Advanced Artificial Intelligence in Biomedicine


392232/ 392240 Schönhuth, Knop Winter 2024/25 Thu 12:00-14:00 X-E0-204 (S) and Thu 10:00-12:00 X-E0-204 (Ü)

:!: The exercises will start subsequent to the presentations, probably in JAN/FEB 2025

Introduction / How to present


introduction-101024.pdf
howtopresent.pdf

How to write reports

how to write reports.pdf

Papers - more follow soon


Date Student Title Authors Year Journal
05.12.2024 Nen Bakraniya Accurate proteome-wide missense variant effect prediction with AlphaMissense Jun Cheng et al. 2023 Science
09.01.2025 Luca Schmidt Accurate structure prediction of biomolecular interactions with AlphaFold 3 Josh Abramson et al. 2024 nature
12.12.2024 Lyon Brown DrugDAGT: a dual-attention graph transformer with contrastive learning improves drug-drug interaction prediction Yaojia Chen et al. 2024 BMC Biology
  MLSNet: a deep learning model for predicting transcription factor binding sites YuchuanZhang et al. 2024 Briefings in Bioinformatics
MSlocPRED: deep transfer learning-based identification of multi-label mRNA sub cellular localisation YunZuo et al. 2024 Briefings in Bioinformatics
23.01.2025 Angelica Gutu scDFN: enhancing single-cell RNA-seq clustering with Deep Fusion networks Tianxiang Liu et al. 2024 Briefings in Bioinformatics
  DeepPGD: A Deep Learning Model for DNA Methylation Prediction Using Temporal Convolution, BiLSTM, and Attention Mechanism Shoryu Teragawa et al. 2024 International Journal of Molecular Sciences
19.12.2024 Chantal Wust Biomedical literature mining: graph kernel-based learning for gene–gene interaction extraction Ai-Ru Hsieh et al. 2024  European Journal of Medical Research
Sequence modeling and design from molecular to genome scale with Evo Eric Nguyen et al. 2024 biorxiv
28.11.2024 John Shahla Caduceus: Bi-Directional Equivariant Long-Range DNA Sequence Modeling Yair Schiff et al. 2024 arXiv
Flow Matching for Generative Modeling Yaron Lipman et al. 2023 arXiv
16.01.2025 Fatih Altundas Learning single-cell perturbation responses using neural optimal transport Charlotte Bunne et al. 2023 nature
09.01.2025 Philip Frese Privacy-preserving decentralized learning methods for biomedical applications Mohammad Tajabadi et al. 2024 ScienceDirect
Integrate Any Omics: Towards genome-wide data integration for patient stratification Shihao Ma 2024 arXiv
28.11.2024 Racha Bekhouche DeepTTA: a transformer-based model for predicting cancer drug response Likun Jiang et al. 2022 Briefings in Bioinformatics
23.01.2025 Henrik Folz Discovery of drug–omics associations in type 2 diabetes with generative deep-learning models Rosa Lundbye Allesøe et al. 2023 Nature Biotechnology
SE(3)-Transformers: 3D Roto-Translation Equivariant Attention Networks Fabian B. Fuchs et al. 2020 34th Conference on Neural Information Processing Systems (NeurIPS 2020)
DIFFDOCK: DIFFUSION STEPS, TWISTS, AND TURNS FOR MOLECULAR DOCKING Gabriele Corso et al. 2023 ICLR
21.11.2024 Fabian Molls EQUIBIND: Geometric Deep Learning for Drug Binding Structure Prediction HannesStärk et al. 2022 39th International Conference on Machine Learning
05.12.2024 Felix Dyck HyenaDNA: Long-Range Genomic Sequence Modeling at Single Nucleotide Resolution Eric Nguyen et al. 2023 NeurIPS 2023
19.12.2024 Alexander Hüdepohl Missing Values and Imputation in Healthcare Data: Can Interpretable Machine Learning Help? Zhi Chen et al. 2023 Conference on Health, Inference, and Learning (CHIL)
16.01.2025 Joyce Abigail Funk Explainable Automated Coding of Clinical Notes using Hierarchical Label-wise Attention Networks and Label Embedding Initialisation Hang Dong et al. 2021 Journal of Biomedical Informatics
21.11.2024 Bhautik Lukhi BioGPT: Generative Pre-trained Transformer for Biomedical Text Generation and Mining Renqian Luo et al. 2022 Briefings in Bioinformatics
12.12.2024 Ismail Ceyhan Antigen-Specific Antibody Design and Optimization with Diffusion-Based Generative Models for Protein Structures Shitong Luo et al. 2022 NeurIPS

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