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496 results on '"Lin, Siyu"'

1. Efficient, gigapixel-scale, aberration-free whole slide scanner using angular ptychographic imaging with closed-form solution

Author

Zhao, Shi, Zhou, Haowen, Lin, Siyu, Cao, Ruizhi, and Yang, Changhuei

Subjects
Physics - Optics, Electrical Engineering and Systems Science - Image and Video Processing
Abstract

Whole slide imaging provides a wide field-of-view (FOV) across cross-sections of biopsy or surgery samples, significantly facilitating pathological analysis and clinical diagnosis. Such high-quality images that enable detailed visualization of cellular and tissue structures are essential for effective patient care and treatment planning. To obtain such high-quality images for pathology applications, there is a need for scanners with high spatial bandwidth products, free from aberrations, and without the requirement for z-scanning. Here we report a whole slide imaging system based on angular ptychographic imaging with a closed-form solution (WSI-APIC), which offers efficient, tens-of-gigapixels, large-FOV, aberration-free imaging. WSI-APIC utilizes oblique incoherent illumination for initial high-level segmentation, thereby bypassing unnecessary scanning of the background regions and enhancing image acquisition efficiency. A GPU-accelerated APIC algorithm analytically reconstructs phase images with effective digital aberration corrections and improved optical resolutions. Moreover, an auto-stitching technique based on scale-invariant feature transform ensures the seamless concatenation of whole slide phase images. In our experiment, WSI-APIC achieved an optical resolution of 772 nm using a 10x/0.25 NA objective lens and captures 80-gigapixel aberration-free phase images for a standard 76.2 mm x 25.4 mm microscopic slide.

Published
2024

2. Latent Chemical Space Searching for Plug-in Multi-objective Molecule Generation

Author

Liu, Ningfeng, Yu, Jie, Xiu, Siyu, Zhao, Xinfang, Lin, Siyu, Qiang, Bo, Zheng, Ruqiu, Jin, Hongwei, Zhang, Liangren, and Liu, Zhenming

Subjects
Quantitative Biology - Biomolecules, Computer Science - Machine Learning, Computer Science - Neural and Evolutionary Computing
Abstract

Molecular generation, an essential method for identifying new drug structures, has been supported by advancements in machine learning and computational technology. However, challenges remain in multi-objective generation, model adaptability, and practical application in drug discovery. In this study, we developed a versatile 'plug-in' molecular generation model that incorporates multiple objectives related to target affinity, drug-likeness, and synthesizability, facilitating its application in various drug development contexts. We improved the Particle Swarm Optimization (PSO) in the context of drug discoveries, and identified PSO-ENP as the optimal variant for multi-objective molecular generation and optimization through comparative experiments. The model also incorporates a novel target-ligand affinity predictor, enhancing the model's utility by supporting three-dimensional information and improving synthetic feasibility. Case studies focused on generating and optimizing drug-like big marine natural products were performed, underscoring PSO-ENP's effectiveness and demonstrating its considerable potential for practical drug discovery applications.

Published
2024

4. FPM-INR: Fourier ptychographic microscopy image stack reconstruction using implicit neural representations

Author

Zhou, Haowen, Feng, Brandon Y., Guo, Haiyun, Lin, Siyu, Liang, Mingshu, Metzler, Christopher A., and Yang, Changhuei

Subjects
Physics - Optics, Electrical Engineering and Systems Science - Image and Video Processing
Abstract

Image stacks provide invaluable 3D information in various biological and pathological imaging applications. Fourier ptychographic microscopy (FPM) enables reconstructing high-resolution, wide field-of-view image stacks without z-stack scanning, thus significantly accelerating image acquisition. However, existing FPM methods take tens of minutes to reconstruct and gigabytes of memory to store a high-resolution volumetric scene, impeding fast gigapixel-scale remote digital pathology. While deep learning approaches have been explored to address this challenge, existing methods poorly generalize to novel datasets and can produce unreliable hallucinations. This work presents FPM-INR, a compact and efficient framework that integrates physics-based optical models with implicit neural representations (INR) to represent and reconstruct FPM image stacks. FPM-INR is agnostic to system design or sample types and does not require external training data. In our demonstrated experiments, FPM-INR substantially outperforms traditional FPM algorithms with up to a 25-fold increase in speed and an 80-fold reduction in memory usage for continuous image stack representations., Comment: Project Page: https://hwzhou2020.github.io/FPM-INR-Web/

Published
2023

5. A Novel Fault Location Method of Distribution Network Based on Dynamic Quantum Genetic Algorithm

Author

Wen, Juan, Qu, Xing, Wen, Ling, Lin, Siyu, Xiao, Qiankang, Angrisani, Leopoldo, Series Editor, Arteaga, Marco, Series Editor, Chakraborty, Samarjit, Series Editor, Chen, Jiming, Series Editor, Chen, Shanben, Series Editor, Chen, Tan Kay, Series Editor, Dillmann, Rüdiger, Series Editor, Duan, Haibin, Series Editor, Ferrari, Gianluigi, Series Editor, Ferre, Manuel, Series Editor, Jabbari, Faryar, Series Editor, Jia, Limin, Series Editor, Kacprzyk, Janusz, Series Editor, Khamis, Alaa, Series Editor, Kroeger, Torsten, Series Editor, Li, Yong, Series Editor, Liang, Qilian, Series Editor, Martín, Ferran, Series Editor, Ming, Tan Cher, Series Editor, Minker, Wolfgang, Series Editor, Misra, Pradeep, Series Editor, Mukhopadhyay, Subhas, Series Editor, Ning, Cun-Zheng, Series Editor, Nishida, Toyoaki, Series Editor, Oneto, Luca, Series Editor, Panigrahi, Bijaya Ketan, Series Editor, Pascucci, Federica, Series Editor, Qin, Yong, Series Editor, Seng, Gan Woon, Series Editor, Speidel, Joachim, Series Editor, Veiga, Germano, Series Editor, Wu, Haitao, Series Editor, Zamboni, Walter, Series Editor, Tan, Kay Chen, Series Editor, Yang, Qingxin, editor, Li, Zewen, editor, and Luo, An, editor

Published
2024
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6. Influence of Wall-Attached Antenna Distance on Channel in Tunnel Scenario

Author

Liu, Yao, Ding, Jianwen, Sun, Bin, Lin, Siyu, Wang, Wei, Angrisani, Leopoldo, Series Editor, Arteaga, Marco, Series Editor, Chakraborty, Samarjit, Series Editor, Chen, Jiming, Series Editor, Chen, Shanben, Series Editor, Chen, Tan Kay, Series Editor, Dillmann, Rüdiger, Series Editor, Duan, Haibin, Series Editor, Ferrari, Gianluigi, Series Editor, Ferre, Manuel, Series Editor, Jabbari, Faryar, Series Editor, Jia, Limin, Series Editor, Kacprzyk, Janusz, Series Editor, Khamis, Alaa, Series Editor, Kroeger, Torsten, Series Editor, Li, Yong, Series Editor, Liang, Qilian, Series Editor, Martín, Ferran, Series Editor, Ming, Tan Cher, Series Editor, Minker, Wolfgang, Series Editor, Misra, Pradeep, Series Editor, Mukhopadhyay, Subhas, Series Editor, Ning, Cun-Zheng, Series Editor, Nishida, Toyoaki, Series Editor, Oneto, Luca, Series Editor, Panigrahi, Bijaya Ketan, Series Editor, Pascucci, Federica, Series Editor, Qin, Yong, Series Editor, Seng, Gan Woon, Series Editor, Speidel, Joachim, Series Editor, Veiga, Germano, Series Editor, Wu, Haitao, Series Editor, Zamboni, Walter, Series Editor, Zhang, Junjie James, Series Editor, Tan, Kay Chen, Series Editor, Yang, Jianwei, editor, Diao, Lijun, editor, Yao, Dechen, editor, and An, Min, editor

Published
2024
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8. Protocol for vision transformer-based evaluation of drug potency using images processed by an optimized Sobel operator

Author

Wang, Yongheng, Zhang, Weidi, Wu, Yi, Qu, Chuyuan, Hu, Hongru, Lee, Teresa, Lin, Siyu, Zhang, Jiawei, Lam, Kit S, and Wang, Aijun

Subjects
Information and Computing Sciences, Medicinal and Biomolecular Chemistry, Chemical Sciences, Substance Misuse, Drug Abuse (NIDA only), Neurosciences, Prevention, 5.1 Pharmaceuticals, Development of treatments and therapeutic interventions, Biotechnology and bioengineering, Cancer, Computer sciences, High Throughput Screening, Microscopy
Abstract

Conventional approaches for screening anticancer drugs rely on chemical reactions, which are time consuming, labor intensive, and costly. Here, we present a protocol for label-free and high-throughput assessment of drug efficacy using a vision transformer and a Conv2D. We describe the steps for cell culture, drug treatment, data collection, and preprocessing. We then detail the building of deep learning models and their use to predict drug potency. This protocol can be adapted for screening chemicals that affect the density or morphological features of cells. For complete details on the use and execution of this protocol, please refer to Wang et al.1.

Published
2023

11. Higher Education and Creative Economy in East Asia: Co(Labor)Ation and Knowledge Socialism in the Creative University

Author

Zhang, Xiyuan, Yodpet, Worapot, Reindl, Stefan, Tian, Hongjun, Gou, Minghan, Li, Zongchen, Lin, Siyu, Song, Ruijie, Wang, Wenjing, Jandric, Petar, and Jackson, Liz

Abstract

This paper is a complete student-led, student-edited collective writing project (CWP) conducted virtually in Spring 2022 throughout the course Knowledge Socialism taught by professor Michael Peters for the Faculty of Education, Beijing Normal university. The CWP involves 4 international, 5 domestic Ph.D. students, and 2 senior Western scholars as reviewers, revealing their thoughts, arguments, understanding, and criticisms towards the creative economy status in East Asian countries (Japan and China mostly) higher education as reflected in the knowledge socialism narratives. Xiyuan as the lead author, co-editing with Woraport and Stefan, assigned each section to other authors and successfully devoted themself to organizing, proofreading, and revising the paper. Through a month of collective work, the final version of the paper elaborates on the contribution of East Asian creative universities and the economy as a whole to the knowledge socialism through co(labor)ation, with implications to the creative labors cultivation and shifted roles of students.

Published
2023
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27. Multi-atlas Segmentation of the Aorta from 4D Flow MRI: Comparison of Several Fusion Strategies

Author

Marin-Castrillon, Diana M., Boucher, Arnaud, Lin, Siyu, Bernard, Chloe, Morgant, Marie-Catherine, Cochet, Alexandre, Lalande, Alain, Bouchot, Olivier, Presles, Benoit, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Woeginger, Gerhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Puyol Antón, Esther, editor, Pop, Mihaela, editor, Martín-Isla, Carlos, editor, Sermesant, Maxime, editor, Suinesiaputra, Avan, editor, Camara, Oscar, editor, Lekadir, Karim, editor, and Young, Alistair, editor

Published
2022
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30. Overexpressed Poldip2 Incurs Retinal Fibrosis via the TGF-β1/SMAD3 Signaling Pathway in Diabetic Retinopathy.

Author

Ji, Zhiyu, Lin, Siyu, Gui, Siyu, Gao, Jie, Cao, Fan, Guan, Yiming, Ni, Qinyu, Chen, Keyang, Tao, Liming, and Zhengxuan, Jiang

Subjects
DIABETIC retinopathy, RHODOPSIN, ADENO-associated virus, PROTEIN expression, CELLULAR signal transduction
Abstract

Retinal fibrosis is one of the major features of diabetic retinopathy (DR). Our recent research has shown that Poldip2 can affect early DR through oxidative stress, but whether Poldip2 would regulate retinal fibrosis during DR development is still enigmatic. Here, diabetic Sprague-Dawley (SD) rats were induced with streptozotocin (STZ) and treated with adeno-associated virus serotype 9–polymerase-δ interacting protein 2 (Poldip2) shRNA, while human adult retinal pigment epithelial (ARPE-19) cells were treated with high glucose or Poldip2 siRNA. We identified that in STZ-induced DR rats and ARPE-19 cells treated with high glucose, the expression of Poldip2, transforming growth factor-β1 (TGF-β1), phosphorylated-SMAD3/SMAD3, MMP9, COL-1, FN, and CTGF increased while the expression of cadherin decreased. However, deleting Poldip2 inhibited the TGF-β1/SMAD3 signaling pathway and attenuated the above protein expression in vivo and in vitro. Mechanistically, we found that Poldip2 promotes the activation of SMAD3, facilitates its nuclear translocation through interacting with it, and significantly enhances the expression of fibrosis makers. Collectively, Poldip2 was identified is a novel regulator of DR fibrosis and is expected to become a therapeutic target for PDR. Article Highlights: To investigate the role of polymerase-δ interacting protein 2 (Poldip2) in retinal fibrosis during diabetic retinopathy (DR) development. Does Poldip2 regulate retinal fibrosis in DR, and what are the underlying mechanisms? Poldip2 upregulation in DR correlates with increased expression of fibrotic markers, while Poldip2 deletion inhibits the transforming growth factor-β1/SMAD3 pathway, reducing fibrosis-related protein levels. Poldip2 emerges as a novel regulator of DR fibrosis, suggesting therapeutic potential for treating proliferative diabetic retinopathy. [ABSTRACT FROM AUTHOR]

Published
2024
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37. An Agent-Based Market Simulator for Back-Testing Deep Reinforcement Learning Based Trade Execution Strategies

Author

Lin, Siyu, Beling, Peter A., Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Woeginger, Gerhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Mantoro, Teddy, editor, Lee, Minho, editor, Ayu, Media Anugerah, editor, Wong, Kok Wai, editor, and Hidayanto, Achmad Nizar, editor

Published
2021
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39. A Deep Reinforcement Learning Framework for Optimal Trade Execution

Author

Lin, Siyu, Beling, Peter A., Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Woeginger, Gerhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Dong, Yuxiao, editor, Ifrim, Georgiana, editor, Mladenić, Dunja, editor, Saunders, Craig, editor, and Van Hoecke, Sofie, editor

Published
2021
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50. Inhalation of 2, 4-Di-tert-butylphenol-Loaded Micelles Suppresses Respiratory Syncytial Virus Infection in Mice

Author

Zhang, Ke, primary, Guo, Mingyang, additional, Peng, Jianqing, additional, Guo, Pengcheng, additional, Wang, Qin, additional, Shen, Huyan, additional, Chen, Fang, additional, Zhang, Pingping, additional, Lin, Siyu, additional, Gao, Han, additional, Peng, Hong, additional, Mou, Rong, additional, Huang, Jiandong, additional, Wang, Jianxin, additional, and Luo, Yu-si, additional

Published
2023
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