BioXcepTion

KVIS-VISTEC & MWIT-VISTEC Computational Research Team

About BioXcepTion

BioXcepTion is a student research team that encourages conducting cutting-edge research with a particular emphasis on Computational Biology, Computational Chemistry, and Artificial Intelligence. The team is achieved by cooperating between:

1) Scalable Data Systems Lab (SCADS), School of Information Science and Technology (IST), Vidyasirimedhi Institute of Science and Technology (VISTEC), Thailand

2) Kamnoetvidya Science Academy (KVIS), Thailand, and

3) Mahidol Wittayanusorn School (MWIT), Thailand.

It was founded in 2017 by students interested in Biological and Chemical Sciences as well as Computer Science. Our team is highly specialized in the domains of machine learning and deep learning, with the goal of resolving structural biology and structural chemistry problems.

Our research focus lies in Molecular Property & Interaction, Molecular Design & Discovery, and Molecular Representation & Learning with the goal of developing an leading to the understanding of molecular science knowledge that can be developed for innovation and industry applications. The main research employs knowledge relevant to Biochemistry & Molecular Biology, Chemistry, Pharmaceutical Sciences, and Computer Science, together with computational techniques such as Machine Learning, Deep Learning, Computational Biology, and Computational Chemistry.

1. Molecular Property & Interaction – focuses on the relationship of biomolecules structure, leading to predict molecular properties and interactions.

2. Molecular Design & Discovery – focuses on the structure of molecules and biomolecules, with the goal of discovering, designing, and understanding molecular phenomena.

3. Molecular Representation & Learning – focuses on designing and developing model architectures and feature engineering strategies that result in enhanced prediction in machine learning and deep learning processes.

MISSION

1. Promote computational science research involves in biology and chemistry

2. Promote scientific learning and discovery in biochemistry, biology, and molecular biology along with computer science 

3. Promote research presentation and publication in international conferences and peer-reviewed journals

4. Promote the development of essential skills for living in the community and modern world

5. Counseling for further study in science, engineering, and technology

Our Identity

Research Focuses

1. Machine learning and deep learning model development for predicting drug response to accelerate drug discovery

2. Discovery of novel inhibitors for emerging infectious diseases (EIDs) and non-communicable diseases (NCDs)

3. Molecular dynamics of biological macromolecules to understand mechanisms and reactions

Basic Knowledge

Recommended Introductory Videos

What is a protein?
By: RCSB

A basic introduction to drugs, drug targets, and molecular interactions
By: Schrödinger

Machine learning roadmap
By: Daniel Bourke

The 7 steps of machine learning
By: Google Cloud Tech

Introduction to Structural Bioinformatics

Machine Learning for Molecular Chemistry

Recommended Online Courses & Resources

Dept. Computer Engineering, Chulalongkorn University

By: Dept. Computer Engineering, Chulalongkorn University

Meet our team

( Senior Advisors, Co-founders, and Research Alumni )

Jiramet Kinchakawat

KVIS#1

(Senior Advisor & Co-founder)

Dept. Bio and Brain Engineering, KAIST, South Korea (KAIST Scholarship)

Thanakrit Wongsatit

KVIS#2

(Senior Advisor & Co-founder)

Dept. Bio and Brain Engineering, KAIST, South Korea (KAIST Scholarship)

Anupap Chauyjaroensuk

KVIS#2

(Senior Advisor & Co-founder)

Dept. Biological Sciences, Kyoto University, Japan (Monbukagakusho: MEXT Scholarship)

Chawapon Tritipchatsakun

KVIS#3

(Research Alumni: 2018-2019)

Dept. Bio and Brain Engineering, KAIST, South Korea (KAIST Scholarship)

Thanis Prucksikanont

KVIS#3

(Research Alumni: 2018-2019)

Faculty of Medicine Ramathibodi Hospital, Mahidol University, Thailand

Natthakan Saeng-nil

KVIS#5

(Research Alumni: 2019-2021)

Computer Engineering with a Second Major in Business Program, Nanyang Technological University (NTU), Singapore (ASEAN Undergraduate Scholarship)

Puri Virakarin

KVIS#5

(Research Alumni: 2019-2021)

Computer Engineering with Management (Double Major) Program, National University of Singapore (NUS), Singapore (ASEAN Undergraduate Scholarship)

Parajaree Ungudonpakdee

KVIS#5

(Research Alumni: 2020-2021)

Faculty of Medicine, Chiang Mai University, Thailand

Thanasan Kumdee

KVIS#5

(Research Alumni: 2020-2021)

Monbukagakusho: MEXT Scholarship in Natural Sciences, Japan

Pawit Kaewnuratchadasorn

MWIT#29

(Research Alumni: 2021-2021)

Faculty of Medicine Siriraj Hospital, Mahidol University, Thailand

Nattawin Yamprasert

MWIT#29

(Research Alumni: 2021-2021)

Digital Engineering Program, Sirindhorn International Institute of Technology (SIIT), Thammasat University, Thailand (Scholarships for Talented Students in Science & Technology)

Wutthipong Chongchareansanti

MWIT#29

(Research Alumni: 2021-2021)

Faculty of Medicine Siriraj Hospital, Mahidol University, Thailand

( Student Researchers : 2020- )

Theeradon Sakpetch

KVIS#6

Kamnoetvidya Science Academy

Phandej Soisamuth

KVIS#6

Kamnoetvidya Science Academy

( Student Researchers : 2021- )

Tisorn Naphattalung

KVIS#7

Kamnoetvidya Science Academy

Surapa Panjaphakdee

KVIS#7

Kamnoetvidya Science Academy

Matin Kositchutima

KVIS#7

Kamnoetvidya Science Academy

( Research Advisors )

Pimsiri Danphitsanuparn

KVIS Teacher

Kamnoetvidya Science Academy

Thanasan Nilsu

KVIS TeacheR

Kamnoetvidya Science Academy

Sarote Boonseng

MWIT Teacher

Mahidol Wittayanusorn School

Bundit Boonyarit

Ph.D. student

VISTEC

Sarana Nutanong

Principal Investigator

VISTEC

Our Achievements

2022–2023

Semi-Supervised Learning with Graph Neural Networks to Improve the Predictive Performance of Drug Response for HIV-1 Protease Inhibitors

Fair: The 8th ASEAN Student Science Project Competition (ASPC 2022), Thailand

Date: May 16 & June 18, 2022

By: 1. Theeradon Sakpetch and 2. Phandej Soisamuth

Advisors: 1. Thanasan Nilsu and 2. Bundit Boonyarit

2021–2022

CANDraGAT: A Hybrid Fragment-Based Graph Attention Network To Improve Cancer Drug Response Prediction

Link: https://projectboard.world/isef/project/86556

Fair: Regeneron International Science and Engineering Fair 2022 (Regeneron ISEF 2022), Atlanta, Georgia, USA

Date: May 7  – 13, 2022

By: 1. Pawit Kaewnuratchadasorn, 2. Nattawin Yamprasert, and 3. Wutthipong Chongchareansanti

Advisors: 1. Sarote Boonseng and 2. Bundit Boonyarit

Semi-Supervised Learning with Graph Neural Networks for Drug Response Prediction Leads Discovery of HIV Inhibitors

Fair: Genius Olympiad 2022, USA

Date: May 16 & June 18, 2022

By: 1. Theeradon Sakpetch and 2. Phandej Soisamuth

Advisors: 1. Thanasan Nilsu and 2. Bundit Boonyarit

Hybrid Graph Attention Networks Toward the Drug Sensitivity Prediction for Precision Oncology using Molecular Structure and Pharmacogenomic Data

Fair: Young Scientist Competition 2022 (YSC2022), Thailand

Date: March 7, 2022

By: 1. Pawit Kaewnuratchadasorn, 2. Nattawin Yamprasert, and 3. Wutthipong Chongchareansanti

Advisors: 1. Sarote Boonseng and 2. Bundit Boonyarit

Semi-Supervised Learning with Graph Neural Networks for Drug Response Prediction Leads Discovery of HIV Inhibitors

Fair: Young Scientist Competition 2022 (YSC2022), Thailand

Date: March 7, 2022

By: 1. Theeradon Sakpetch and 2. Phandej Soisamuth

Advisors: 1. Thanasan Nilsu and 2. Bundit Boonyarit

Machine Learning Enables Prediction for Enzyme Kinetics of Glycosidases Based on Molecular Descriptors and Physicochemical Properties

Fair: Young Scientist Competition 2022 (YSC2022), Thailand

Date: January 31, 2022

By: 1. Tisorn Naphattalung, 2. Surapa Panjaphakdee, and 3. Matin Kositchutima

Advisors: 1. Thanasan Nilsu and 2. Bundit Boonyarit

Deep Transfer Learning-Based Heart Failure Drug Classification on Small Datasets 

Fair: 5th KVIS Invitational Science Fair (5th KVIS-ISF), Thailand

Date: January 28, 2022

By: 1. Parajaree Ungudonpakdee and 2. Thanasan Kumdee

Advisors: 1. Thanasan Nilsu and 2. Bundit Boonyarit

Application of Machine Learning Technique Assisted Prediction of Bioactivities of Ligands in Targeted Drug Discovery Process of Lung Cancer for EGFR Target

Fair: 5th KVIS Invitational Science Fair (5th KVIS-ISF), Thailand

Date: January 28, 2022

By: 1. Natthakan Saeng-nil and 2. Puri Virakarin

Advisors: 1. Thanasan Nilsu and 2. Bundit Boonyarit

EGFRNet: Transfer and Multi-Task Learning Based on Graph Convolutional Network Toward Multi-Target Drug Discovery Against Cancers for EGFR-Family Proteins

Fair: Graduation ceremony for Vidyasirimedhi Institute of Science and Technology & Kamnoetvidya Science Academy, Thailand

Date: November 16, 2021

By: 1. Natthakan Saeng-nil and 2. Puri Virakarin

Advisors: 1. Thanasan Nilsu and 2. Bundit Boonyarit

Deep Transfer Learning-Based Heart Failure Drug Classification on Small Datasets 

Fair: Asia Pacific Conference of Young Scientists 2021 (APCYS 2021), Mexico

Date: September 27 – October 1, 2021

By: 1. Parajaree Ungudonpakdee and 2. Thanasan Kumdee

Advisors: 1. Thanasan Nilsu and 2. Bundit Boonyarit

An Integrated Multi-Task and Transfer Learning With Graph Convolutional Network Assisted Drug Response Prediction Leads Discovery of HIV/HCV Co-Inhibitors

Fair: International Students’ Science Fair 2021 & The 3rd Beihang International Science Fair (ISSF-BHISF 2021), China

Date: July 16 – 19, 2021

By: 1. Theeradon Sakpetch and 2. Phandej Soisamuth

Advisors: 1. Thanasan Nilsu and 2. Bundit Boonyarit

Deep Transfer Learning-Based Hit Compound Classification for Therapeutic Targets in Heart Failure Drug Discovery on Small Datasets 

Fair: The Virtual Korea Science Academy of KAIST Science Fair (KSASF) 2021, South Korea

Date: June 29 – July 1, 2021

By: 1. Parajaree Ungudonpakdee and 2. Thanasan Kumdee

Advisors: 1. Thanasan Nilsu and 2. Bundit Boonyarit

An Integrated Multi-Task and Transfer Learning With Graph Convolutional Network Assisted Drug Response Prediction Leads Discovery of HIV/HCV Co-Inhibitors

Fair: The Virtual Korea Science Academy of KAIST Science Fair (KSASF) 2021, South Korea

Date: June 29 – July 1, 2021

By: 1. Theeradon Sakpetch and 2. Phandej Soisamuth

Advisors: 1. Thanasan Nilsu and 2. Bundit Boonyarit

2020–2021

EGFRNet: Transfer and Multi-Task Learning Based on Graph Convolutional Network Toward Multi-Target Drug Discovery Against Cancers for EGFR-Family Proteins

Link: https://projectboard.world/isef/project/56057

Fair: Regeneron International Science and Engineering Fair 2021 (Regeneron ISEF 2021), USA

Date: May 4 & 16 – 21, 2021

By: 1. Natthakan Saeng-nil and 2. Puri Virakarin

Advisors: 1. Thanasan Nilsu and 2. Bundit Boonyarit

Application of Machine Learning Technique Assisted Prediction of Bioactivities of Ligands in Targeted Drug Discovery Process of Lung Cancer for EGFR Target

Fair: Genius Olympiad 2021, USA (Postponed from 2020 due to COVID-19)

Date: May 15 & June 12, 2021

By: 1. Puri Virakarin and 2. Natthakan Saeng-nil

Advisors: 1. Thanasan Nilsu and 2. Bundit Boonyarit

Application of Machine Learning Technique Assisted Prediction of Bioactivities of Ligands in Targeted Drug Discovery Process of Lung Cancer for EGFR Target

Link: http://www.school.ioffe.ru/readings/2021/results2.html

Fair: The XXXI International Scientific Student Conference Sakharov Readings, Russia

Date: May 15, 2021

By: 1. Natthakan Saeng-nil and 2. Puri Virakarin

Advisors: 1. Thanasan Nilsu and 2. Bundit Boonyarit

Deep Transfer Learning-Based Hit Compound Classification for Therapeutic Targets in Heart Failure Drug Discovery on Small Datasets 

Link: https://internat.msu.ru/en/sunc-msu/educational-projects-en/the-kolmogorov-readings/21-kolmogorov-readings/

Fair: The 21st Kolmogorov Readings, Russia

Date: May 3 – 6, 2021

By: 1. Parajaree Ungudonpakdee and 2. Thanasan Kumdee

Advisors: 1. Thanasan Nilsu and 2. Bundit Boonyarit

Application of Machine Learning Technique Assisted Prediction of Bioactivities of Ligands in Targeted Drug Discovery Process of Lung Cancer for EGFR Target

Fair: Young Scientist Competition 2021 (YSC2021), Thailand

Date: March 4 & 19, 2021

By: 1. Natthakan Saeng-nil and 2. Puri Virakarin

Advisors: 1. Thanasan Nilsu and 2. Bundit Boonyarit

An Integrated Multi-Task Learning and Transfer Learning-Based Approach for Structure-Property Landscapes Leads Drug Discovery for Protease Inhibitors of HIV and HCV

Fair: Young Scientist Competition 2021 (YSC2021), Thailand

Date: January 25 & 31, 2021

By: 1. Theeradon Sakpetch and 2. Phandej Soisamuth

Advisors: 1. Thanasan Nilsu and 2. Bundit Boonyarit

LigEGFR: Deep Learning-Assisted Drug Discovery for Lung Cancer

Fair: International Music, Science, Engineering Energy Fair 2020 (BUCA IMSEF 2020), Turkey

Date: December 14 – 18, 2020

By: 1. Natthakan Saeng-nil and 2. Puri Virakarin

Advisors: 1. Thanasan Nilsu and 2. Bundit Boonyarit

Deep Transfer Learning-Based Hit Compound Classification for Therapeutic Targets in Heart Failure Drug Discovery on Small Datasets 

Fair: Young Scientist Competition 2021 (YSC2021), Thailand

Date: December 10 – 11, 2020

By: 1. Parajaree Ungudonpakdee and 2. Thanasan Kumdee

Advisors: 1. Thanasan Nilsu and 2. Bundit Boonyarit

LigEGFR: Deep Learning-Assisted Drug Discovery Process of Lung Cancer for EGFR Target

Fair: Japan Super Science Fair 2020 (18th JSSF), Japan

Date: November 7 – 8, 2020

By: 1. Natthakan Saeng-nil and 2. Puri Virakarin

Advisors: 1. Thanasan Nilsu and 2. Bundit Boonyarit

LigEGFR: Deep Learning-Assisted Drug Discovery for Lung Cancer

Fair: AI-JAM US Online Competition 2020, Silicon Valley, USA

Date: September 19, 2020

By: 1. Puri Virakarin and 2. Natthakan Saeng-nil

Advisors: 1. Thanasan Nilsu and 2. Bundit Boonyarit

2019–2020

Application of Machine Learning Technique Assisted Prediction of Bioactivities of Ligands in Targeted Drug Discovery Process of Lung Cancer for EGFR Target

Fair: Young Scientist Competition 2020 (YSC2020), Thailand

Date: July 27, 2020

By: 1. Natthakan Saeng-nil and 2. Puri Virakarin

Advisors: 1. Thanasan Nilsu and 2. Bundit Boonyarit

Computational Analysis of Glucagon Receptor (GCGR) and Antagonists Structure for Further Screening Anti-diabetics compounds

Fair: Canada–Wide Science Fair 2020, Canada (Cancelled due to COVID-19)

Date: May 9 – 15, 2020

By: 1. Chawapon Tritipchatsakun and 2. Thanis Prucksikanont

Advisors: 1. Pimsiri Danphitsanuparn and 2. Bundit Boonyarit

Application of Machine Learning Technique Assisted Prediction of Bioactivities of Ligands in Targeted Drug Discovery Process of Lung Cancer for EGFR Target

Fair: Young Scientist Competition 2020 (YSC2020), Thailand

Date: January 31, 2020

By: 1. Puri Virakarin and 2. Natthakan Saeng-nil

Advisors: 1. Thanasan Nilsu and 2. Bundit Boonyarit

Computational Analysis of Glucagon Receptor (GCGR) and Antagonists Structure for Further Screening Anti-diabetics compounds

Fair: 16th International Students’ Science Fair (ISSF 2020) and 3rd KVIS Invitation Science Fair, 2020, Thailand

Date: January 15 – 20, 2020

By: 1. Chawapon Tritipchatsakun and 2. Thanis Prucksikanont

Advisors: 1. Pimsiri Danphitsanuparn and 2. Bundit Boonyarit

Computational Analysis of Glucagon Receptor (GCGR) and Antagonists Structure for Further Screening Anti-diabetics compounds

Fair: Graduation ceremony for Vidyasirimedhi Institute of Science and Technology & Kamnoetvidya Science Academy, Thailand

Date: November 11, 2019

By: 1. Chawapon Tritipchatsakun and 2. Thanis Prucksikanont

Advisors: 1. Pimsiri Danphitsanuparn and 2. Bundit Boonyarit

2018–2019

Studies on structure of glucagon receptor (GCGR) related to type 2 diabetes pathogenesis by computational biophysics methods

Fair: Singapore International Science Challenge – International Students’ Science Fair 2019 (SISC-ISSF 2019), Singapore

Date: March 17 – 22, 2019

By: 1. Chawapon Tritipchatsakun and 2. Thanis Prucksikanont

Advisors: 1. Pimsiri Danphitsanuparn and 2. Bundit Boonyarit

Our Publication

(1) Puri Virakarin, Natthakan Saengnil, Bundit Boonyarit, Jiramet Kinchagawat, Rattasat Laotaew, Treephop Saeteng, Thanasan Nilsu, Naravut Suvannang, Thanyada Rungrotmongkol, and Sarana Nutanong. “LigEGFR: Spatial graph embedding and molecular descriptors assisted bioactivity prediction of ligand molecules for epidermal growth factor receptor on a cell line-based dataset.” bioRxiv (2020).

DOI: https://doi.org/10.1101/2020.12.24.423424

Website: http://ligegfr.vistec.ist/

Contact
Bundit Boonyarit
Email: [email protected]

Scalable Data Systems Lab (SCADS)
School of Information Science and Technology (IST)
Vidyasirimedhi Institute of Science and Technology (VISTEC)

555 Moo 1, Pa Yup Nai, Wang Chan, Rayong 21210, THAILAND