy. Both the tracking and detection algorithms are optimized utilizing optical tracking information. The information is introduced into the tracking network to define the search patch update strategy and form a trajectory reference to correct tracking results. In the detection network, the original image is processed according to the needle insertion position and current position given by the optical localization system to locate a coarse region, and the depth-score criterion is adopted to optimize detection results. Extensive experiments demonstrate that our approach achieves promising tip tracking and detection performance with tip localization errors of 1.11 ± 0.59 mm and 1.17 ± 0.70 mm, respectively. Moreover, we establish a paired dataset consisting of ultrasound images and their corresponding spatial tip coordinates acquired from the optical tracking system and conduct real puncture experiments to verify the effectiveness of the proposed methods. Our approach significantly improves needle visualization and provides physicians with visual guidance for posture adjustment.

Self-supervised Human Activity Recognition (HAR) has been gradually gaining a lot of attention in ubiquitous computing community. Its current focus primarily lies in how to overcome the challenge of manually labeling complicated and intricate sensor data from wearable devices, which is often hard to interpret. However, current self-supervised algorithms encounter three main challenges: performance variability caused by data augmentations in contrastive learning paradigm, limitations imposed by traditional self-supervised models, and the computational load deployed on wearable devices by current mainstream transformer encoders. To comprehensively tackle these challenges, this paper proposes a powerful self-supervised approach for HAR from a novel perspective of denoising autoencoder, the first of its kind to explore how to reconstruct masked sensor data built on a commonly employed, well-designed, and computationally efficient fully convolutional network. Extensive experiments demonstrate that our proposed Masked Convolutional AutoEncoder (MaskCAE) outperforms current state-of-the-art algorithms in self-supervised, fully supervised, and semi-supervised situations without relying on any data augmentations, which fills the gap of masked sensor data modeling in HAR area. Visualization analyses show that our MaskCAE could effectively capture temporal semantics in time series sensor data, indicating its great potential in modeling abstracted sensor data. An actual implementation is evaluated on an embedded platform.

Automated segmentation of liver tumors in CT scans is pivotal for diagnosing and treating liver cancer, offering a valuable alternative to labor-intensive manual processes and ensuring the provision of accurate and reliable clinical assessment. However, the inherent variability of liver tumors, coupled with the challenges posed by blurred boundaries in imaging characteristics, presents a substantial obstacle to achieving their precise segmentation. In this paper, we propose a novel dual-branch liver tumor segmentation model, SBCNet, to address these challenges effectively. Specifically, our proposed method introduces a contextual encoding module, which enables a better identification of tumor variability using an advanced multi-scale adaptive kernel. Moreover, a boundary enhancement module is designed for the counterpart branch to enhance the perception of boundaries by incorporating contour learning with the Sobel operator. Finally, we propose a hybrid multi-task loss function, concurrently concerning tumors' scale and boundary features, to foster interaction across different tasks of dual branches, further improving tumor segmentation. Experimental validation on the publicly available LiTS dataset demonstrates the practical efficacy of each module, with SBCNet yielding competitive results compared to other state-of-the-art methods for liver tumor segmentation.

For a long time, the prevention and control of COVID-19 has received significant attention. A crucial aspect of controlling the disease's spread is the epidemiological survey of patients and the subsequent analysis of epidemiological survey reports (case reports). However, current mainstream analysis approaches are all made manually. This manual method is time-consuming and manpower-intensive. This paper designs an automated visual epidemiological survey analysis (AVESA) framework for the epidemiological survey on COVID-19. AVESA designs a deep neural network for information extraction from case reports and automatically constructs an epidemiological knowledge graph based on predefined pattern. Moreover, a multi-dimensional knowledge reasoning model is developed for conducting knowledge reasoning in the complete COVID-19 epidemiological knowledge graph. In the entity extraction sub-task and multi-task extraction sub-task, AVESA achieved F1 scores of 85.12% and 92.29% respectively on the constructed dataset, significantly outperforming the standalone information extraction models. In full-graph computing, all three experiments align closely with manual analysis standards. In the risk analysis experiment, the weighted PageRank algorithm showed an average improvement of 11.21% in Top_Recall_n% over the standard PageRank algorithm. In the community detection experiment, the weighted Louvain algorithm showed a mere 4.34% community difference rate compared to manual analysis.

Recently, psychophysiological computing has received considerable attention. Due to easy acquisition at a distance and less conscious initiation, gait-based emotion recognition is considered as a valuable research branch in the field of psychophysiological computing. However, most existing methods rarely explore the spatio-temporal context of gait, which limits the ability to capture the higher-order relationship between emotion and gait. In this paper, we utilize a range of research, including psychophysiological computing and artificial intelligence, to propose an integrated emotion perception framework called EPIC, which can find novel joint topology and generate thousands of synthetic gaits by spatio-temporal interaction context. First, we analyze the joint coupling among non-adjacent joints by calculating Phase Lag Index (PLI), which can discover the latent connection among body joints. Second, to synthesize more sophisticated and accurate gait sequences, we explore the effect of spatio-temporal constraints, and propose a new loss function that utilizes the Dynamic Time Warping (DTW) algorithm and pseudo-velocity curve to constrain the output of Gated Recurrent Units (GRU). Finally, Spatial Temporal Graph Convolution Networks (ST-GCN) is used to classify emotions using the generation and the real data. Experimental results demonstrate our approach achieves the accuracy of 89.66%, and outperforms the state-of-the-art methods on Emotion-Gait dataset.

Inrecent years, significant progress has been made in the field of learning from positive and unlabeled examples (PU learning), particularly in the context of advancing image and text classification tasks. However, applying PU learning to semi-supervised disease classification remains a formidable challenge, primarily due to the limited availability of labeled medical images. In the realm of medical image-aided diagnosis algorithms, numerous theoretical and practical obstacles persist. The research on PU learning for medical image-assisted diagnosis holds substantial importance, as it aims to reduce the time spent by professional experts in classifying images. Unlike natural images, medical images are typically accompanied by a scarcity of annotated data, while an abundance of unlabeled cases exists. Addressing these challenges, this paper introduces a novel generative model inspired by Hölder divergence, specifically designed for semi-supervised disease classification using positive and unlabeled medical image data. In this paper, we present a comprehensive formulation of the problem and establish its theoretical feasibility through rigorous mathematical analysis. To evaluate the effectiveness of our proposed approach, we conduct extensive experiments on five benchmark datasets commonly used in PU medical learning: BreastMNIST, PneumoniaMNIST, BloodMNIST, OCTMNIST, and AMD. The experimental results clearly demonstrate the superiority of our method over existing approaches based on KL divergence. Notably, our approach achieves state-of-the-art performance on all five disease classification benchmarks. By addressing the limitations imposed by limited labeled data and harnessing the untapped potential of unlabeled medical images, our novel generative model presents a promising direction for enhancing semi-supervised disease classification in the field of medical image analysis.

Recent studies have demonstrated the benefit of extracting and fusing pulse signals from multi-scale region-of-interests (ROIs). However, these methods suffer from heavy computational load. This paper aims to effectively utilize multi-scale rPPG features with a more compact architecture. Inspired by recent research works exploring two-path architecture that leverages global and local information with bidirectional bridge in between. This paper designs a novel architecture Global-Local Interaction and Supervision Network (GLISNet), which uses a local path to learn representations in the original scale and a global path to learn representations in the other scale capturing multi-scale information. A light-weight rPPG signal generation block is attached to the output of each path that maps the pulse representation to the pulse output. A hybrid loss function is utilized enabling the local and global representations to learn directly from the training data. Extensive experiments are conducted on two publicly available datasets, and results demonstrate that GLISNet achieves superior performance in terms of signal-to-noise ratio (SNR), mean absolute error (MAE), and root mean squared error (RMSE). In terms of SNR, GLISNet has an increase of 4.41% compared with the second best algorithm PhysNet on PURE dataset. The MAE has a decrease of 13.16% compared with the second best algorithm DeeprPPG on UBFC-rPPG dataset. The RMSE has a decrease of 26.29% compared with the second best algorithm PhysNet on UBFC-rPPG dataset. Experiments on MIHR dataset demonstrates the robustness of GLISNet under low-light environment.

This paper presents new methods to detect eating from wrist motion. Our main novelty is that we analyze a full day of wrist motion data as a single sample so that the detection of eating occurrences can benefit from diurnal context. We develop a two-stage framework to facilitate a feasible full-day analysis. The first-stage model calculates local probabilities of eating P(E w ) within windows of data, and the second-stage model calculates enhanced probabilities of eating P(E d ) by treating all P(E w ) within a single day as one sample. The framework also incorporates an augmentation technique, which involves the iterative retraining of the first-stage model. This allows us to generate a sufficient number of day-length samples from datasets of limited size. We test our methods on the publicly available Clemson All-Day (CAD) dataset and FreeFIC dataset, and find that the inclusion of day-length analysis substantially improves accuracy in detecting eating episodes. We also benchmark our results against several state-of-the-art methods. Our approach achieved an eating episode true positive rate (TPR) of 89% with 1.4 false positives per true positive (FP/TP), and a time weighted accuracy of 84%, which are the highest accuracies reported on the CAD dataset. Our results show that the daily pattern classifier substantially improves meal detections and in particular reduces transient false detections that tend to occur when relying on shorter windows to look for individual ingestion or consumption events.

Objective: Electrocardiogram (ECG) signals have wide-ranging applications in various fields, and thus it is crucial to identify clean ECG signals under different sensors and collection scenarios. Despite the availability of a variety of deep learning algorithms for ECG quality assessment, these methods still lack generalization across different datasets, hindering their widespread use., Methods: In this paper, an effective model named Swin Denoising AutoEncoder (SwinDAE) is proposed. Specifically, SwinDAE uses a DAE as the basic architecture, and incorporates a 1D Swin Transformer during the feature learning stage of the encoder and decoder. SwinDAE was first pre-trained on the public PTB-XL dataset after data augmentation, with the supervision of signal reconstruction loss and quality assessment loss. Specially, the waveform component localization loss is proposed in this paper and used for joint supervision, guiding the model to learn key information of signals. The model was then fine-tuned on the finely annotated BUT QDB dataset for quality assessment., Results: SwinDAE achieved 0.02-0.13 mean F1 score improvement on the BUT QDB dataset compared to multiple deep learning methods, and demonstrated applicability on two other datasets., Conclusion: The proposed SwinDAE shows strong generalization ability on different datasets, and surpasses other state-of-the-art deep learning methods on multiple evaluation metrics. In addition, the statistical analysis for SwinDAE prove the significance of the performance and the rationality of the prediction., Significance: SwinDAE can learn the commonality between high-quality ECG signals, exhibiting excellent performance in the application of cross-sensors and cross-collection scenarios.

Increasingly serious health problems have made the usage of computed tomography surge. Therefore, algorithms for processing CT images are becoming more and more abundant. These algorithms can lessen the harm of cumulative radiation in CT technology for the patient while eliminating the noise of image caused by dose reduction. However, the mainstream CNN-based algorithms are inefficient when dealing with features in broad regions. Inspired by the large receptive field of transformer framework, this paper designs an end-to-end low-dose CT (LDCT) denoising network based on the transformer. The overall network contains a main branch and dual side branches. Specifically, the overlapping-free window-based self-attention transformer block is adopted on the main branch to realize image denoising. On the dual side branches, we propose double enhancement module to enrich edge, texture, and context information of LDCT images. Meanwhile, the receptive field of network is further enlarged after processing, which is helpful for building model's long-range dependencies. The outputs of the side branches are concatenated for enhancing information and generating high-quality CT images. In addition, to better train the network, we introduce a compound loss function including mean squared error (MSE), multi-scale perceptual (MSP), and Sobel-L1 (SL) to make the denoised image closer to the targeted norm-dose CT (NDCT) image. Lastly, we conducted experiments on two clinical datasets including abdomen, head, and chest LDCT images with 25%, 25%, and 10% of the full dose, respectively. The experimental results demonstrated that the proposed DEformer achieved better denoising performance than the existing algorithms.

In this paper, we present a novel MI classification method based on multi-band convolutional neural network (CNN) with band-dependent kernel sizes, named MBK-CNN, to improve classification performance, by resolving the subject dependency issue of the widely used CNN-based approaches due to the kernel size optimization problem. The proposed structure exploits the frequency diversity of the EEG signals and simultaneously resolves the subject dependent kernel size issue. EEG signal is decomposed into overlapping multi-band and passed through multiple CNNs (termed 'branch-CNNs') with different kernel sizes to generate frequency dependent features, which are combined by a simple weighted sum. In contrast to the existing works where single-band multi-branch CNNs with different kernel sizes are used to resolve the subject dependency issue, a unique kernel size per frequency band is used. To prevent possible overfitting induced by a weighted sum, each branch-CNN is additionally trained by tentative cross entropy loss while overall network is optimized by the end-to-end cross entropy loss, which is named amalgamated cross entropy loss. In addition, we further propose multi-band CNN with enhanced spatial diversity, named MBK-LR-CNN, by replacing each branch-CNN with several sub branch-CNNs applied for channel subsets (termed 'local region') to improve the classification performance. We evaluated the performance of the proposed methods, MBK-CNN and MBK-LR-CNN, on publicly available datasets, BCI Competition IV dataset 2a and High Gamma Dataset. The experimental results confirm the performance improvement of the proposed methods compared to the currently existing MI classification methods.

Vessel segmentation is crucial in many medical image applications, such as detecting coronary stenoses, retinal vessel diseases and brain aneurysms. However, achieving high pixel-wise accuracy, complete topology structure and robustness to various contrast variations are critical and challenging, and most existing methods focus only on achieving one or two of these aspects. In this paper, we present a novel approach, the affinity feature strengthening network (AFN), which jointly models geometry and refines pixel-wise segmentation features using a contrast-insensitive, multiscale affinity approach. Specifically, we compute a multiscale affinity field for each pixel, capturing its semantic relationships with neighboring pixels in the predicted mask image. This field represents the local geometry of vessel segments of different sizes, allowing us to learn spatial- and scale-aware adaptive weights to strengthen vessel features. We evaluate our AFN on four different types of vascular datasets: X-ray angiography coronary vessel dataset (XCAD), portal vein dataset (PV), digital subtraction angiography cerebrovascular vessel dataset (DSA) and retinal vessel dataset (DRIVE). Extensive experimental results demonstrate that our AFN outperforms the state-of-the-art methods in terms of both higher accuracy and topological metrics, while also being more robust to various contrast changes.

This paper focuses on activity recognition using a single wearable inertial measurement sensor placed on the subject's chest. The ten activities that need to be identified include lying down, standing, sitting, bending and walking, among others. The activity recognition approach is based on using and identifying a transfer function associated with each activity. The appropriate input and output signals for each transfer function are first determined based on the norms of the sensor signals excited by that specific activity. Then the transfer function is identified using training data and a Wiener filter based on the auto-correlation and cross-correlation of the output and input signals. The activity occurring in real-time is recognized by computing and comparing the input-output errors associated with all the transfer functions. The performance of the developed system is evaluated using data from a group of Parkinson's disease subjects, including data obtained in a clinical setting and data obtained through remote home monitoring. On average, the developed system provides better than 90% accuracy in identifying each activity as it occurs. Activity recognition is particularly useful for PD patients in order to monitor their level of activity, characterize their postural instability and recognize high risk-activities in real-time that could lead to falls.

One of the major goals in gene expression data analysis is to explore and discover groups of genes and groups of biological conditions with meaningful relationships. While this problem can be addressed by algorithms, their results require an analysis within context, since they may be affected by many side processes -such as tissue differentiation- that could hinder the target goal. Visual analytics-based methods for exploratory analysis of the gene expression matrix (GEM) are essential in biomedical research since they allow us to frame the analysis within the user's knowledge domain. In this paper, we present a visual analytics approach to discover relevant connections between genes and samples based on linking a reordered GEM heatmap and dual 2D projections of its rows and columns, which can be recomputed conditioned by subsets of genes and/or samples selected by the user during the analysis. We demonstrate the capability of our approach to discover relevant knowledge in three case studies involving two cancer types plus normal tissue from the TCGA database.

The present paper introduces a novel method, named AutoEncoder-Filter Bank Common Spatial Patterns (AE-FBCSP), to decode imagined movements from electroencephalography (EEG). AE-FBCSP is an extension of the well-established FBCSP and is based on a global (cross-subject) and subsequent transfer learning subject-specific (intra-subject) approach. A multi-way extension of AE-FBCSP is also introduced in this paper. Features are extracted from high-density EEG (64 electrodes), by means of FBCSP, and used to train a custom AE, in an unsupervised way, to project the features into a compressed latent space. Latent features are used to train a supervised classifier (feed forward neural network) to decode the imagined movement. The proposed method was tested using a public dataset of EEGs collected from 109 subjects. The dataset consists of right-hand, left-hand, both hands, both feet motor imagery and resting EEGs. AE-FBCSP was extensively tested in the 3-way classification (right hand vs left hand vs resting) and also in the 2-way, 4-way and 5-way ones, both in cross- and intra-subject analysis. AE-FBCSP outperformed standard FBCSP in a statistically significant way (p > 0.05) and achieved a subject-specific average accuracy of 89.09% in the 3-way classification. The proposed methodology performed subject-specific classification better than other comparable methods in the literature, applied to the same dataset, also in the 2-way, 4-way and 5-way tasks. One of the most interesting outcomes is that AE-FBCSP remarkably increased the number of subjects that responded with a very high accuracy, which is a fundamental requirement for BCI systems to be applied in practice.

Respiration rate is an important healthcare indicator, and it has become a popular research topic in remote healthcare applications with Internet of Things. Existing respiration monitoring systems have limitations in terms of convenience, comfort, and privacy, etc. This paper presents a contactless and real-time respiration monitoring system, the so-called Wi-Breath, based on off-the-shelf WiFi devices. The system monitors respiration with both the amplitude and phase difference of the WiFi channel state information (CSI), which is sensitive to human body micro movement. The phase information of the CSI signal is considered and both the amplitude and phase difference are used. For better respiration detection accuracy, a signal selection method is proposed to select an appropriate signal from the amplitude and phase difference based on a support vector machine (SVM) algorithm. Experimental results demonstrate that the Wi-Breath achieves an accuracy of 91.2% for respiration detection, and has a 17.0% reduction in average error in comparison with state-of-the-art counterparts.

Co-administration of two or more drugs simultaneously can result in adverse drug reactions. Identifying drug-drug interactions (DDIs) is necessary, especially for drug development and for repurposing old drugs. DDI prediction can be viewed as a matrix completion task, for which matrix factorization (MF) appears as a suitable solution. This paper presents a novel Graph Regularized Probabilistic Matrix Factorization (GRPMF) method, which incorporates expert knowledge through a novel graph-based regularization strategy within an MF framework. An efficient and sounded optimization algorithm is proposed to solve the resulting non-convex problem in an alternating fashion. The performance of the proposed method is evaluated through the DrugBank dataset, and comparisons are provided against state-of-the-art techniques. The results demonstrate the superior performance of GRPMF when compared to its counterparts.

With the development of modern cameras, more physiological signals can be obtained from portable devices like smartphone. Some hemodynamically based non-invasive video processing applications have been applied for blood pressure classification and blood glucose prediction objectives for unobtrusive physiological monitoring at home. However, this approach is still under development with very few publications. In this paper, we propose an end-to-end framework, entitled cocktail causal container, to fuse multiple physiological representations and to reconstruct the correlation between frequency and temporal information during multi-task learning. Cocktail causal container processes hematologic reflex information to classify blood pressure and blood glucose. Since the learning of discriminative features from video physiological representations is quite challenging, we propose a token feature fusion block to fuse the multi-view fine-grained representations to a union discrete frequency space. A causal net is used to analyze the fused higher-order information, so that the framework can be enforced to disentangle the latent factors into the related endogenous association that corresponds to down-stream fusion information to improve the semantic interpretation. Moreover, a pair-wise temporal frequency map is developed to provide valuable insights into extraction of salient photoplethysmograph (PPG) information from fingertip videos obtained by a standard smartphone camera. Extensive comparisons have been implemented for the validation of cocktail causal container using a Clinical dataset and PPG-BP benchmark. The root mean square error of 1.329±0.167 for blood glucose prediction and precision of 0.89±0.03 for blood pressure classification are achieved in Clinical dataset.

A plethora of healthcare data is produced every day due to the proliferation of prominent technologies such as Internet of Medical Things (IoMT). Digital-driven smart devices like wearable watches, wristbands and bracelets are utilized extensively in modern healthcare applications. Mining valuable information from the data distributed at the owners' level is useful, but it is challenging to preserve data privacy. Federated learning (FL) has swiftly surged in popularity due to its efficacy in dealing privacy vulnerabilities. Recent studies have demonstrated that Gradient Inversion Attack (GIA) can reconstruct the input data by leaked gradients, previous work demonstrated the achievement of GIA in very limited scenarios, such as the label repetition rate of the target sample being low and batch sizes being smaller than 48. In this paper, a novel method of End-to-End Gradient Inversion (E2EGI) is proposed. Compared to the state-of-the-art method, E2EGI's Minimum Loss Combinatorial Optimization (MLCO) has the ability to realize reconstructed samples with higher similarity, and the Distributed Gradient Inversion algorithm can implement GIA with batch sizes of 8 to 256 on deep network models (such as ResNet-50) and ImageNet datasets. A new Label Reconstruction algorithm is developed that relies only on the gradient information of the target model, which can achieve a label reconstruction accuracy of 81% in one batch sample with a label repetition rate of 96%, a 27% improvement over the state-of-the-art method. This proposed work can underpin data security assessments for healthcare federated learning.

In this paper, we describe a design methodology to design distributed neural network architectures that can perform efficient inference within sensor networks with communication bandwidth constraints. The different sensor channels are distributed across multiple sensor devices, which have to exchange data over bandwidth-limited communication channels to solve a classification task. Our design methodology starts from a centralized neural network and transforms it into a distributed architecture in which the channels are distributed over different nodes. The distributed network consists of two parallel branches, whose outputs are fused at the fusion center. The first branch collects classification results from local, node-specific classifiers while the second branch compresses each node's signal and then reconstructs the multi-channel time series for classification at the fusion center. We further improve bandwidth gains by dynamically activating the compression path when the local classifications do not suffice. We validate this method on a motor execution task in an emulated EEG sensor network and analyze the resulting bandwidth-accuracy trade-offs. Our experiments show that the proposed framework enables up to a factor 20 in bandwidth reduction and factor 9 in power reduction with minimal loss (up to 2%) in classification accuracy compared to the centralized baseline on the demonstrated task. The proposed method offers a way to transform a centralized architecture to a distributed, bandwidth-efficient network amenable for low-power sensor networks. While the application focus of this paper is on wearable brain-computer interfaces, the proposed methodology can be applied in other sensor network-like applications as well.

The privacy protection and data security problems existing in the healthcare framework based on the Internet of Medical Things (IoMT) have always attracted much attention and need to be solved urgently. In the teledermatology healthcare framework, the smartphone can acquire dermatology medical images for remote diagnosis. The dermatology medical image is vulnerable to attacks during transmission, resulting in malicious tampering or privacy data disclosure. Therefore, there is an urgent need for a watermarking scheme that doesn't tamper with the dermatology medical image and doesn't disclose the dermatology healthcare data. Federated learning is a distributed machine learning framework with privacy protection and secure encryption technology. Therefore, this paper presents a robust zero-watermarking scheme based on federated learning to solve the privacy and security issues of the teledermatology healthcare framework. This scheme trains the sparse autoencoder network by federated learning. The trained sparse autoencoder network is applied to extract image features from the dermatology medical image. Image features are undergone to two-dimensional Discrete Cosine Transform (2D-DCT) in order to select low-frequency transform coefficients for creating zero-watermarking. Experimental results show that the proposed scheme has more robustness to the conventional attack and geometric attack and achieves superior performance when compared with other zero-watermarking schemes. The proposed scheme is suitable for the specific requirements of medical images, which neither changes the important information contained in medical images nor divulges privacy data.

Analysis of high dimensional biomedical data such as microarray gene expression data and mass spectrometry images, is crucial to provide better medical services including cancer subtyping, protein homology detection, etc. Clustering is a fundamental cognitive task which aims to group unlabeled data into multiple clusters based on their intrinsic similarities. However, for most clustering methods, including the most widely used K-means algorithm, all features of the high dimensional data are considered equally in relevance, which distorts the performance when clustering high-dimensional data where there exist many redundant variables and correlated variables. In this paper, we aim at addressing the problem of the high dimensional bioinformatics data clustering and propose a new correlation induced clustering, CoIn, to capture complex correlations among high dimensional data and guarantee the correlation consistency within each cluster. We evaluate the proposed method on a high dimensional mass spectrometry dataset of liver cancer tumor to explore the metabolic differences on tissues and discover the intra-tumor heterogeneity (ITH). By comparing the results of baselines and ours, it has been found that our method produces more explainable and understandable results for clinical analysis, which demonstrates the proposed clustering paradigm has the potential with application to knowledge discovery in high dimensional bioinformatics data.

Locating diseases in chest X-ray images with few careful annotations saves large human effort. Recent works approached this task with innovative weakly-supervised algorithms such as multi-instance learning (MIL) and class activation maps (CAM), however, these methods often yield inaccurate or incomplete regions. One of the reasons is the neglection of the pathological implications hidden in the relationship across anatomical regions within each image and the relationship across images. In this paper, we argue that the cross-region and cross-image relationship, as contextual and compensating information, is vital to obtain more consistent and integral regions. To model the relationship, we propose the Graph Regularized Embedding Network (GREN), which leverages the intra-image and inter-image information to locate diseases on chest X-ray images. GREN uses a pre-trained U-Net to segment the lung lobes, and then models the intra-image relationship between the lung lobes using an intra-image graph to compare different regions. Meanwhile, the relationship between in-batch images is modeled by an inter-image graph to compare multiple images. This process mimics the training and decision-making process of a radiologist: comparing multiple regions and images for diagnosis. In order for the deep embedding layers of the neural network to retain structural information (important in the localization task), we use the Hash coding and Hamming distance to compute the graphs, which are used as regularizers to facilitate training. By means of this, our approach achieves the state-of-the-art result on NIH chest X-ray dataset for weakly-supervised disease localization. Our codes are accessible online.

Deformation decomposition serves as a good solution for deformable image registration when the deformation is large. Current deformation decomposition methods can be categorized into cascade-based methods and pyramid-based methods. However, cascade-based methods suffer from heavy computational burdens and long inference time due to their structures of repeated subnetworks, while the effectiveness of pyramid-based methods is constrained by their limited numbers of resolution levels. In this paper, to address both the insufficient and inefficient decomposition problems in current deformation decomposition methods, we propose a recursive decomposition network (RDN) to offer a novel solution for deformable image registration. Stage-wise recursion can efficiently decompose a large deformation into different pyramid estimation stages without using repeated subnetworks like in cascade-based methods. Level-wise recursion can sufficiently decompose the deformation inside each resolution level instead of only one-time estimation like in pyramid-based methods. Extensive experiments and ablation studies on two representative datasets validate the effectiveness and efficiency of our proposed RDN.

Segmentation of retinal vessels on fundus images plays a critical role in the diagnosis of micro-vascular and ophthalmological diseases. Although being extensively studied, this task remains challenging due to many factors including the highly variable vessel width and poor vessel-background contrast. In this paper, we propose a multiscale feature interaction network (MFI-Net) for retinal vessel segmentation, which is a U-shaped convolutional neural network equipped with the pyramid squeeze-and-excitation (PSE) module, coarse-to-fine (C2F) module, deep supervision, and feature fusion. We extend the SE operator to multiscale features, resulting in the PSE module, which uses the channel attention learned at multiple scales to enhance multiscale features and enables the network to handle the vessels with variable width. We further design the C2F module to generate and re-process the residual feature maps, aiming to preserve more vessel details during the decoding process. The proposed MFI-Net has been evaluated against several public models on the DRIVE, STARE, CHASE_DB1, and HRF datasets. Our results suggest that both PSE and C2F modules are effective in improving the accuracy of MFI-Net, and also indicate that our model has superior segmentation performance and generalization ability over existing models on four public datasets.

The development of activity recognition based on multi-modal data makes it possible to reduce human intervention in the process of monitoring. This paper proposes an efficient and cost-effective multi-modal sensing framework for activity monitoring, it can automatically identify human activities based on multi-modal data, and provide help to patients with moderate disabilities. The multi-modal sensing framework for activity monitoring relies on parallel processing of videos and inertial data. A new supervised adaptive multi-modal fusion method (AMFM) is used to process multi-modal human activity data. Spatio-temporal graph convolution network with adaptive loss function (ALSTGCN) is proposed to extract skeleton sequence features, and long short-term memory fully convolutional network (LSTM-FCN) module with adaptive loss function is adapted to extract inertial data features. An adaptive learning method is proposed at the decision level to learn the contribution of the two modalities to the classification results. The effectiveness of the algorithm is demonstrated on two public multi-modal datasets (UTD-MHAD and C-MHAD) and a new multi-modal dataset H-MHAD collected from our laboratory. The results show that the performance of the AMFM approach on three datasets is better than the performance of the video or the inertial-based single-modality model. The class-balanced cross-entropy loss function further improves the model performance based on the H-MHAD dataset. The accuracy of action recognition is 91.18%, and the recall rate of falling activity is 100%. The results illustrate that using multiple heterogeneous sensors to realize automatic process monitoring is a feasible alternative to the manual response.

Automatic spine and vertebra segmentation from X-ray spine images is a critical and challenging problem in many computer-aid spinal image analysis and disease diagnosis applications. In this paper, a two-stage automatic segmentation framework for spine X-ray images is proposed, which can firstly locate the spine regions (including backbone, sacrum and ilium) in the coarse stage and then identify eighteen vertebrae (i.e., cervical vertebra 7, thoracic vertebra 1-12 and lumbar vertebra 1-5) with isolate and clear boundary in the fine stage. A novel Attention Gate based dual-pathway Network (AGNet) composed of context and edge pathways is designed to extract semantic and boundary information for segmentation of both spine and vertebra regions. Multi-scale supervision mechanism is applied to explore comprehensive features and an Edge aware Fusion Mechanism (EFM) is proposed to fuse features extracted from the two pathways. Some other image processing skills, such as centralized backbone clipping, patch cropping and convex hull detection are introduced to further refine the vertebra segmentation results. Experimental validations on spine X-ray images dataset and vertebrae dataset suggest that the proposed AGNet achieves superior performance compared with state-of-the-art segmentation methods, and the coarse-to-fine framework can be implemented in real spinal diagnosis systems.

Targeted therapy for one for a set of genes has made it possible to apply precision medicine for different patients due to the existence of tumor heterogeneity. However, how to regulate those genes are still problematic. One of the natural regulators of genes is microRNAs. Thus, a better understanding of the miRNA-gene interaction mechanism might contribute to future diagnosis, prevention, and cancer therapy. The interactions between microRNA and genes play an essential role in molecular genetics. The in-vivo experiments validating the relationships between them are time-consuming, money-costly, and labor-intensive. With the development of high-throughput technology, we dealt with tons of biological data. However, extracting features from tremendous raw data and making a mathematical model is still a challenging topic. Machine learning and deep learning algorithms have become powerful tools in dealing with biological data. Inspired by this, in this paper, we propose a model that combines features/embedding extraction methods, deep learning algorithms, and a voting system. We leverage doc2vec to generate sequential embedding from molecular sequences. The role2vec, GCN, and GMM for geometrical embedding were generated from the complex network from similarity and pair-wise datasets. For the deep learning algorithms, we leveraged LSTM and Bi-LSTM according to different embedding and features. Finally, we adopted a voting system to balance results from different data sources. The results have shown that our voting system could achieve a higher AUC than the existing benchmark. The case studies demonstrate that our model could reveal potential relationships between miRNAs and genes. The source code, features, and predictive results can be downloaded at https://github.com/Xshelton/SRG-vote.

The visual quality of ultrasound (US) images is crucial for clinical diagnosis and treatment. The main source of image quality degradation is the inherent speckle noise generated during US image acquisition. Current deep learning-based methods cannot preserve the maximum boundary contrast when removing noise and speckle. In this paper, we address the issue by proposing a novel wavelet-based generative adversarial network (GAN) for real-time high-quality US image reconstruction, viz. WGAN-DUS. First, we propose a batch normalization module (BNM) to balance the importance of each sub-band image and fuse sub-band features simultaneously. Then, a wavelet reconstruction module (WRM) integrated with a cascade of wavelet residual channel attention block (WRCAB) is proposed to extract distinctive sub-band features used to reconstruct denoised images. A gradual tuning strategy is proposed to fine-tune our generator for better despeckling performance. We further propose a wavelet-based discriminator and a comprehensive loss function to effectively suppress speckle noise and preserve the image features. Besides, we have designed an algorithm to estimate the noise levels during despeckling of real US images. The performance of our network was then evaluated on natural, synthetic, simulated and clinical US images and compared against various despeckling methods. To verify the feasibility of WGAN-DUS, we further extend our work to uterine fibroid segmentation with the denoised US image of the proposed approach. Experimental result demonstrates that our proposed method is feasible and can be generalized to clinical applications for despeckling of US images in real-time without losing its fine details.

Single-cell clustering is a crucial task of scRNA-seq analysis, which reveals the natural grouping of cells. However, due to the high noise and high dimension in scRNA-seq data, how to effectively and accurately identify cell types from a great quantity of cell mixtures is still a challenge. Considering this, in this paper, we propose a novel subspace clustering algorithm termed SLRRSC. This method is developed based on the low-rank representation model, and it aims to capture the global and local properties inherent in data. In order to make the LRR matrix describe the spatial relationship of samples more accurately, we introduce the manifold-based graph regularization and similarity constraint into the LRR-based method SLRRSC. The graph regularization can preserve the local geometric structure of the data in low-rank decomposition, so that the low-rank representation matrix contains more local structure information. By imposing similarity constraint on the low-rank matrix, the similarity information between sample pairs is further introduced into the SLRRSC model to improve the learning ability of low-rank method for global structure. At the same time, the similarity constraint makes the low-rank representation matrix symmetric, which makes it better interpretable in clustering application. We compare the effectiveness of the SLRRSC algorithm with other single-cell clustering methods on simulated data and real single-cell datasets. The results show that this method can obtain more accurate sample similarity matrix and effectively solve the problem of cell type recognition.

Cancer genome data generally consists of multiple views from different sources. These views provide different levels of information about gene activity, as well as more comprehensive cancer information. The low-rank representation (LRR) method, as a powerful subspace clustering method, has been extended and applied in cancer data research. Although the multi-view learning methods based on low rank representation have achieved good results in cancer multi-omics analysis because they fully consider the consistency and complementarity between views, these methods have some shortcomings in mining the potential local geometry of data. In view of this, this paper proposes a new method named Multi-view Random-walk Graph regularization Low-Rank Representation (MRGLRR) to comprehensively analyze multi-view genomics data. This method uses multi-view model to find the common centroid of view. By constructing a joint affinity matrix to learn the low-rank subspace representation of multiple sets of data, the hidden information of each view is fully obtained. In addition, this method introduces random walk graph regularization constraint to obtain more accurate similarity between samples. Different from the traditional graph regularization constraint, after constructing the KNN graph, we use the random walk algorithm to obtain the weight matrix. The random walk algorithm can retain more local geometric information and better learn the topological structure of the data. What's more, a feature gene selection strategy suitable for multi-view model is proposed to find more differentially expressed genes with research value. Experimental results show that our method is better than other representative methods in terms of clustering and feature gene selection for cancer multi-omics data.

Neuron tracing from optical image is critical in understanding brain function in diseases. A key problem is to trace discontinuous filamentary structures from noisy background, which is commonly encountered in neuronal and some medical images. Broken traces lead to cumulative topological errors, and current methods were hard to assemble various fragmentary traces for correct connection. In this paper, we propose a graph connectivity theoretical method for precise filamentary structure tracing in neuron image. First, we build the initial subgraphs of signals via a region-to-region based tracing method on CNN predicted probability. CNN technique removes noise interference, whereas its prediction for some elongated fragments is still incomplete. Second, we reformulate the global connection problem of individual or fragmented subgraphs under heuristic graph restrictions as a dynamic linear programming function via minimizing graph connectivity cost, where the connected cost of breakpoints are calculated using their probability strength via minimum cost path. Experimental results on challenging neuronal images proved that the proposed method outperformed existing methods and achieved similar results of manual tracing, even in some complex discontinuous issues. Performances on vessel images indicate the potential of the method for some other tubular objects tracing.

Study of pairwise genetic interactions, such as mutually exclusive mutations, has led to understanding of underlying mechanisms in cancer. Investigation of various combinatorial motifs within networks of such interactions can lead to deeper insights into its mutational landscape and inform therapy development. One such motif called the Between-Pathway Model (BPM) represents redundant or compensatory pathways that can be therapeutically exploited. Finding such BPM motifs is challenging since most formulations require solving variants of the NP-complete maximum weight bipartite subgraph problem. In this paper we design an algorithm based on Integer Linear Programming (ILP) to solve this problem. In our experiments, our approach outperforms the best previous method to mine BPM motifs. Further, our ILP-based approach allows us to easily model additional application-specific constraints. We illustrate this advantage through a new application of BPM motifs that can potentially aid in finding combination therapies to combat cancer.

Hard sample selection can effectively improve model convergence by extracting the most representative samples from a training set. However, due to the large capacity of medical images, existing sampling strategies suffer from insufficient exploitation for hard samples or high time cost for sample selection when adopted by 3D patch-based models in the field of multi-organ segmentation. In this paper, we present a novel and effective online hard patch mining (OHPM) algorithm. In our method, an average shape model that can be mapped with all training images is constructed to guide the exploration of hard patches and aggregate feedback from predicted patches. The process of hard mining is formalized as a multi-armed bandit problem and solved with bandit algorithms. With the shape model, OHPM requires negligible time consumption and can intuitively locate difficult anatomical areas during training. The employment of bandit algorithms ensures online and sufficient hard mining. We integrate OHPM with advanced segmentation networks and evaluate them on two datasets containing different anatomical structures. Comparative experiments with other sampling strategies demonstrate the superiority of OHPM in boosting segmentation performance and improving model convergence. The results in each dataset with each network suggest that OHPM significantly outperforms other sampling strategies by nearly 2% average Dice score.

The analysis of molecular cavities, where ligands interact with protein structures, plays a critical role in protein structure-based drug design. However, it is a challenge because of the ambiguous definition of the cavity boundaries in most cavity detection methods. The cavities are mostly calculated by input parameters, which are difficult for users to visualize cavities in interactive ways. In this paper, we propose a novel method for the interactive exploration of cavity calculation and visualization. Firstly, the proposed method combines the two solvent-excluded surfaces (SES) models of a given protein to define the boundaries and provides cavity emission points. Secondly, the system provides a user-guided interactive method to allow users to select cavities by simply clicking operations and to track the cavity identify and filling process based on position constraints. Finally, the selected cavities are represented with the colorful depth perception method. Experiments show that our work can effectively identify and calculate cavities.

Precise quantification of tree-like structures from biomedical images, such as neuronal shape reconstruction and retinal blood vessel caliber estimation, is increasingly important in understanding normal function and pathologic processes in biology. Some handcrafted methods have been proposed for this purpose in recent years. However, they are designed only for a specific application. In this paper, we propose a shape analysis algorithm, DeepRayburst, that can be applied to many different applications based on a Multi-Feature Rayburst Sampling (MFRS) and a Dual Channel Temporal Convolutional Network (DC-TCN). Specifically, we first generate a Rayburst Sampling (RS) core containing a set of multidirectional rays. Then the MFRS is designed by extending each ray of the RS to multiple parallel rays which extract a set of feature sequences. A Gaussian kernel is then used to fuse these feature sequences and outputs one feature sequence. Furthermore, we design a DC-TCN to make the rays terminate on the surface of tree-like structures according to the fused feature sequence. Finally, by analyzing the distribution patterns of the terminated rays, the algorithm can serve multiple shape analysis applications of tree-like structures. Experiments on three different applications, including soma shape reconstruction, neuronal shape reconstruction, and vessel caliber estimation, confirm that the proposed method outperforms other state-of-the-art shape analysis methods, which demonstrate its flexibility and robustness.

AI healthcare applications rely on sensitive electronic healthcare records (EHRs) that are scarcely labelled and are often distributed across a network of the symbiont institutions. It is challenging to train the effective machine learning models on such data. In this work, we propose dynamic neural graphs based federated learning framework to address these challenges. The proposed framework extends Reptile, a model agnostic meta-learning (MAML) algorithm, to a federated setting. However, unlike the existing MAML algorithms, this paper proposes a dynamic variant of neural graph learning (NGL) to incorporate unlabelled examples in the supervised training setup. Dynamic NGL computes a meta-learning update by performing supervised learning on a labelled training example while performing metric learning on its labelled or unlabelled neighbourhood. This neighbourhood of a labelled example is established dynamically using local graphs built over the batches of training examples. Each local graph is constructed by comparing the similarity between embedding generated by the current state of the model. The introduction of metric learning on the neighbourhood makes this framework semi-supervised in nature. The experimental results on the publicly available MIMIC-III dataset highlight the effectiveness of the proposed framework for both single and multi-task settings under data decentralisation constraints and limited supervision.

Objective: Human-curated diseaseontologies are widely used for diagnostic evaluation, treatment and data comparisons over time, and clinical decision support. The classification principles underlying these ontologies are guided by the analysis of observable pathological similarities between disorders, often based on anatomical or histological principles. Although, thanks to recent advances in molecular biology, disease ontologies are slowly changing to integrate the etiological and genetic origins of diseases, nosology still reflects this "reductionist" perspective. Proximity relationships of disease modules (hereafter DMs) in the human interactome network are now increasingly used in diagnostics, to identify pathobiologically similar diseases and to support drug repurposing and discovery. On the other hand, similarity relations induced from structural proximity of DMs also have several limitations, such as incomplete knowledge of disease-gene relationships and reliability of clinical trials to assess their validity. The purpose of the study described in this paper is to shed more light on disease similarities by analyzing the relationship between categorical proximity of diseases in human-curated ontologies and structural proximity of the related DMs in the interactome., Method: We propose a method (and related algorithms) to automatically induce a hierarchical structure from proximity relations between DMs, and to compare this structure with a human-curated disease taxonomy., Results: We demonstrate that the proposed method allows to systematically analyze commonalities and differences among structural and categorical similarity of human diseases, help refine and extend human disease classification systems, and identify promising network areas where new disease-gene interactions can be discovered.