18 results on '"Nan-Yow Chen"'
Search Results
2. LYNSU: automated 3D neuropil segmentation of fluorescent images for Drosophila brains
- Author
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Kai-Yi Hsu, Chi-Tin Shih, Nan-Yow Chen, and Chung-Chuan Lo
- Subjects
fluorescence image ,U-net ,YOLO ,connectomics ,image segmentation ,anatomical analysis ,Neurosciences. Biological psychiatry. Neuropsychiatry ,RC321-571 - Abstract
The brain atlas, which provides information about the distribution of genes, proteins, neurons, or anatomical regions, plays a crucial role in contemporary neuroscience research. To analyze the spatial distribution of those substances based on images from different brain samples, we often need to warp and register individual brain images to a standard brain template. However, the process of warping and registration may lead to spatial errors, thereby severely reducing the accuracy of the analysis. To address this issue, we develop an automated method for segmenting neuropils in the Drosophila brain for fluorescence images from the FlyCircuit database. This technique allows future brain atlas studies to be conducted accurately at the individual level without warping and aligning to a standard brain template. Our method, LYNSU (Locating by YOLO and Segmenting by U-Net), consists of two stages. In the first stage, we use the YOLOv7 model to quickly locate neuropils and rapidly extract small-scale 3D images as input for the second stage model. This stage achieves a 99.4% accuracy rate in neuropil localization. In the second stage, we employ the 3D U-Net model to segment neuropils. LYNSU can achieve high accuracy in segmentation using a small training set consisting of images from merely 16 brains. We demonstrate LYNSU on six distinct neuropils or structures, achieving a high segmentation accuracy comparable to professional manual annotations with a 3D Intersection-over-Union (IoU) reaching up to 0.869. Our method takes only about 7 s to segment a neuropil while achieving a similar level of performance as the human annotators. To demonstrate a use case of LYNSU, we applied it to all female Drosophila brains from the FlyCircuit database to investigate the asymmetry of the mushroom bodies (MBs), the learning center of fruit flies. We used LYNSU to segment bilateral MBs and compare the volumes between left and right for each individual. Notably, of 8,703 valid brain samples, 10.14% showed bilateral volume differences that exceeded 10%. The study demonstrated the potential of the proposed method in high-throughput anatomical analysis and connectomics construction of the Drosophila brain.
- Published
- 2024
- Full Text
- View/download PDF
3. Using Graph Attention Network to Reversely Design GaN MIS-HEMTs Based on Hand-Drawn Characteristics
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Yi-Ming Tseng, Bang-Ren Chen, Wei-Cheng Lin, Wen-Jay Lee, Nan-Yow Chen, and Tian-Li Wu
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GaN power HEMTs ,hand-drawn characteristics ,reverse designs ,Electrical engineering. Electronics. Nuclear engineering ,TK1-9971 - Abstract
In this work, the methodology using Graph Attention Network (GAT) for the reserve design in GaN power MIS-HEMTs based on hand-drawn characteristics is demonstrated for the first-time. The hand-drawn ID-VG characteristic is constructed by Ramer-Douglas-Peucker algorithm. Then, the extracted information is sent to the Graph Attention Network to receive the corresponding device design variables, including tAlGaN, recessed depth, Al%, Lg, Lgd, and Lgs. Less than 30 seconds is consumed to generate the design variables and less than 8% of the differences in the key extracted parameters, such as threshold voltage (Vth), On-state current (Ion), and subthreshold slope (SS), can be achieved by comparing hand-drawn ID-VG and simulated ID-VG characteristic based on the design variables from GAT model. Therefore, the developed GAT approach is promising for the reverse design of GaN power MIS-HEMTs, which can provide users with efficient and valuable design suggestions to optimize the devices toward the targeting performance.
- Published
- 2023
- Full Text
- View/download PDF
4. Device simulations with A U-Net model predicting physical quantities in two-dimensional landscapes
- Author
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Wen-Jay Lee, Wu-Tsung Hsieh, Bin-Horn Fang, Kuo-Hsing Kao, and Nan-Yow Chen
- Subjects
Medicine ,Science - Abstract
Abstract Although Technology Computer-Aided Design (TCAD) simulation has paved a successful and efficient way to significantly reduce the cost of experiments under the device design, it still encounters many challenges as the semiconductor industry goes through rapid development in recent years, i.e. Complex 3D device structures, power devices. Recently, although machine learning has been proposed to enable the simulation acceleration and inverse‑design of devices, which can quickly and accurately predict device performance, up to now physical quantities (such as electric field, potential energy, quantum-mechanically confined carrier distributions, and so on) being essential for understanding device physics can still only be obtained by traditional time-consuming self-consistent calculation. In this work, we employ a modified U-Net and train the models to predict the physical quantities of a MOSFET in two-dimensional landscapes for the first time. Errors in predictions by the two models have been analyzed, which shows the importance of a sufficient amount of data to prediction accuracy. The computation time for one landscape prediction with high accuracy by our well-trained U-Net model is much faster than the traditional approach. This work paves the way for interpretable predictions of device simulations based on convolutional neural networks.
- Published
- 2023
- Full Text
- View/download PDF
5. Artificial intelligence deep learning for 3D IC reliability prediction
- Author
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Po-Ning Hsu, Kai-Cheng Shie, Kuan-Peng Chen, Jing-Chen Tu, Cheng-Che Wu, Nien-Ti Tsou, Yu-Chieh Lo, Nan-Yow Chen, Yong-Fen Hsieh, Mia Wu, Chih Chen, and King-Ning Tu
- Subjects
Medicine ,Science - Abstract
Abstract Three-dimensional integrated circuit (3D IC) technologies have been receiving much attention recently due to the near-ending of Moore’s law of minimization in 2D IC. However, the reliability of 3D IC, which is greatly influenced by voids and failure in interconnects during the fabrication processes, typically requires slow testing and relies on human’s judgement. Thus, the growing demand for 3D IC has generated considerable attention on the importance of reliability analysis and failure prediction. This research conducts 3D X-ray tomographic images combining with AI deep learning based on a convolutional neural network (CNN) for non-destructive analysis of solder interconnects. By training the AI machine using a reliable database of collected images, the AI can quickly detect and predict the interconnect operational faults of solder joints with an accuracy of up to 89.9% based on non-destructive 3D X-ray tomographic images. The important features which determine the “Good” or “Failure” condition for a reflowed microbump, such as area loss percentage at the middle cross-section, are also revealed.
- Published
- 2022
- Full Text
- View/download PDF
6. Engineer design process assisted by explainable deep learning network
- Author
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Chia-Wei Hsu, An-Cheng Yang, Pei-Ching Kung, Nien-Ti Tsou, and Nan-Yow Chen
- Subjects
Medicine ,Science - Abstract
Abstract Engineering simulation accelerates the development of reliable and repeatable design processes in various domains. However, the computing resource consumption is dramatically raised in the whole development processes. Making the most of these simulation data becomes more and more important in modern industrial product design. In the present study, we proposed a workflow comprised of a series of machine learning algorithms (mainly deep neuron networks) to be an alternative to the numerical simulation. We have applied the workflow to the field of dental implant design process. The process is based on a complex, time-dependent, multi-physical biomechanical theory, known as mechano-regulatory method. It has been used to evaluate the performance of dental implants and to assess the tissue recovery after the oral surgery procedures. We provided a deep learning network (DLN) with calibrated simulation data that came from different simulation conditions with experimental verification. The DLN achieves nearly exact result of simulated bone healing history around implants. The correlation of the predicted essential physical properties of surrounding bones (e.g. strain and fluid velocity) and performance indexes of implants (e.g. bone area and bone-implant contact) were greater than 0.980 and 0.947, respectively. The testing AUC values for the classification of each tissue phenotype were ranging from 0.90 to 0.99. The DLN reduced hours of simulation time to seconds. Moreover, our DLN is explainable via Deep Taylor decomposition, suggesting that the transverse fluid velocity, upper and lower parts of dental implants are the keys that influence bone healing and the distribution of tissue phenotypes the most. Many examples of commercial dental implants with designs which follow these design strategies can be found. This work demonstrates that DLN with proper network design is capable to replace complex, time-dependent, multi-physical models/theories, as well as to reveal the underlying features without prior professional knowledge.
- Published
- 2021
- Full Text
- View/download PDF
7. Prediction of Bone Healing around Dental Implants in Various Boundary Conditions by Deep Learning Network
- Author
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Pei-Ching Kung, Chia-Wei Hsu, An-Cheng Yang, Nan-Yow Chen, and Nien-Ti Tsou
- Subjects
deep learning ,data-driven ,tissue differentiation ,bone healing ,Biology (General) ,QH301-705.5 ,Chemistry ,QD1-999 - Abstract
Tissue differentiation varies based on patients’ conditions, such as occlusal force and bone properties. Thus, the design of the implants needs to take these conditions into account to improve osseointegration. However, the efficiency of the design procedure is typically not satisfactory and needs to be significantly improved. Thus, a deep learning network (DLN) is proposed in this study. A data-driven DLN consisting of U-net, ANN, and random forest models was implemented. It serves as a surrogate for finite element analysis and the mechano-regulation algorithm. The datasets include the history of tissue differentiation throughout 35 days with various levels of occlusal force and bone properties. The accuracy of day-by-day tissue differentiation prediction in the testing dataset was 82%, and the AUC value of the five tissue phenotypes (fibrous tissue, cartilage, immature bone, mature bone, and resorption) was above 0.86, showing a high prediction accuracy. The proposed DLN model showed the robustness for surrogating the complex, time-dependent calculations. The results can serve as a design guideline for dental implants.
- Published
- 2023
- Full Text
- View/download PDF
8. NeuroRetriever: Automatic Neuron Segmentation for Connectome Assembly
- Author
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Chi-Tin Shih, Nan-Yow Chen, Ting-Yuan Wang, Guan-Wei He, Guo-Tzau Wang, Yen-Jen Lin, Ting-Kuo Lee, and Ann-Shyn Chiang
- Subjects
neuroimage processing ,drosophila ,segmenation ,tracing ,connectome ,Neurosciences. Biological psychiatry. Neuropsychiatry ,RC321-571 - Abstract
Segmenting individual neurons from a large number of noisy raw images is the first step in building a comprehensive map of neuron-to-neuron connections for predicting information flow in the brain. Thousands of fluorescence-labeled brain neurons have been imaged. However, mapping a complete connectome remains challenging because imaged neurons are often entangled and manual segmentation of a large population of single neurons is laborious and prone to bias. In this study, we report an automatic algorithm, NeuroRetriever, for unbiased large-scale segmentation of confocal fluorescence images of single neurons in the adult Drosophila brain. NeuroRetriever uses a high-dynamic-range thresholding method to segment three-dimensional morphology of single neurons based on branch-specific structural features. Applying NeuroRetriever to automatically segment single neurons in 22,037 raw brain images, we successfully retrieved 28,125 individual neurons validated by human segmentation. Thus, automated NeuroRetriever will greatly accelerate 3D reconstruction of the single neurons for constructing the complete connectomes.
- Published
- 2021
- Full Text
- View/download PDF
9. 26th Annual Computational Neuroscience Meeting (CNS*2017): Part 2
- Author
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Leonid L. Rubchinsky, Sungwoo Ahn, Wouter Klijn, Ben Cumming, Stuart Yates, Vasileios Karakasis, Alexander Peyser, Marmaduke Woodman, Sandra Diaz-Pier, James Deraeve, Eliana Vassena, William Alexander, David Beeman, Pawel Kudela, Dana Boatman-Reich, William S. Anderson, Niceto R. Luque, Francisco Naveros, Richard R. Carrillo, Eduardo Ros, Angelo Arleo, Jacob Huth, Koki Ichinose, Jihoon Park, Yuji Kawai, Junichi Suzuki, Hiroki Mori, Minoru Asada, Sorinel A. Oprisan, Austin I. Dave, Tahereh Babaie, Peter Robinson, Alejandro Tabas, Martin Andermann, André Rupp, Emili Balaguer-Ballester, Henrik Lindén, Rasmus K. Christensen, Mari Nakamura, Tania R. Barkat, Zach Tosi, John Beggs, Davide Lonardoni, Fabio Boi, Stefano Di Marco, Alessandro Maccione, Luca Berdondini, Joanna Jędrzejewska-Szmek, Daniel B. Dorman, Kim T. Blackwell, Christoph Bauermeister, Hanna Keren, Jochen Braun, João V. Dornas, Eirini Mavritsaki, Silvio Aldrovandi, Emma Bridger, Sukbin Lim, Nicolas Brunel, Anatoly Buchin, Clifford Charles Kerr, Anton Chizhov, Gilles Huberfeld, Richard Miles, Boris Gutkin, Martin J. Spencer, Hamish Meffin, David B. Grayden, Anthony N. Burkitt, Catherine E. Davey, Liangyu Tao, Vineet Tiruvadi, Rehman Ali, Helen Mayberg, Robert Butera, Cengiz Gunay, Damon Lamb, Ronald L. Calabrese, Anca Doloc-Mihu, Víctor J. López-Madrona, Fernanda S. Matias, Ernesto Pereda, Claudio R. Mirasso, Santiago Canals, Alice Geminiani, Alessandra Pedrocchi, Egidio D’Angelo, Claudia Casellato, Ankur Chauhan, Karthik Soman, V. Srinivasa Chakravarthy, Vignayanandam R. Muddapu, Chao-Chun Chuang, Nan-yow Chen, Mehdi Bayati, Jan Melchior, Laurenz Wiskott, Amir Hossein Azizi, Kamran Diba, Sen Cheng, Elena Y. Smirnova, Elena G. Yakimova, Anton V. Chizhov, Nan-Yow Chen, Chi-Tin Shih, Dorian Florescu, Daniel Coca, Julie Courtiol, Viktor K. Jirsa, Roberto J. M. Covolan, Bartosz Teleńczuk, Richard Kempter, Gabriel Curio, Alain Destexhe, Jessica Parker, Alexander N. Klishko, Boris I. Prilutsky, Gennady Cymbalyuk, Felix Franke, Andreas Hierlemann, Rava Azeredo da Silveira, Stefano Casali, Stefano Masoli, Martina Rizza, Martina Francesca Rizza, Yinming Sun, Willy Wong, Faranak Farzan, Daniel M. Blumberger, Zafiris J. Daskalakis, Svitlana Popovych, Shivakumar Viswanathan, Nils Rosjat, Christian Grefkes, Silvia Daun, Damiano Gentiletti, Piotr Suffczynski, Vadym Gnatkovski, Marco De Curtis, Hyeonsu Lee, Se-Bum Paik, Woochul Choi, Jaeson Jang, Youngjin Park, Jun Ho Song, Min Song, Vicente Pallarés, Matthieu Gilson, Simone Kühn, Andrea Insabato, Gustavo Deco, Katharina Glomb, Adrián Ponce-Alvarez, Petra Ritter, Adria Tauste Campo, Alexander Thiele, Farah Deeba, P. A. Robinson, Sacha J. van Albada, Andrew Rowley, Michael Hopkins, Maximilian Schmidt, Alan B. Stokes, David R. Lester, Steve Furber, Markus Diesmann, Alessandro Barri, Martin T. Wiechert, David A. DiGregorio, Alexander G. Dimitrov, Catalina Vich, Rune W. Berg, Antoni Guillamon, Susanne Ditlevsen, Romain D. Cazé, Benoît Girard, Stéphane Doncieux, Nicolas Doyon, Frank Boahen, Patrick Desrosiers, Edward Laurence, Louis J. Dubé, Russo Eleonora, Daniel Durstewitz, Dominik Schmidt, Tuomo Mäki-Marttunen, Florian Krull, Francesco Bettella, Christoph Metzner, Anna Devor, Srdjan Djurovic, Anders M. Dale, Ole A. Andreassen, Gaute T. Einevoll, Solveig Næss, Torbjørn V. Ness, Geir Halnes, Eric Halgren, Klas H. Pettersen, Marte J. Sætra, Espen Hagen, Alina Schiffer, Axel Grzymisch, Malte Persike, Udo Ernst, Daniel Harnack, Udo A. Ernst, Nergis Tomen, Stefano Zucca, Valentina Pasquale, Giuseppe Pica, Manuel Molano-Mazón, Michela Chiappalone, Stefano Panzeri, Tommaso Fellin, Kelvin S. Oie, David L. Boothe, Joshua C. Crone, Alfred B. Yu, Melvin A. Felton, Isma Zulfiqar, Michelle Moerel, Peter De Weerd, Elia Formisano, Kelvin Oie, Piotr Franaszczuk, Roland Diggelmann, Michele Fiscella, Domenico Guarino, Jan Antolík, Andrew P. Davison, Yves Frègnac, Benjamin Xavier Etienne, Flavio Frohlich, Jérémie Lefebvre, Encarni Marcos, Maurizio Mattia, Aldo Genovesio, Leonid A. Fedorov, Tjeerd M.H. Dijkstra, Louisa Sting, Howard Hock, Martin A. Giese, Laure Buhry, Clément Langlet, Francesco Giovannini, Christophe Verbist, Stefano Salvadé, Michele Giugliano, James A. Henderson, Hendrik Wernecke, Bulcsú Sándor, Claudius Gros, Nicole Voges, Paulina Dabrovska, Alexa Riehle, Thomas Brochier, Sonja Grün, Yifan Gu, Pulin Gong, Grégory Dumont, Nikita A. Novikov, Boris S. Gutkin, Parul Tewatia, Olivia Eriksson, Andrei Kramer, Joao Santos, Alexandra Jauhiainen, Jeanette H. Kotaleski, Jovana J. Belić, Arvind Kumar, Jeanette Hellgren Kotaleski, Masanori Shimono, Naomichi Hatano, Subutai Ahmad, Yuwei Cui, Jeff Hawkins, Johanna Senk, Karolína Korvasová, Tom Tetzlaff, Moritz Helias, Tobias Kühn, Michael Denker, PierGianLuca Mana, David Dahmen, Jannis Schuecker, Sven Goedeke, Christian Keup, Katja Heuer, Rembrandt Bakker, Paul Tiesinga, Roberto Toro, Wei Qin, Alex Hadjinicolaou, Michael R. Ibbotson, Tatiana Kameneva, William W. Lytton, Lealem Mulugeta, Andrew Drach, Jerry G. Myers, Marc Horner, Rajanikanth Vadigepalli, Tina Morrison, Marlei Walton, Martin Steele, C. Anthony Hunt, Nicoladie Tam, Rodrigo Amaducci, Carlos Muñiz, Manuel Reyes-Sánchez, Francisco B. Rodríguez, Pablo Varona, Joseph T. Cronin, Matthias H. Hennig, Elisabetta Iavarone, Jane Yi, Ying Shi, Bas-Jan Zandt, Werner Van Geit, Christian Rössert, Henry Markram, Sean Hill, Christian O’Reilly, Rodrigo Perin, Huanxiang Lu, Alexander Bryson, Michal Hadrava, Jaroslav Hlinka, Ryosuke Hosaka, Mark Olenik, Conor Houghton, Nicolangelo Iannella, Thomas Launey, Rebecca Kotsakidis, Jaymar Soriano, Takatomi Kubo, Takao Inoue, Hiroyuki Kida, Toshitaka Yamakawa, Michiyasu Suzuki, Kazushi Ikeda, Samira Abbasi, Amber E. Hudson, Detlef H. Heck, Dieter Jaeger, Joel Lee, Skirmantas Janušonis, Maria Luisa Saggio, Andreas Spiegler, William C. Stacey, Christophe Bernard, Davide Lillo, Spase Petkoski, Mark Drakesmith, Derek K. Jones, Ali Sadegh Zadeh, Chandra Kambhampati, Jan Karbowski, Zeynep Gokcen Kaya, Yair Lakretz, Alessandro Treves, Lily W. Li, Joseph Lizier, Cliff C. Kerr, Timothée Masquelier, Saeed Reza Kheradpisheh, Hojeong Kim, Chang Sub Kim, Julia A. Marakshina, Alexander V. Vartanov, Anastasia A. Neklyudova, Stanislav A. Kozlovskiy, Andrey A. Kiselnikov, Kanako Taniguchi, Katsunori Kitano, Oliver Schmitt, Felix Lessmann, Sebastian Schwanke, Peter Eipert, Jennifer Meinhardt, Julia Beier, Kanar Kadir, Adrian Karnitzki, Linda Sellner, Ann-Christin Klünker, Lena Kuch, Frauke Ruß, Jörg Jenssen, Andreas Wree, Paula Sanz-Leon, Stuart A. Knock, Shih-Cheng Chien, Burkhard Maess, Thomas R. Knösche, Charles C. Cohen, Marko A. Popovic, Jan Klooster, Maarten H.P. Kole, Erik A. Roberts, Nancy J. Kopell, Daniel Kepple, Hamza Giaffar, Dima Rinberg, Alex Koulakov, Caroline Garcia Forlim, Leonie Klock, Johanna Bächle, Laura Stoll, Patrick Giemsa, Marie Fuchs, Nikola Schoofs, Christiane Montag, Jürgen Gallinat, Ray X. Lee, Greg J. Stephens, Bernd Kuhn, Luiz Tauffer, Philippe Isope, Katsuma Inoue, Yoshiyuki Ohmura, Shogo Yonekura, Yasuo Kuniyoshi, Hyun Jae Jang, Jeehyun Kwag, Marc de Kamps, Yi Ming Lai, Filipa dos Santos, K. P. Lam, Peter Andras, Julia Imperatore, Jessica Helms, Tamas Tompa, Antonieta Lavin, Felicity H. Inkpen, Michael C. Ashby, Nathan F. Lepora, Aaron R. Shifman, John E. Lewis, Zhong Zhang, Yeqian Feng, Christian Tetzlaff, Tomas Kulvicius, Yinyun Li, Rodrigo F. O. Pena, Davide Bernardi, Antonio C. Roque, Benjamin Lindner, Sebastian Vellmer, Ausra Saudargiene, Tiina Maninen, Riikka Havela, Marja-Leena Linne, Arthur Powanwe, Andre Longtin, Jesús A. Garrido, Joe W. Graham, Salvador Dura-Bernal, Sergio L. Angulo, Samuel A. Neymotin, and Srdjan D. Antic
- Subjects
Neurosciences. Biological psychiatry. Neuropsychiatry ,RC321-571 ,Neurophysiology and neuropsychology ,QP351-495 - Published
- 2017
- Full Text
- View/download PDF
10. Differential synchrotron X-ray imaging markers based on the renal microvasculature for tubulointerstitial lesions and glomerulopathy
- Author
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Yu-Chuan Lin, Yeukuang Hwu, Guo-Shu Huang, Michael Hsiao, Tsung-Tse Lee, Shun-Min Yang, Ting-Kuo Lee, Nan-Yow Chen, Sung-Sen Yang, Ann Chen, and Shuk-Man Ka
- Subjects
Medicine ,Science - Abstract
Abstract High resolution synchrotron microtomography capable of revealing microvessels in three dimensional (3D) establishes distinct imaging markers of mouse kidney disease strongly associated to renal tubulointerstitial (TI) lesions and glomerulopathy. Two complementary mouse models of chronic kidney disease (CKD), unilateral ureteral obstruction (UUO) and focal segmental glomerulosclerosis (FSGS), were used and five candidates of unique 3D imaging markers were identified. Our characterization to differentially reflect the altered microvasculature of renal TI lesions and/or glomerulopathy demonstrated these image features can be used to differentiate the disease status and the possible cause therefore qualified as image markers. These 3D imaging markers were further correlated with the histopathology and renal microvessel-based molecular study using antibodies against vascular endothelial cells (CD31), the connective tissue growth factor or the vascular endothelial growth factor. We also found that these 3D imaging markers individually characterize the development of renal TI lesions or glomerulopathy, quantitative and integrated use of all of them provide more information for differentiating the two renal conditions. Our findings thus establish a practical strategy to characterize the CKD-associated renal injuries by the microangiography-based 3D imaging and highlight the impact of dysfunctional microvasculature as a whole on the pathogenesis of the renal lesions.
- Published
- 2017
- Full Text
- View/download PDF
11. Engineer design process assisted by explainable deep learning network
- Author
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Pei Ching Kung, An-Cheng Yang, Chia Wei Hsu, Nan Yow Chen, and Nien-Ti Tsou
- Subjects
Multidisciplinary ,Computer simulation ,Product design ,Computer science ,business.industry ,Process (engineering) ,Deep learning ,medicine.medical_treatment ,Science ,Computational science ,Article ,Mechanical engineering ,Network planning and design ,Workflow ,Computational methods ,medicine ,Design process ,Medicine ,Artificial intelligence ,business ,Dental implant ,Biomedical engineering ,Simulation - Abstract
Engineering simulation accelerates the development of reliable and repeatable design processes in various domains. However, the computing resource consumption is dramatically raised in the whole development processes. Making the most of these simulation data becomes more and more important in modern industrial product design. In the present study, we proposed a workflow comprised of a series of machine learning algorithms (mainly deep neuron networks) to be an alternative to the numerical simulation. We have applied the workflow to the field of dental implant design process. The process is based on a complex, time-dependent, multi-physical biomechanical theory, known as mechano-regulatory method. It has been used to evaluate the performance of dental implants and to assess the tissue recovery after the oral surgery procedures. We provided a deep learning network (DLN) with calibrated simulation data that came from different simulation conditions with experimental verification. The DLN achieves nearly exact result of simulated bone healing history around implants. The correlation of the predicted essential physical properties of surrounding bones (e.g. strain and fluid velocity) and performance indexes of implants (e.g. bone area and bone-implant contact) were greater than 0.980 and 0.947, respectively. The testing AUC values for the classification of each tissue phenotype were ranging from 0.90 to 0.99. The DLN reduced hours of simulation time to seconds. Moreover, our DLN is explainable via Deep Taylor decomposition, suggesting that the transverse fluid velocity, upper and lower parts of dental implants are the keys that influence bone healing and the distribution of tissue phenotypes the most. Many examples of commercial dental implants with designs which follow these design strategies can be found. This work demonstrates that DLN with proper network design is capable to replace complex, time-dependent, multi-physical models/theories, as well as to reveal the underlying features without prior professional knowledge.
- Published
- 2021
12. Differential synchrotron X-ray imaging markers based on the renal microvasculature for tubulointerstitial lesions and glomerulopathy
- Author
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Ting-Kuo Lee, Ann Chen, Yu-Chuan Lin, Yeukuang Hwu, Guo-Shu Huang, Shun-Min Yang, Michael Hsiao, Shuk-Man Ka, Sung-Sen Yang, T. K. Lee, and Nan-Yow Chen
- Subjects
0301 basic medicine ,CD31 ,Male ,Pathology ,medicine.medical_specialty ,Science ,030232 urology & nephrology ,Kidney ,urologic and male genital diseases ,Article ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Focal segmental glomerulosclerosis ,Imaging, Three-Dimensional ,Glomerulopathy ,Medicine ,Animals ,Renal Insufficiency, Chronic ,Microvessel ,Mice, Inbred BALB C ,Multidisciplinary ,Neovascularization, Pathologic ,business.industry ,medicine.disease ,Vascular endothelial growth factor ,030104 developmental biology ,medicine.anatomical_structure ,chemistry ,Microangiography ,Microvessels ,business ,Tomography, X-Ray Computed ,Algorithms ,Biomarkers ,Synchrotrons ,Kidney disease - Abstract
High resolution synchrotron microtomography capable of revealing microvessels in three dimensional (3D) establishes distinct imaging markers of mouse kidney disease strongly associated to renal tubulointerstitial (TI) lesions and glomerulopathy. Two complementary mouse models of chronic kidney disease (CKD), unilateral ureteral obstruction (UUO) and focal segmental glomerulosclerosis (FSGS), were used and five candidates of unique 3D imaging markers were identified. Our characterization to differentially reflect the altered microvasculature of renal TI lesions and/or glomerulopathy demonstrated these image features can be used to differentiate the disease status and the possible cause therefore qualified as image markers. These 3D imaging markers were further correlated with the histopathology and renal microvessel-based molecular study using antibodies against vascular endothelial cells (CD31), the connective tissue growth factor or the vascular endothelial growth factor. We also found that these 3D imaging markers individually characterize the development of renal TI lesions or glomerulopathy, quantitative and integrated use of all of them provide more information for differentiating the two renal conditions. Our findings thus establish a practical strategy to characterize the CKD-associated renal injuries by the microangiography-based 3D imaging and highlight the impact of dysfunctional microvasculature as a whole on the pathogenesis of the renal lesions.
- Published
- 2017
13. An FET With a Source Tunneling Barrier Showing Suppressed Short-Channel Effects for Low-Power Applications.
- Author
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Yu-Feng Hsieh, Si-Hua Chen, Meng-Hsueh Chiang, Lu, Darsen D., Kuo-Hsing Kao, Nan-Yow Chen, Wen-Jay Lee, Jyun-Hwei Tsai, and Chun-Nan Chen
- Subjects
QUANTUM tunneling ,FIELD-effect transistors ,THRESHOLD voltage ,GREEN'S functions ,NONEQUILIBRIUM statistical mechanics - Abstract
A device design technique using tunneling barriers (TBs) for reducing the short-channel effects (SCEs) is proposed. By introducing TBs at the source and drain junctions of a Si FET, the threshold voltage (V
th ) roll-off can be significantly suppressed. This is because the TBs weaken the electrical coupling between drain bias and transmission/current spectrum in energy. Specifically, as compared with a conventional FET, the Vth roll-off for channel length reduction from 20 to 5 nm is mitigated by more than 40% when a thin TB is embedded at the source junction. This paper further reveals that the TB at the source junction dominates the physical mechanism minimizing the SCEs of the TBFET, and thus the device performance can be improved appreciably by removing the TB at the drain side and by decreasing the TB height at the source side. [ABSTRACT FROM AUTHOR]- Published
- 2018
- Full Text
- View/download PDF
14. Large-scale quantitative analysis of neurons via morphological structures by Fast Automatically Structural Tracing Algorithm (FAST)
- Author
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Nan-Yow Chen, Guan-Wei He, Chi-Tin Shih, Kuan-Peng Chen, Ann-Shyn Chiang, Yu-Tai Ching, and Ting-Yuan Wang
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Modularity (networks) ,Similarity (geometry) ,Computational neuroscience ,Quantitative Biology::Neurons and Cognition ,Computer science ,General Neuroscience ,Schematic ,Tracing ,Cellular and Molecular Neuroscience ,Poster Presentation ,Isomap ,Algorithm ,Branch point ,TRACE (psycholinguistics) - Abstract
Quantitative analysis of neurons is a very important issue in neural science especially after numerous three-dimensional neural images in Drosophila brains were taken from confocal laser scanning microscope [1]. However, analyzing these messy data is mostly by human being with some semi-automatic software packages so far. Not only the task is very labor intensive but also the result is susceptible to errors and usually lacks objectivity. Therefore, fast and accurate analyzing tools are crucial and very desirable. Recently, we developed a computational algorithm, FAST (Fast Automatically Structural Tracing algorithm), which can trace neurons and get characteristic quantities of neuron fibers from their morphology in a very efficient way. These characteristic quantities (called SIs, Structural Indexes) are, for example, number of branch points, number of end points, cross section area of fibers, branch angle of fibers, distribution of fiber length, curvature of fibers, and innervation in neuropils, etc. After structural indexes of neuron fibers were obtained, isomap [2] and modularity [3] methods are applied to classify neurons without depending on human intervention. The isomap method can defined the similarity between neurons by geodesic paths in a high-dimensional manifold as well as the modularity method can find the best community structure of classification by optimization, i.e., to maximize the intra module connections as many as possible and to minimize the inter module connections as few as possible. With these tools, large-scale neural morphological structures, their annotations as well as quantified characteristics, and neural classifications can be facilely and reliably retrieved as useful data for computational neuroscience. Figure 1 A schematic diagram for innervation table and classification results of local neurons in olfactory system of Drosophila.
- Published
- 2015
15. Detecting small lung tumors in mouse models by refractive-index microradiology
- Author
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Chia-Chi Chien, Hongjie Xue, Yuh-Cheng Yang, Yeukuang Hwu, Jianqi Sun, Weisheng(岳伟胜) Yue, Chang-Hai Wang, Giorgio Margaritondo, Yan(李燕) Li, Guilin(张桂林) Zhang, Lisa X. Xu, Yen-Ta Lu, Pan-Chyr Yang, Ting-Kuo Lee, Jung Ho Je, Yu-Tai Ching, T. F. Shih, Ping(刘平) Liu, Nan-Yow Chen, Chien-Hung Lu, Chien, Chia-Chi, Zhang, Guilin, Hwu, Y, Liu, Ping, Yue, Weisheng, Sun, Jianqi, Li, Yan, Xue, Hongjie, Xu, Lisaxuemin, Wang, Changhai, Chen, Nanyow, Lu, Chienhung, Lee, Ting-Kuo, Yang, Yuhcheng, Lu, Yenta, Ching, Yutai, Shih, T F, Yang, Pan-Chyr, Je, Jungho, and Margaritondo, G
- Subjects
Male ,medicine.medical_specialty ,Lung Neoplasms ,Phase contrast microscopy ,Radiography ,Biochemistry ,Analytical Chemistry ,law.invention ,Mice ,law ,Cell Line, Tumor ,Spectroscopy, Fourier Transform Infrared ,medicine ,Carcinoma ,Mammography ,Animals ,Medical physics ,synchrotron x-ray imaging ,Lung cancer ,Lung ,real-time imaging ,medicine.diagnostic_test ,business.industry ,Brain Neoplasms ,Cancer ,Glioma ,Reference Standards ,medicine.disease ,Rats ,Disease Models, Animal ,lung cancer ,medicine.anatomical_structure ,Tomography ,Collagen ,business ,Nuclear medicine - Abstract
Refractive-index (phase-contrast) radiology was able to detect lung tumors less than 1 mm in live mice. Significant micromorphology differences were observed in the microradiographs between normal, inflamed, and lung cancer tissues. This was made possible by the high phase contrast and by the fast image taking that reduces the motion blur. The detection of cancer and inflammation areas by phase contrast microradiology and microtomography was validated by bioluminescence and histopathological analysis. The smallest tumor detected is less than 1 mm3 with accuracy better than 1 × 10−3 mm3. This level of performance is currently suitable for animal studies, while further developments are required for clinical application. Refereed/Peer-reviewed
- Published
- 2011
16. Effective potentials for Folding Proteins
- Author
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Zheng-Yao Su, Nan-Yow Chen, and Chung-Yu Mou
- Subjects
Protein Denaturation ,Protein Folding ,Protein Conformation ,FOS: Physical sciences ,General Physics and Astronomy ,Nerve Tissue Proteins ,Sequence (biology) ,Condensed Matter - Soft Condensed Matter ,Protein Structure, Secondary ,Hydrophobic effect ,Lattice protein ,Native state ,Condensed Matter - Statistical Mechanics ,Quantitative Biology::Biomolecules ,Statistical Mechanics (cond-mat.stat-mech) ,biology ,Hydrogen bond ,Chemistry ,Water ,Hydrogen Bonding ,Folding (chemistry) ,Kinetics ,Chemical physics ,biology.protein ,Soft Condensed Matter (cond-mat.soft) ,Thermodynamics ,Protein folding ,Protein G ,Hydrophobic and Hydrophilic Interactions ,Mathematics - Abstract
A coarse-grained off-lattice model that is not biased in any way to the native state is proposed to fold proteins. To predict the native structure in a reasonable time, the model has included the essential effects of water in an effective potential. Two new ingredients, the dipole-dipole interaction and the local hydrophobic interaction, are introduced and are shown to be as crucial as the hydrogen bonding. The model allows successful folding of the wild-type sequence of protein G and may have provided important hints to the study of protein folding., 4 pages, 4 figures, to appear in Physical Review Letters
- Published
- 2006
17. Large-scale segmentation and tracing for neurons in Drosophila brain by Fast Automatically Structural Tracing Algorithm (FASTA)
- Author
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Wen-Wei Liao, Ting-Kuo Lee, Nan-Yow Chen, Yu-Tai Ching, Ting-Yuan Wang, Guan-Wei He, Meng-Fu Maxwell Shih, Chi-Tin Shih, Li-An Chu, and Ann-Shyn Chiang
- Subjects
Commercial software ,Computational neuroscience ,Confocal laser scanning microscope ,Computer science ,General Neuroscience ,ComputingMethodologies_IMAGEPROCESSINGANDCOMPUTERVISION ,Tracing ,computer.software_genre ,Cellular and Molecular Neuroscience ,Laser scanning microscope ,Voxel ,Poster Presentation ,Segmentation ,Algorithm ,computer - Abstract
Recently, numerous three-dimensional neural images in Drosophila brains were taken from confocal laser scanning microscope [1]. However, how to obtain useful neuronal information from these messy raw data is very challenging. In order to conquer this problem, two critical issues need to be addressed: the first is to segment the image of single neuron from image data; the second is to trace the neuron fibers for quantitative analysis. Therefore, a robust segmentation process and an efficient tracing algorithm for single neuron are crucial and very desirable. At present there are methods and commercial software packages for these functions. But it requires a viewer to use his/her vision and judgment to segment and trace the neurons. Not only the task is very labor intensive but also the result is susceptible to errors and is usually lack of objectivity. Here we proposed an automatic procedure to segment and trace neural image data on a large scale. We first developed a new algorithm, Fast Automatically Structural Tracing Algorithm (FASTA), which encodes all image voxels on the idea of source field method and traces whole neuron via these codelets with some stopping criteria. Then, all image data were segmented into several single-neuron images with reasonable intensity threshold by using of FASTA iteratively. With this automatic procedure, single-neuron images and their annotations as well as quantified characteristics can be facilely and reliably retrieved as useful data for computational neuroscience. Figure 1
- Published
- 2013
18. Large-scale segmentation and tracing for neurons in Drosophila brain by Fast Automatically Structural Tracing Algorithm (FASTA).
- Author
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Nan-Yow Chen, Meng-Fu Maxwell Shih, Chi-Tin Shih, Guan-Wei He, Ting-Yuan Wang, Li-An Chu, Wen-Wei Liao, Yu-Tai Ching, Ting-Kuo Lee, and Ann-Shyn Chiang
- Subjects
- *
NEURONS , *DROSOPHILA , *BRAIN - Abstract
An abstract of the article "Large-scale segmentation and tracing for neurons in drosophila brain by Fast Automatically Structural Tracing Algorithm (FASTA)" by Nan-Yow Chen and colleagues is presented.
- Published
- 2013
- Full Text
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