Binary Classification Quantum Neural Network Model Based on Optimized Grover Algorithm.

We focus on the problem that the Grover algorithm is not suitable for the completely unknown proportion of target solutions. Considering whether the existing quantum classifier used by the current quantum neural network (QNN) to complete the classification task can solve the problem of the classical classifier, this paper proposes a binary quantum neural network classifical model based on an optimized Grover algorithm based on partial diffusion. Trial and error is adopted to extend the partial diffusion quantum search algorithm with the known proportion of target solutions to the unknown state, and to apply the characteristics of the supervised learning of the quantum neural network to binary classify the classified data. Experiments show that the proposed method can effectively retrieve quantum states with similar features. The test accuracy of BQM retrieval under the depolarization noise at the 20th period can reach 97% when the depolarization rate is 0.1. It improves the retrieval accuracy by about 4% and 10% compared with MSE and BCE in the same environment.

Integration of Human Protein Sequence and Protein-Protein Interaction Data by Graph Autoencoder to Identify Novel Protein-Abnormal Phenotype Associations.

Understanding gene functions and their associated abnormal phenotypes is crucial in the prevention, diagnosis and treatment against diseases. The Human Phenotype Ontology (HPO) is a standardized vocabulary for describing the phenotype abnormalities associated with human diseases. However, the current HPO annotations are far from completion, and only a small fraction of human protein-coding genes has HPO annotations. Thus, it is necessary to predict protein-phenotype associations using computational methods. Protein sequences can indicate the structure and function of the proteins, and interacting proteins are more likely to have same function. It is promising to integrate these features for predicting HPO annotations of human protein. We developed GraphPheno, a semi-supervised method based on graph autoencoders, which does not require feature engineering to capture deep features from protein sequences, while also taking into account the topological properties in the protein-protein interaction network to predict the relationships between human genes/proteins and abnormal phenotypes. Cross validation and independent dataset tests show that GraphPheno has satisfactory prediction performance. The algorithm is further confirmed on automatic HPO annotation for no-knowledge proteins under the benchmark of the second Critical Assessment of Functional Annotation, 2013-2014 (CAFA2), where GraphPheno surpasses most existing methods. Further bioinformatics analysis shows that predicted certain phenotype-associated genes using GraphPheno share similar biological properties with known ones. In a case study on the phenotype of abnormality of mitochondrial respiratory chain, top prioritized genes are validated by recent papers. We believe that GraphPheno will help to reveal more associations between genes and phenotypes, and contribute to the discovery of drug targets.

Low-cost thermal imaging with machine learning for non-invasive diagnosis and therapeutic monitoring of pneumonia.

Rapid screening and early treatment of lung infection are essential for effective control of many epidemics such as Coronavirus Disease 2019 (COVID-19). Recent studies have demonstrated the potential correlation between lung infection and the change of back skin temperature distribution. Based on these findings, we propose to use low-cost, portable and rapid thermal imaging in combination with image-processing algorithms and machine learning analysis for non-invasive and safe detection of pneumonia. The proposed method was tested in 69 subjects (30 normal adults, 11 cases of fever without pneumonia, 19 cases of general pneumonia and 9 cases of COVID-19) where both RGB and thermal images were acquired from the back of each subject. The acquired images were processed automatically in order to extract multiple location and shape features that distinguish normal subjects from pneumonia patients at a high accuracy of 93 % . Furthermore, daily assessment of two pneumonia patients by the proposed method accurately predicted the clinical outcomes, coincident with those of laboratory tests. Our pilot study demonstrated the technical feasibility of portable and intelligent thermal imaging for screening and therapeutic assessment of pneumonia. The method can be potentially implemented in under-resourced regions for more effective control of respiratory epidemics.

Applying limiting entropy to quantify the alignment of collagen fibers by polarized light imaging.

Collagen alignment has shown clinical significance in a variety of diseases. For instance, vulvar lichen sclerosus (VLS) is characterized by homogenization of collagen fibers with increasing risk of malignant transformation. To date, a variety of imaging techniques have been developed to visualize collagen fibers. However, few works focused on quantifying the alignment quality of collagen fiber. To assess the level of disorder of local fiber orientation, the homogeneity index (HI) based on limiting entropy is proposed as an indicator of disorder. Our proposed methods are validated by verification experiments on Poly Lactic Acid (PLA) filament phantoms with controlled alignment quality of fibers. A case study on 20 VLS tissue biopsies and 14 normal tissue biopsies shows that HI can effectively characterize VLS tissue from normal tissue (P < 0.01). The classification results are very promising with a sensitivity of 93% and a specificity of 95%, which indicated that our method can provide quantitative assessment for the alignment quality of collagen fibers in VLS tissue and aid in improving histopathological examination of VLS.

Simulating orientation and polarization characteristics of dense fibrous tissue by electrostatic spinning of polymeric fibers.

Phantoms simulating polarization characteristics of soft tissue play an important role in the development, calibration, and validation of diagnostic polarized imaging devices and of therapeutic strategy, in both laboratory and clinical settings. We propose to fabricate optical phantoms that simulate polarization characteristics of dense fibrous tissues by bonding electrospun polylactic acid (PLA) fibers between polydimethylsiloxane (PDMS) substrate with a groove. Increasing the rotational speed of an electrospinning collector helps improve the orientation of the electrospun fibers. The phantoms simulate the polarization characteristics of dense fibrous tissue of collagenous fibroma and healthy skin with high fidelity. Our experiments demonstrate the technical potential of using such phantoms for validation and calibration of polarimetric medical devices.