Effective knowledge graph embeddings based on multidirectional semantics relations for polypharmacy side effects prediction.

MOTIVATION: Polypharmacy is the combined use of drugs for the treatment of diseases. However, it often shows a high risk of side effects. Due to unnecessary interactions of combined drugs, the side effects of polypharmacy increase the risk of disease and even lead to death. Thus, obtaining abundant and comprehensive information on the side effects of polypharmacy is a vital task in the healthcare industry. Early traditional methods used machine learning techniques to predict side effects. However, they often make costly efforts to extract features of drugs for prediction. Later, several methods based on knowledge graphs are proposed. They are reported to outperform traditional methods. However, they still show limited performance by failing to model complex relations of side effects among drugs. RESULTS: To resolve the above problems, we propose a novel model by further incorporating complex relations of side effects into knowledge graph embeddings. Our model can translate and transmit multidirectional semantics with fewer parameters, leading to better scalability in large-scale knowledge graphs. Experimental evaluation shows that our model outperforms state-of-the-art models in terms of the average area under the ROC and precision-recall curves. AVAILABILITY AND IMPLEMENTATION: Code and data are available at: https://github.com/galaxysunwen/MSTE-master.

A Genetic Algorithm-Based Ensemble Learning Framework for Drug Combination Prediction.

Combination therapy is a promising clinical treatment strategy for cancer and other complex diseases. Multiple drugs can target multiple proteins and pathways, greatly improving the therapeutic effect and slowing down drug resistance. To narrow the search space of synergistic drug combinations, many prediction models have been developed. However, drug combination datasets always have the characteristics of class imbalance. Synergistic drug combinations receive the most attention in clinical application but are in small numbers. To predict synergistic drug combinations in different cancer cell lines, in this study, we propose a genetic algorithm-based ensemble learning framework, GA-DRUG, to address the problems of class imbalance and high dimensionality of input data. The cell-line-specific gene expression profiles under drug perturbations are used to train GA-DRUG, which contains imbalanced data processing and the search of global optimal solutions. Compared to 11 state-of-the-art algorithms, GA-DRUG achieves the best performance and significantly improves the prediction performance in the minority class (Synergy). The ensemble framework can effectively correct the classification results of a single classifier. In addition, the cellular proliferation experiment performed on several previously unexplored drug combinations further confirms the predictive ability of GA-DRUG.

MRDFF: A deep forest based framework for CT whole heart segmentation.

Automatic whole heart segmentation plays an important role in the treatment and research of cardiovascular diseases. In this paper, we propose an improved Deep Forest framework, named Multi-Resolution Deep Forest Framework (MRDFF), which accomplishes whole heart segmentation in two stages. We extract the heart region by binary classification in the first stage, thus avoiding the class imbalance problem caused by too much background. The results of the first stage are then subdivided in the second stage to obtain accurate cardiac substructures. In addition, we also propose hybrid feature fusion, multi-resolution fusion and multi-scale fusion to further improve the segmentation accuracy. Experiments on the public dataset MM-WHS show that our model can achieve comparable accuracy in about half the training time of neural network models.

Domain-Adaptive Prototype-Recalibrated Network with Transductive Learning Paradigm for Intelligent Fault Diagnosis under Various Limited Data Conditions.

In real industrial scenarios, intelligent fault diagnosis based on data-driven methods has been widely researched in the past decade. However, data scarcity is widespread in fault diagnosis tasks owning to the difficulties in collecting adequate data. As a result, there is an increasing demand for both researchers and engineers for fault identification with scarce data. To address this issue, an innovative domain-adaptive prototype-recalibrated network (DAPRN) based on a transductive learning paradigm and prototype recalibration strategy (PRS) is proposed, which has the potential to promote the generalization ability from the source domain to target domain in a few-shot fault diagnosis. Within this scheme, the DAPRN is composed of a feature extractor, a domain discriminator, and a label predictor. Concretely, the feature extractor is jointly optimized by the minimization of few-shot classification loss and the maximization of domain-discriminative loss. The cosine similarity-based label predictor, which is promoted by the PRS, is exploited to avoid the bias of naïve prototypes in the metric space and recognize the health conditions of machinery in the meta-testing process. The efficacy and advantage of DAPRN are validated by extensive experiments on bearing and gearbox datasets compared with seven popular and well-established few-shot fault diagnosis methods. In practical application, the proposed DAPRN is expected to solve more challenging few-shot fault diagnosis scenarios and facilitate practical fault identification problems in modern manufacturing.

3D vasculature segmentation using localized hybrid level-set method.

BACKGROUND: Intensity inhomogeneity occurs in many medical images, especially in vessel images. Overcoming the difficulty due to image inhomogeneity is crucial for the segmentation of vessel image. METHODS: This paper proposes a localized hybrid level-set method for the segmentation of 3D vessel image. The proposed method integrates both local region information and boundary information for vessel segmentation, which is essential for the accurate extraction of tiny vessel structures. The local intensity information is firstly embedded into a region-based contour model, and then incorporated into the level-set formulation of the geodesic active contour model. Compared with the preset global threshold based method, the use of automatically calculated local thresholds enables the extraction of the local image information, which is essential for the segmentation of vessel images. RESULTS: Experiments carried out on the segmentation of 3D vessel images demonstrate the strengths of using locally specified dynamic thresholds in our level-set method. Furthermore, both qualitative comparison and quantitative validations have been performed to evaluate the effectiveness of our proposed model. CONCLUSIONS: Experimental results and validations demonstrate that our proposed model can achieve more promising segmentation results than the original hybrid method does.

A Distance Transformation Deep Forest Framework With Hybrid-Feature Fusion for CXR Image Classification.

Detecting pneumonia, especially coronavirus disease 2019 (COVID-19), from chest X-ray (CXR) images is one of the most effective ways for disease diagnosis and patient triage. The application of deep neural networks (DNNs) for CXR image classification is limited due to the small sample size of the well-curated data. To tackle this problem, this article proposes a distance transformation-based deep forest framework with hybrid-feature fusion (DTDF-HFF) for accurate CXR image classification. In our proposed method, hybrid features of CXR images are extracted in two ways: hand-crafted feature extraction and multigrained scanning. Different types of features are fed into different classifiers in the same layer of the deep forest (DF), and the prediction vector obtained at each layer is transformed to form distance vector based on a self-adaptive scheme. The distance vectors obtained by different classifiers are fused and concatenated with the original features, then input into the corresponding classifier at the next layer. The cascade grows until DTDF-HFF can no longer gain benefits from the new layer. We compare the proposed method with other methods on the public CXR datasets, and the experimental results show that the proposed method can achieve state-of-the art (SOTA) performance. The code will be made publicly available at https://github.com/hongqq/DTDF-HFF.

A Training-Free Infant Spontaneous Movement Assessment Method for Cerebral Palsy Prediction Based on Videos.

OBJECTIVE: Early diagnosis of infant cerebral palsy (CP) is very important for infant health. In this paper, we present a novel training-free method to quantify infant spontaneous movements for predicting CP. METHODS: Unlike other classification methods, our method turns the assessment into a clustering task. First, the joints of the infant are extracted by the current pose estimation algorithm, and the skeleton sequence is segmented into multiple clips through a sliding window. Then we cluster the clips and quantify infant CP by the number of cluster classes. RESULTS: The proposed method was tested on two datasets, and achieved state-of-the-arts (SOTAs) on both datasets using the same parameters. What's more, our method is interpretable with visualized results. CONCLUSION: The proposed method can quantify abnormal brain development in infants effectively and be used in different datasets without training. SIGNIFICANCE: Limited by small samples, we propose a training-free method for quantifying infant spontaneous movements. Unlike other binary classification methods, our work not only enables continuous quantification of infant brain development, but also provides interpretable conclusions by visualizing the results. The proposed spontaneous movement assessment method significantly advances SOTAs in automatically measuring infant health.

Bionic intelligent ankle-foot prosthesis based on the conjugate curved surface.

Given the poor biomimetic motion of traditional ankle-foot prostheses, it is of great significance to develop an intelligent prosthesis that can realize the biomimetic mechanism of human feet and ankles. To this end, we presented a bionic intelligent ankle-foot prosthesis based on the complex conjugate curved surface. The proposed prosthesis is mainly composed of the rolling conjugated joints with a bionic design and the carbon fiber energy-storage foot. We investigated the flexibility of the prosthetic ankle joint movement, and the ability of the prosthetic foot to absorb ground impact during the gait cycle. Experimental results showed the matching of the ankle/toe position relationship of the human foot during simulated walking, which is helpful to realize the biomimetic motion of the human foot and ankle. It can also help therapists and clinicians provide better rehabilitation for lower-limb amputees.

A hybrid deep forest-based method for predicting synergistic drug combinations.

Combination therapy is a promising approach in treating multiple complex diseases. However, the large search space of available drug combinations exacerbates challenge for experimental screening. To predict synergistic drug combinations in different cancer cell lines, we propose an improved deep forest-based method, ForSyn, and design two forest types embedded in ForSyn. ForSyn handles imbalanced and high-dimensional data in medium-/small-scale datasets, which are inherent characteristics of drug combination datasets. Compared with 12 state-of-the-art methods, ForSyn ranks first on four metrics for eight datasets with different feature combinations. We conduct a systematic analysis to identify the most appropriate configuration parameters. We validate the predictive value of ForSyn with cell-based experiments on several previously unexplored drug combinations. Finally, a systematic analysis of feature importance is performed on the top contributing features extracted by ForSyn. The resulting key genes may play key roles on corresponding cancers.

A direct slicing technique for the 3D printing of implicitly represented medical models.

In conventional medical image printing methods, volumetric medical data needs to be conversed into STereo Lithography (STL) format, the most commonly used format for representing geometric models for 3D printing. However, this STL conversion process is not only time consuming, but more importantly, it often leads to the loss of accuracy. It has become a critical factor hindering the printing efficiency and precision of organ models. By examining the key characteristics of discrete medical volume data, this paper proposes a direct slicing technique for printing implicitly represented 3D medical models. The proposed method mainly consists of three algorithms: (1) A layer-based contour extraction algorithm for discrete volume data; (2) An inner shell construction algorithm based on discrete point differential indentation; (3) An infill generation algorithm based on the constructed virtual contour and scan lines. The proposed method has been applied to the slicing of several organ models for experiments, and the ratios of time cost and memory cost between the conventional method and the proposed method are about 4-100 and 1.1 to 1.4 respectively, which demonstrate that the proposed method has a great improvement in both time and space performance when compared with the conventional STL-based method. Our technique extends the direct input format of geometric models for additive manufacturing. That is, discrete volume data can be used as a direct input for additive manufacturing without conversion to STL format.

Human 3D pose estimation in a lying position by RGB-D images for medical diagnosis and rehabilitation.

Posture recognition in the human lying position is of great significance for the rehabilitation evaluation of lying patients and the diagnosis of infants with early cerebral palsy. In this paper, we proposed a novel method for human 3D pose estimation in a lying position with the RGB image and corresponding depth information. Firstly, we employ current pose estimation method on RGB images to achieve the human full body 2D keypoints. By combining the depth information and coordinate transformation, the 3D movement of human in lying position can be obtained. We validate our method with two public datasets. The results show that the accuracy can reach the state-of-the-art.

[A clinical and genetic analysis of a pedigree with two 46,XY patients suffering from 17alpha-hydroxylase deficiency].

OBJECTIVE: To investigate the molecular defects of CYP17A1 gene in a pedigree with two 46,XY patients suffering from 17alpha-hydroxylase deficiency (17-OHD) and explore the steroid biosynthetic difference in carriers of 17-OHD before and after adrenocorticotrophic hormone (ACTH) test. METHODS: Clinical data and hormone profiles were collected from the members of the pedigree. CYP17A1 genotyping was performed in the patients and family members with PCR-direct sequencing. A short ACTH test was evaluated in some cases. RESULTS: The CYP17 genes of the patients were proved to hold a homozygous mutation with a base deletion and a base transversion (TAC/AA) in exon 6, which produced a missense mutation of Tyr-->Lys at codon 329 and changed the open reading frame following this codon. The hormone response of the carriers after ACTH stimulation was abnormal between the patients and normal controls. CONCLUSION: 17-OHD in this family was caused by CYP17A1 mutation (TAC329AA); some hormonal response to ACTH stimulation was abnormal in carriers.

A Light Spot Humanoid Motion Paradigm Modulated by the Change of Brightness to Recognize the Stride Motion Frequency.

The steady-state visual evoked potential (SSVEP)-based brain-computer interface (BCI) usually has the advantages of high information transfer rate (ITR) and no need for training. However, low frequencies, such as the human stride motion frequency, cannot easily induce SSVEP. To solve this problem, a light spot humanoid motion paradigm modulated by the change of brightness was designed in this study. The characteristics of the brain response to the motion paradigm modulated by the change of brightness were analyzed for the first time. The results showed that the designed paradigm could induce not only the high flicker frequency but also the modulation frequencies between the change of brightness and the motion in the primary visual cortex. Thus, the stride motion frequency can be recognized through the modulation frequencies by using the designed paradigm. Also, in an online experiment, this paradigm was employed to control a lower limb robot to achieve same frequency stimulation, which meant that the visual stimulation frequency was the same as the motion frequency of the robot. Also, canonical correlation analysis (CCA) was used to distinguish three different stride motion frequencies. The average accuracies of the classification in three walking speeds using the designed paradigm with the same and different high frequencies reached 87 and 95% respectively. Furthermore, the angles of the knee joint of the robot were obtained to demonstrate the feasibility of the electroencephalograph (EEG)-driven robot with same stimulation.

Human action recognition based on kinematic similarity in real time.

Human action recognition using 3D pose data has gained a growing interest in the field of computer robotic interfaces and pattern recognition since the availability of hardware to capture human pose. In this paper, we propose a fast, simple, and powerful method of human action recognition based on human kinematic similarity. The key to this method is that the action descriptor consists of joints position, angular velocity and angular acceleration, which can meet the different individual sizes and eliminate the complex normalization. The angular parameters of joints within a short sliding time window (approximately 5 frames) around the current frame are used to express each pose frame of human action sequence. Moreover, three modified KNN (k-nearest-neighbors algorithm) classifiers are employed in our method: one for achieving the confidence of every frame in the training step, one for estimating the frame label of each descriptor, and one for classifying actions. Additional estimating of the frame's time label makes it possible to address single input frames. This approach can be used on difficult, unsegmented sequences. The proposed method is efficient and can be run in real time. The research shows that many public datasets are irregularly segmented, and a simple method is provided to regularize the datasets. The approach is tested on some challenging datasets such as MSR-Action3D, MSRDailyActivity3D, and UTD-MHAD. The results indicate our method achieves a higher accuracy.

GPU accelerating technique for rendering implicitly represented vasculatures.

With the flooding datasets of medical Computed Tomography (CT) and Magnetic Resonance Imaging (MRI), implicit modeling techniques are increasingly applied to reconstruct the human organs, especially the vasculature. However, displaying implicitly represented geometric objects arises heavy computational burden. In this study, a Graphics Processing Unit (GPU) accelerating technique was developed for high performance rendering of implicitly represented objects, especially the vasculatures. The experimental results suggested that the rendering performance was greatly enhanced via exploiting the advantages of modern GPUs.

Microarray data classification based on ensemble independent component selection.

Independent component analysis (ICA) has been widely deployed to the analysis of microarray datasets. Although it was pointed out that after ICA transformation, different independent components (ICs) are of different biological significance, the IC selection problem is still far from fully explored. In this paper, we propose a genetic algorithm (GA) based ensemble independent component selection (EICS) system. In this system, GA is applied to select a set of optimal IC subsets, which are then used to build diverse and accurate base classifiers. Finally, all base classifiers are combined with majority vote rule. To show the validity of the proposed method, we apply it to classify three DNA microarray data sets involving various human normal and tumor tissue samples. The experimental results show that our ensemble method obtains stable and satisfying classification results when compared with several existing methods.