BioXcepTion

KVIS Computational Research Team

BioXcepTion Membership Recruitment 2021

If you have a passion for machine learning integrated with biology and chemistry, We invite you to be a part of our research team

We would like to invite all of KVIS batch 7 (grade 10) students to apply for the BioXcepTion research team. The students will receive an opportunity to collaborate with Scalable Data Systems Lab (SCADS), School of Information Science and Technology (IST), Vidyasirimedhi Institute of Science and Technology (VISTEC).

KVIS co-advisor: Dr. Thanasan Nilsu – KVIS Biology Teacher
VISTEC co-advisor: Bundit Boonyarit – Ph.D. student, VISTEC
Number of team(s) accepted: 1 team (only 2 students)

Research theme: Machine learning for enzyme engineering / biocatalysis

Keywords: Computational biology, Computational chemistry, Structural bioinformatics, Machine learning, Deep learning, Biocatalysis, Enzyme engineering

Deadline of Application Submission

  • 00Days
  • 00Hours
  • 00Minutes
  • 00Seconds

About BioXcepTion

BioXcepTion is a student research team that encourages to promoting advanced scientific and technological research with a particular emphasis on Computational Biology, Computational Chemistry, and Artificial Intelligence. The team is achieved by cooperating between Scalable Data Systems Lab (SCADS), School of Information Science and Technology (IST), Vidyasirimedhi Institute of Science and Technology (VISTEC), and Kamnoetvidya Science Academy (KVIS). 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. Machine learning and deep learning model development for enzyme engineering and biocatalysis

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

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

Basic Knowledge

What is a protein?

By: RCSB

A basic introduction to drugs, drug targets, and molecular interactions

By: Schrödinger

Basic computational chemistry and drug development

By: Schrödinger

Introduction to structural bioinformatics

Machine learning roadmap

By: Daniel Bourke

The 7 steps of machine learning

By: Google Cloud Tech

Meet our team

( Research Students : 2017-2018 )

Jiramet Kinchakawat

KVIS#1

Dept. Bio and Brain Engineering, KAIST, South Korea

Thanakrit Wongsatit

KVIS#2

Dept. Bio and Brain Engineering, KAIST, South Korea

Anupap Chauyjaroensuk

KVIS#2

Dept. Biological Sciences, Kyoto University, Japan

Chawapon Tritipchatsakun

KVIS#3

Dept. Bio and Brain Engineering, KAIST, South Korea

Thanis Prucksikanont

KVIS#3

Dept. Medicine Ramathibodi Hospital, Mahidol University, Thailand

( Research Students : 2019-2020 )

Natthakan Saeng-nil

KVIS#5

Kamnoetvidya Science Academy

Puri Virakarin

KVIS#5

Kamnoetvidya Science Academy

( Research Students : 2020-2021 )

Parajaree Ungudonpakdee

KVIS#5

Kamnoetvidya Science Academy

Thanasan Kumdee

KVIS#5

Kamnoetvidya Science Academy

Theeradon Sakpetch

KVIS#6

Kamnoetvidya Science Academy

Phandej Soisamuth

KVIS#6

Kamnoetvidya Science Academy

( Research Students : 2021-2022 )

Tisorn Naphattalung

KVIS#7

Kamnoetvidya Science Academy

Surapa Panjaphakdee

KVIS#7

Kamnoetvidya Science Academy

Matin Kositchutima

KVIS#7

Kamnoetvidya Science Academy

( Advisors )

Pimsiri Danphitsanuparn

KVIS Teacher

Kamnoetvidya Science Academy

Thanasan Nilsu

KVIS Teacher

Kamnoetvidya Science Academy

Tanawan Leeboonngam

KVIS Teacher

Kamnoetvidya Science Academy

Bundit Boonyarit

Ph.D. student

VISTEC

Sarana Nutanong

Principal Investigator

VISTEC

Our Achievements

2021–2022

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

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

Fair: Young Scientist Competition 2022 (YSC2022), Thailand

Date: October 8, 2021

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 of Enzyme and Substrate

Fair: Young Scientist Competition 2022 (YSC2022), Thailand

Date: October 8, 2021

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: 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