AIST5040 PhysAI and GenAI for Natural Science

AIST5040 PhysAI and GenAI for Natural Science
(a.k.a. AI for Science)

Department of Computer Science and Engineering
The Chinese University of Hong Kong
2026-2027 Term 1

Description

This course introduces PhysAI and GenAI as complementary approaches to natural scientific discovery. PhysAI refers to physics-inspired AI models that embed domain knowledge, physical laws, and invariances into learning frameworks, enabling models to achieve greater robustness, accuracy, and interpretability. In contrast, GenAI leverages generative modeling to create hypotheses, design candidates, and explore novel scientific paradigms beyond the limits of existing data. Together, PhysAI and GenAI form a powerful synergy: PhysAI accelerates and strengthens established paradigms, while GenAI opens pathways to entirely new directions of research. Through this integration, PhysAI and GenAI hold the potential to transform discovery in chemistry, materials science, and biology.

Advisory: Students are expected to have taken AIST1000 or AIST3120 or AIST4010 or AIST4030 or AIST5030 or CSCI3230 or CSCI3320.

Reference Materials

Syllabus

Fri 10:30am - 1:30pm, Lee Shau Kee Building 514

	Date	Topics	References & Presentation Topics
Week 1	Sep 11th	Overview of AI for Science
Week 2	Sep 18th	AI & Physics Foundation: GenAI #1	(PhysAI for) Density Estimation Autoregressive Models PixelCNN, NeurIPS'16 Transformer, NeurIPS'17 VAR, NeurIPS'24 Energy-Based Model EBM, Wikipedia Contrastive Learning CD, AISTATS'05 NCE, AISTATS'10 GAN, NeurIPS'14 Score-Based Models Score Matching, JMLR'05 Nonequilibrium Thermodynamics, ICML'15 NCSN, NeurIPS'19 SDE (VE & VP), ICLR'21 Variational Model VAE, ICLR'14 DDPM, NeurIPS'20 EDM, NeurIPS'22 Flow-Based Models Flow Matching, ICLR'23 Rectified Flow, ICLR'23 K-Flow, ICLR'26 PhysAI for PDE PINN, JCP'19 Neural Operator, JMLR'23 PhysAI for Symmetry Geom3D, NeurIPS'23 InertialAR, ICML'26 PhysAI for Interpretability GraphCG, TMLR'24 PDETraversal, ICML'23
Week 3	Sep 25th	AI & Physics Foundation: GenAI #2 PhysAI
Week 4	Oct 2nd	AI & Physics Foundation: Transfer Learning, Multi-modal Learning, Large Language Model, Foundation Model, and World Model #1	SSL Contrastive SSL CPC / InfoNCE, arXiv'18 InfoMax, ICLR'19 SimCLR, ICML'20 Alignment and Uniformity, ICML'20 DINO, ICCV'21 Non-contrastive SSL BYOL, NeurIPS'20 SimSiam, CVPR'21 DirectPred, ICML'21 MAE SSL Summary GraphMVP, ICLR'22 Key Architecture U-Net, MICCAI'15 ResNet, CVPR'16 Transformer, NeurIPS'17 ViT, ICLR'21 RoPE, Neurocomputing'24 Mamba, COLM'24 ViT Series ViT, ICLR'21 U-ViT, CVPR'23 DiT, ICCV'23 SiT, ECCV'24 MM-DiT, ICML'24 REPA, ICLR'25 iREPA, ICLR'26 RAE, ICLR'26 JEPA Series JEPA, OpenReview'22 I-JEPA, CVPR'23 V-JEPA, ICLR'24 LeJEPA, arXiv'25 Others Position: LLMs Can't Jump, ICML'26
Week 5	Oct 9th	AI & Physics Foundation: Transfer Learning, Multi-modal Learning, Large Language Model, Foundation Model, and World Model #2 Guest Lecture by Ziyu Li: Topics: World Model
Week 6	Oct 16th	PhysAI for Chemistry: Molecular Representation and Property Prediction, Energy and Force, AI MD	Molecular Representations (String/1D) SMILES, JCICS'88 SELFIES, Mach. Learn.: Sci. Technol.'20 Molecular Property Prediction (Graph/2D) Neural Fingerprints, NeurIPS'15 MPNN, ICML'17 D-MPNN, JCIM'19 Geometric & Equivariant Molecular Learning SchNet, NeurIPS'17 SE(3)-Transformer, NeurIPS'20 EGNN, ICML'21 SEGNN, ICLR'22 Geom3D, NeurIPS'23 Uni-Mol, ICLR'23 Neural Potentials & Molecular Dynamics Deep Potential, PRL'18 NequIP, Nat. Commun.'22 Allegro, Nat. Commun.'23 Molecular Pretraining N-Gram Graph, NeurIPS'19 GraphCL, NeurIPS'20 GraphMVP, ICLR'22 GeoSSL, ICLR'23 MoleculeSDE, ICML'23 DrugCLIP, Science'26 Molecule-Text-3D Multimodal Learning 3D-MolT5, ICLR'25 3D-MoLM, ICLR'24 Quantum Chemistry, Electronic Structure & Baselines GFN2-xTB, JCTC'19 Charge Density Prediction, NeurIPS'24
Week 7	Oct 23rd	GenAI for Chemistry: Molecule Generation and Optimization, Reaction Prediction, Retrosynthesis and Synthesis Planning	Molecular Sequence Generation Molecular VAE, ACS Cent. Sci.'18 Grammar VAE, ICML'17 Molecular Graph Generation JT-VAE, ICML'18 GraphAF, ICLR'20 DiGress, ICLR'23 Molecular Conformation Generation ConfGF, ICML'21 MoleculeSDE, ICML'23 Joint Molecular Structure Generation G-SchNet, NeurIPS'19 MiDi, ICML'23 InertialAR, ICML'26 Goal-Directed Generation & Molecular Optimization GCPN, NeurIPS'18 REINVENT, J. Cheminform.'17 Molecule-Text Representation, Retrieval & Generation MolT5, EMNLP'22 KV-PLM, Sci. Rep.'22 MoleculeSTM, Nat. Mach. Intell.'23 Reaction Prediction & Atom Mapping Molecular Transformer, ACS Cent. Sci.'19 RXNMapper, Sci. Adv.'21 Retrosynthesis & Synthesis Planning Retro*, ICML'20 Graph2Graphs, ICML'20 Chemistry LLMs & Agents ChemCrow, Nat. Mach. Intell.'24
Week 8	Oct 30th	PhysAI for Biology: Protein Structure, Genome Function, Single-Cell and Gene Regulation Guest Lecture by Yanjing Li: Topics TBD	Protein Language Models & Representation Learning ESM-2, Science'23 ProtTrans, TPAMI'22 Protein Structure & Complex Prediction AlphaFold2, Nature'21 RoseTTAFold, Science'21 ESMFold, Science'23 AlphaFold3, Nature'24 Inverse Folding ProteinMPNN, Science'22 ESM-IF1, ICML'22 Structure Search & Geometric Pretraining Foldseek, Nat. Biotechnol.'24 RigidSSL, ICLR'26 Genome Sequence-to-Function & Variant Effects Enformer, Nat. Methods'21 Nucleotide Transformer, Nat. Methods'25 AlphaGenome, Nature'26 Single-Cell & Gene Regulatory Models Geneformer, Nature'23 scGPT, Nat. Methods'24
Week 9	Nov 6th	GenAI for Biology: Protein Design and Engineering, Cell-State and Perturbation Modeling, Genome and RNA Design, Structure-based Drug Design Guest Lecture by Dr. Yuning You: Topics TBD	Protein Structure Generation Chroma, Nature'23 RFdiffusion, Nature'23 PAR, ICML'26 Protein Sequence Generation ProGen2, Cell Syst.'23 ESM3, Science'25 Protein Conformational Ensembles BioEmu, Science'25 Docking & Binding DiffDock, ICLR'23 Structure-based Drug Design DiffSBDD, Nat. Comput. Sci.'24 NucleusDiff, PNAS'25 NeuralMD, Nat. Commun.'25 Multimodal Biomolecular Design ProteinDT, Nat. Mach. Intell.'25 ChatDrug, ICLR'24 BioMatrix, arXiv'26 LOGOS, arXiv'26 Genome Foundation Models & Generative Design Evo, Science'24 Evo 2, Nature'26 ChatNT, Nat. Mach. Intell.'25 Single-Cell Perturbation & Cell-State Generation Squidiff, Nat. Methods'26 RNA Structure & Design RNA-FrameFlow, TMLR'25 DuetRNA, ArXiv'26 Surveys & Benchmarks DNA Foundation Model Benchmark, Nat. Commun.'25
Week 10	Nov 13th	PhysAI for Material Science: Crystallization, Phase Detection	Crystal Representation & Property Prediction CGCNN, PRL'18 MEGNet, Chem. Mater.'19 ALIGNN, npj Comput. Mater.'21 Matformer, NeurIPS'22 Interatomic Potentials & Atomistic Simulation M3GNet, Nat. Comput. Sci.'22 MACE, NeurIPS'22 CHGNet, Nat. Mach. Intell.'23 MatterSim, arXiv'24 GNoME, Nature'23 Phase, Symmetry & Reciprocal-Space Learning Reciprocal-space NN, arXiv'22 NeuralCrystal, NeurIPS AI4Mat Workshop'24
Week 11	Nov 20th	GenAI for Material Science: Material Generation, Structure Generation	Unconditional Crystal Generation CDVAE, ICLR'22 DiffCSP, ICLR'24 FlowMM, ICML'24 CrystalFlow, Nat. Commun.'25 KLDM, arXiv'25 MaskGXT, arXiv'26 Property-Conditioned & Targeted Generation MatterGen, Nature'25 OMatG, ICML'25 ChargeDIFF, Nat. Commun.'26 Language Models & Multimodal Materials Design ChatBattery, arXiv'25 MatterChat, arXiv'25 LLMs for Materials (Perspective), Digital Discovery'24 Porous Materials & MOF Design MOFTransformer, Nat. Mach. Intell.'23 MOFDiff, ICLR'24 ChatMOF, Nat. Commun.'24 GHP-MOFassemble, Commun. Chem.'24 MOFFUSION, Nat. Commun.'25 Surveys & Benchmarks Crystal GenAI Review, npj Comput. Mater.'25 Matbench Discovery, Nat. Mach. Intell.'25
Week 12	Nov 27th	Project Presentation #1
Week 13	Dec 4th	Project Presentation #2 Summary