2019 IEEE 19th International Conference on Bioinformatics and Bioengineering (BIBE)最新文献

Meta-Learning for Avatar Kinematics Reconstruction in Virtual Reality Rehabilitation 虚拟现实康复中虚拟角色运动学重构的元学习

2019 IEEE 19th International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2019-10-01 DOI: 10.1109/BIBE.2019.00117

Cristian Axenie, Armin Becher, Daria Kurz, T. Grauschopf

{"title":"Meta-Learning for Avatar Kinematics Reconstruction in Virtual Reality Rehabilitation","authors":"Cristian Axenie, Armin Becher, Daria Kurz, T. Grauschopf","doi":"10.1109/BIBE.2019.00117","DOIUrl":"https://doi.org/10.1109/BIBE.2019.00117","url":null,"abstract":"Virtual Reality (VR) sensorimotor rehabilitation is still in infancy but will soon require avatars, digital alter-egos of patients' physical selves. Such embodied interfaces could stimulate patients' perception in a rich and highly customized environment, where sensorimotor deficits, such as in Chemotherapy-Induced Peripheral Neuropathy, could be corrected. In such scenarios, motion prediction is a key ingredient for realistic immersion. Yet, such a task lives under hard processing latency constraints and the inherent variability of human motion. We propose a neural network meta-learning system exploiting the underlying correlations in body kinematics with potential to provide, within latency guarantees, personalized VR rehabilitation. The unsupervised meta-learner is able to extract underlying statistics of the motion data by exploiting data regularities in order to describe the underlying manifold, or structure, of motion under sensorimotor deficits. We demonstrate, through preliminary experiments the potential of such a learning system for adaptive kinematics estimation in personalized rehabilitation VR avatars.","PeriodicalId":318819,"journal":{"name":"2019 IEEE 19th International Conference on Bioinformatics and Bioengineering (BIBE)","volume":"34 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116153106","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 4

Stability Investigation Using Hydrogen Bonds for Different Mutations and Drug Resistance in Non-Small Cell Lung Cancer Patients 利用氢键研究非小细胞肺癌患者不同突变和耐药的稳定性

2019 IEEE 19th International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2019-10-01 DOI: 10.1109/BIBE.2019.00030

Avirup Ghosh, Hong Yan

{"title":"Stability Investigation Using Hydrogen Bonds for Different Mutations and Drug Resistance in Non-Small Cell Lung Cancer Patients","authors":"Avirup Ghosh, Hong Yan","doi":"10.1109/BIBE.2019.00030","DOIUrl":"https://doi.org/10.1109/BIBE.2019.00030","url":null,"abstract":"Lung cancer is the predominant reason for cancer deaths. Deletion mutation (del_E746-A750) in the Epidermal growth factor receptor (EGFR) is liable for 40% of Non-small cell lung cancer (NSCLC). However, 70% of the NSCLC active patients acquire T790M drug resistance mutation after progressing with the first-line EGFR Tyrosine kinase inhibitor (TKI). There are many third-generation EGFR-TKIs which are EGFR mutant selective and produced to heal the patients with T790M resistance mutation. Osimertinib is one of the third-generation EGFR TKIs which irreversibly inhibits the EGFR activity after the T790M mutation. Unfortunately, despite having an impressive initial response, 6 out of 15 patients who were diagnosed with third-generation EGFR-TKI would develop a new resistance and the most frequent being C797S mutation at exon 20. Numerous treatment techniques were implemented for patients who have progressed with C797S second resistance mutation, but there is no official fourth-generation EGFR TKI has invented. In our research work, we analyzed the stability changes for each structure in terms of reduction and hydrogen bonds. Our findings provide insight into the diversity of mechanisms through hydrogen bond analysis in different EGFR structures in terms of stability check and highlight the need for therapeutics and fourth-generation TKI to overcome resistance arbitrated by EGFR C797S.","PeriodicalId":318819,"journal":{"name":"2019 IEEE 19th International Conference on Bioinformatics and Bioengineering (BIBE)","volume":"170 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"114153031","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

MemAlign: A Memory Structure to Accelerate Gene Sequencing MemAlign:加速基因测序的记忆结构

2019 IEEE 19th International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2019-10-01 DOI: 10.1109/BIBE.2019.00036

Meysam Roodi, A. Moshovos

{"title":"MemAlign: A Memory Structure to Accelerate Gene Sequencing","authors":"Meysam Roodi, A. Moshovos","doi":"10.1109/BIBE.2019.00036","DOIUrl":"https://doi.org/10.1109/BIBE.2019.00036","url":null,"abstract":"Since 2003, when the human reference genome was discovered, several applications found gene sequencing a promising mechanism to help improve their results. These include studying hereditary diseases, prenatal monitoring and others. Gene sequencing in its typical configuration consists of several elaborate processing stages, each performed by a separate software package. The intermediate results are transferred via large files between gene sequencing different steps, hence making gene sequencing a processing and I/O demanding task. Taking advantage of advances memory speed and capacity and with the ultimate goal of pipelining the gene sequencing steps and avoiding utilizing file storage to communicate intermediate results, in this paper we present MemAlign, a novel pre-sorted memory structure to pipeline the first and second processing steps of gene sequencing; Alignment and Sort. The number of memory locations of MemAlign corresponds the positions on the human reference genome. Combined with techniques to compress the alignment results, MemAlign essentially eliminates the Sort step by storing alignment results in the memory location that corresponds to the alignment position. MemAlign not only speeds up the combined processing time of Alignment and Sort, but also saves the considerable amount of storage required to store the intermediate results between the two steps.","PeriodicalId":318819,"journal":{"name":"2019 IEEE 19th International Conference on Bioinformatics and Bioengineering (BIBE)","volume":"27 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128996854","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Monitoring of Orientation of Cells by Electric Impedance: Test on Oriented Cells Using Micro Striped Grooves Pattern by Photolithography 用电阻抗监测细胞的取向:用光刻技术对定向细胞进行微条纹凹槽图案的测试

2019 IEEE 19th International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2019-10-01 DOI: 10.1109/BIBE.2019.00106

S. Hashimoto, Kazuyuki Abe

{"title":"Monitoring of Orientation of Cells by Electric Impedance: Test on Oriented Cells Using Micro Striped Grooves Pattern by Photolithography","authors":"S. Hashimoto, Kazuyuki Abe","doi":"10.1109/BIBE.2019.00106","DOIUrl":"https://doi.org/10.1109/BIBE.2019.00106","url":null,"abstract":"The electric impedance has been measured to estimate the orientation of cells in vitro. To arrange the orientation, several parallel lines of micro rectangular grooves (1 µm depth, 3 µm width and interval) have been made between a pair of the surface titanium electrodes on the scaffold of glass by the photolithography technique. Two types of arrangements of lines were designed related to the micro grooves: parallel, and perpendicular to the electric line of force between electrodes. C2C12 (mouse myoblast cell line) was cultured on the micro-patterned scaffold. The electric impedance (Z) between electrodes was measured every 24 hours with the sinusoidal electric waves (frequency, 1 kHz < f < 10 MHz; amplitude, v = ± 0.05 V) for three days. The number of oriented cells (Ns) was defined by the number of cells, which cross the straight-line bands of 0.01 mm width connecting between electrodes. The experimental result shows that Z increases with Ns. The phase difference between the voltage and the current is larger at the arrangement of myoblasts oriented in the perpendicular position than that in the parallel position. The present study shows that the measurement of the electric impedance is effective to estimate the orientation of cells.","PeriodicalId":318819,"journal":{"name":"2019 IEEE 19th International Conference on Bioinformatics and Bioengineering (BIBE)","volume":"9 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130483607","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Automatic Detection and Segmentation of Lung Lesions using Deep Residual CNNs 基于深度残差cnn的肺病变自动检测与分割

2019 IEEE 19th International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2019-10-01 DOI: 10.1109/BIBE.2019.00182

João B. S. Carvalho, José-Maria Moreira, Mário A. T. Figueiredo, Nickolas Papanikolaou

引用次数: 6

Neural Network Training Data Profoundly Impacts Texture-Based Intravascular Image Segmentation 神经网络训练数据深刻影响基于纹理的血管内图像分割

2019 IEEE 19th International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2019-10-01 DOI: 10.1109/BIBE.2019.00184

Akshay Gowrishankar, L. Athanasiou, Max L. Olender, E. Edelman

{"title":"Neural Network Training Data Profoundly Impacts Texture-Based Intravascular Image Segmentation","authors":"Akshay Gowrishankar, L. Athanasiou, Max L. Olender, E. Edelman","doi":"10.1109/BIBE.2019.00184","DOIUrl":"https://doi.org/10.1109/BIBE.2019.00184","url":null,"abstract":"Segmentation of variably differentiated and low-frequency elements in a complex image is challenging. Improving sensitivity demands often prohibitive decreases in specificity. This is particularly the case in intravascular imaging, where detection of heterogeneously dispersed lesion elements, which are often less evident than normal structures, is essential. Modalities including optical coherence tomography (OCT) provide cross-sectional images of coronary arteries that reveal atherosclerotic plaques. Manual plaque segmentation is time consuming and error prone; automated methods are quicker but dictate accuracy tradeoffs. We developed a neural network-based method for automatic detection of calcified plaques in OCT images using texture-based features and examined how underlying training data distribution impacts sensitivity and predictive value. The method assesses each pixel, rather than a patch, as an independent unit, enabling precise control of training data distribution while simultaneously decreasing reliance on massive imaging datasets for training. Pixels from 30 manually annotated OCT images of calcified plaques were used to train the neural network. Several texture measures were computed for the local neighborhood of each pixel and used as inputs to a multi-layered neural network. The ratio of pixels of each class in the training dataset was then varied and the resulting network performance was compared. Positive predictive value and sensitivity ranged from 0.69 to 0.77 and 0.35 to 0.86, respectively, as the ratio of non-calcified to calcified pixels varied from around 15 to 1, with inverse changes in specificity. The results clearly demonstrate that appropriately balanced data must be carefully curated with thoughtful consideration of the model's application and the clinical imperative being addressed.","PeriodicalId":318819,"journal":{"name":"2019 IEEE 19th International Conference on Bioinformatics and Bioengineering (BIBE)","volume":"158 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123530054","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

A Social Robot-Based Platform for Prevention of Childhood Obesity 基于社交机器人的儿童肥胖预防平台

2019 IEEE 19th International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2019-10-01 DOI: 10.1109/BIBE.2019.00171

Andreas K Triantafyllidis, Anastasios Alexiadis, Dimosthenis Elmas, K. Votis, D. Tzovaras

引用次数: 9

Preliminary Evaluation of Robotic Transrectal Biopsy System on an Interventional Planning Software 机器人经直肠活检系统在介入计划软件上的初步评价

2019 IEEE 19th International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2019-10-01 DOI: 10.1109/BIBE.2019.00070

J. D. V. Garcia, E. Leiss, M. Karkoub, P. Tsiamyrtzis, N. Tsekos, N. Navkar, S. Balakrishnan, J. Abinahed, A. Al-Ansari, Georges Younes, A. Darweesh, Khalid Al-Rumaihi, E. Christoforou

{"title":"Preliminary Evaluation of Robotic Transrectal Biopsy System on an Interventional Planning Software","authors":"J. D. V. Garcia, E. Leiss, M. Karkoub, P. Tsiamyrtzis, N. Tsekos, N. Navkar, S. Balakrishnan, J. Abinahed, A. Al-Ansari, Georges Younes, A. Darweesh, Khalid Al-Rumaihi, E. Christoforou","doi":"10.1109/BIBE.2019.00070","DOIUrl":"https://doi.org/10.1109/BIBE.2019.00070","url":null,"abstract":"Prostate biopsy is considered as a definitive way for diagnosing prostate malignancies. Urologists are currently moving towards MR-guided prostate biopsies over conventional transrectal ultrasound-guided biopsies for prostate cancer detection. Recently, robotic systems have started to emerge as an assistance tool for urologists to perform MR-guided prostate biopsies. However, these robotic assistance systems are designed for a specific clinical environment and cannot be adapted to modifications or changes applied to the clinical setting and/or workflow. This work presents the preliminary design of a cable-driven manipulator developed to be used in both MR scanners and MR-ultrasound fusion systems. The proposed manipulator design and functionality are evaluated on a simulated virtual environment. The simulation is created on an in-house developed interventional planning software to evaluate the ergonomics and usability. The results show that urologists can benefit from the proposed design of the manipulator and planning software to accurately perform biopsies of targeted areas in the prostate.","PeriodicalId":318819,"journal":{"name":"2019 IEEE 19th International Conference on Bioinformatics and Bioengineering (BIBE)","volume":"29 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121562664","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 20

Blood Flow SPH Simulation with Elastic Deformation of Blood Vessels 血管弹性变形的血流SPH模拟

2019 IEEE 19th International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2019-10-01 DOI: 10.1109/BIBE.2019.00102

Antonio Deusany de Carvalho Junior, H. Bíscaro

引用次数: 3

Importance of Feature Weighing in Cervical Cancer Subtypes Identification 特征加权在宫颈癌亚型鉴定中的重要性

2019 IEEE 19th International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2019-10-01 DOI: 10.1109/BIBE.2019.00024

Madhumita Madhumita, Sushmita Paul

{"title":"Importance of Feature Weighing in Cervical Cancer Subtypes Identification","authors":"Madhumita Madhumita, Sushmita Paul","doi":"10.1109/BIBE.2019.00024","DOIUrl":"https://doi.org/10.1109/BIBE.2019.00024","url":null,"abstract":"Cancer subtypes identification is very important for the advancement of precision cancer disease diagnosis and therapy. It is one of the important components of the personalized medicine framework. Cervical cancer (CC) is one of the leading gynecological cancers that causes deaths in women worldwide. However, there is a lack of studies to identify histological subtypes among the patients suffering from tumor of the uterine cervix. Hence, sub-typing of cancer can help in analyzing shared molecular profiles between different histological subtypes of solid tumors of uterine cervix. With the advancement in technology, large scale multi-omics data are generated. The integration of genomics data generated from different platforms helps in capturing complementary information about the patients. Several computational approaches have been developed that integrate muti-omics data for cancer sub-typing. In this study, mRNA (messenger RNA) and miRNA (microRNA) expression data are integrated to identify the histological subtypes of CC. In this regard, a method is proposed that ranks the biomarkers (mRNA and miRNA) on the basis of their varying expression across the samples. The ranking method generates a weight for every biomarker which is further used to identify the similarity between the samples. A well-known approach named Similarity Network Fusion (SNF) is then applied, followed by Spectral clustering, to identify groups of related samples. This study focuses on the role of weighing the biomarkers prior to their integration and application of the clustering algorithm. The weighing method proposed in this study is compared with some other methods and proved to be more efficient. The proposed method helps in identifying histological subtypes of CC and can also be applied to other types of cancer data where histological subtypes play a key role in designing treatments and therapies.","PeriodicalId":318819,"journal":{"name":"2019 IEEE 19th International Conference on Bioinformatics and Bioengineering (BIBE)","volume":"65 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2019-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"133390781","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0