Deep Learning for Drug Discovery

Organizers

Prof. Dr. Verena Wolf
Gerrit Großmann, MSc
Michael Backenköhler, MSc

Prof. Dr. Olga Kalinina
Ilya Senatorov, MSc (mail)
Roman Joeres, BSc (mail)

This is a joint seminar with the Deep Learning for Drug Discovery Seminar by Prof. Olga Kalinina’s group.

Please contact Gerrit Großmann for questions about the seminar and have [DLDDSeminar] in the subject line. For bioinformatics students, please write a mail with your questions and [DLDDSeminar] in the subject line to Roman Joeres.

Registration

Please use the seminar assignment system to register.
We ask bioinformatic students to apply for Prof. Kalinina’s seminar. (There will be more information about this in the bioinformatics introductory lecture.)
For bioinformatic students: please apply before 04/14/2022 12pm (noon) by sending an email to Roman Joeres with [DLDDSeminar] in the subject line. Please also attach a transcript of records from LSF.

Topic

The discovery of novel therapeutic drugs is extremely costly and time-consuming. In silico (i.e. computational) drug discovery can potentially accelerate this process. However, this method requires exploring the vast chemical space in order to find molecules of interest. High expectations are placed on deep learning methods to simplify this process and provide navigation in the realm of possible molecules.

This seminar focuses on deep learning methods for learning molecular representations, predicting molecular properties and, ultimately, for finding novel molecules with desired properties. Primarily, we examine recent advances in the field of geometric deep learning and graph neural networks.

Organisation

  • This seminar takes place Thursdays 10:15 to 11:45.
  • A kick-off meeting will be held on Thursday, April 21, 2022.
  • The first session will be held two weeks later (Thursday, May 5, 2022).
  • The seminar will take place in-person in E2.1 (ZBI) Room 001.
  • Hybrid participation (via MS Teams) is only possible for people in quarantine or in other well-justified cases. If you are unable to attend more than one session in person, we may ask for a doctor’s certificate.
  • The seminar language is English.
  • The seminar earns you 7 ECTS.
  • The seminar is eligible for bachelor and master students of computer science and related courses.
  • Depending on the study regulations, registration/unregistration in HISPOS/LSF is due by Thursday, May 12, 2022.
  • The seminar includes 10 sessions (with 2 presentations each).
  • Please include [DLDDSeminar] in the subject line of all emails related to the seminar.

Requirements

Prior knowledge of biochemistry is not expected. General background knowledge in deep learning is recommended.

Grade

To pass, you have to attend all sessions (in person), give a presentation, participate in discussions, and submit reports.

The final grade consists of: your presentation (50%), reports (30%), and participation during the seminar discussions (20%).

Presentation (50%)

Identify the key ideas and concepts and give a self-consistent presentation explaining these concepts to your fellow students. The presentation should focus on intutivion and high-level understanding and contextualization, not on technical details. We encourage the students to read related work and explore supplementary material and include it to the presentation where it seems useful (e.g., from related literature, youtube, github, medium articles, OpenReview, etc.).

Send a first draft of your slides as a .pdf file to your supervisor 7 days before the presentation (deadline is Thursdays 23:59). Upload your final slides as a .pdf file to MS Teams before the presentation.

The presentation should be 25 minutes long.

Here are some suggestions for a good presentation:

  • The goal is to tell a (self-consistent and entertaining) story - not to convince us that you understand the paper.
  • Put time and effort into creating visualizations and working out (running) examples.
  • Prioritize concreteness, simplicity, and clarity. 
  • Don’t overcrowd your slides. Try to avoid full sentences and be cautious with bullet points. 
  • Use equations only when necessary, use color-coded equations to improve their readability.
  • Be critical of the authors’ claims, don’t fall for overselling.

Reports (30%)

Every participant has to write a short report for each paper in his/her group (except your own). Each report should be about two to three pages long. The report should contain a short summary of (what you consider to be) the main contribution or most intriguing idea of the paper. Otherwise, you can freely express your own thoughts on the topic. For instance: What did you like/dislike about the paper (both methodically and didactically)? What are connections to other seminar papers? Can you suggest improvements? What do you think is missing?

The report deadline is 14 days after the last presentation (August 4, 23:59).

You can use the Neurips or Springer LNCS Latex template or any other reasonable format (don’t write an abstract). Please use a spell+grammer checker like languagetool or grammarly before submitting.

Please email the report to your advisor.

Discussions (20%)

Read each presented paper in advance (of course, we do not expect you to understand them fully) and actively participate in the discussion. We expect each participant to attend each session.

Content

Compulsory Reading List

Background Knowlege

Paper List and Time Table

Date (DD.MM.YYY) Type Student (Advisor) Topic Group
05.05.2022 B Roshni Biswas (Roman) Convolutional Networks on Graphs for Learning Molecular Fingerprints D
05.05.2022 CS Advait Ganesh Athreya (GG) Neural Message Passing for Quantum Chemistry D
12.05.2022 B Mohammadmahdi Koochali (Roman & Ilya) SeqGAN: Sequence Generative Adversarial Nets with Policy Gradient A
12.05.2022 B Pegah Einaliyan (Roman & Ilya) Objective-Reinforced Generative Adversarial Networks (ORGAN) for Sequence Generation Models A
19.05.2022 CS (MB) Shreyash Arya Junction Tree Variational Autoencoder for Molecular Graph Generation A
19.05.2022 CS (GG) Ashwath Pravin Shetty MolGAN: An implicit generative model for small molecular graphs A
26.05.2022 - - No Session - Christi Himmelfahrt -
02.06.2022 B Nancy Singh (Roman) Hit and Lead Discovery with Explorative RL and Fragment-based Molecule Generation B
02.06.2022 CS (GG) August von Liechtenstein Learning to Extend Molecular Scaffolds with Structural Motifs (presentation did not take place, write a report anyway) C
09.06.2022 B Joel Chavarria Rivera (Ilya) Model agnostic generation of counterfactual explanations for molecules B
16.06.2022 - - No Session - Frohnleichnam -
23.06.2022 CS (MB) Martin Bálint Weisfeiler and Lehman Go Cellular: CW Networks E
23.06.2022 CS (MB) Kartik Teotia E(n) Equivariant Graph Neural Networks E
30.06.2022 B Gilbert El Khouri (Ilya) Molecular machine learning with conformer ensembles C
30.06.2022 B Aleksandra Kushnareva (Ilya) GeoMol: Torsional Geometric Generation of Molecular 3D Conformer Ensembles C
07.07.2022 CS Ibrahim Siddig Ibrahim Eltayeb (MB) SchNet: A continuous-filter convolutional neural network for modeling quantum interactions D
07.07.2022 CS Irem Begüm Gündüz (GG) Spherical Message Passing for 3D Graph Networks C
14.07.2022 B Tanya Malkani (Roman) Self-supervised Graph Transformer on Large-Scale Molecular Data E
14.07.2022 CS Kinaan Aamir Khan (MB) Molecular Transformer: A Model for Uncertainty-Calibrated Chemical Reaction Prediction E
14.07.2022 B Sneha Thomas (Roman) Spec2Mol: An end-to-end deep learning framework for translating MS/MS Spectra to de-novo molecules (originally planned on 9.6.) B
21.07.2022 B Nazligul Keske (Ilya) Drug-target affinity prediction using graph neural network and contact maps D
21.07.2022 CS Mattes Alexander Warning (GG) Iterative Refinement Graph Neural Network for Antibody Sequence-Structure Co-design B

The type indicates weather a paper is suggest for bioinformatics (B) or CS sutends.






Image Credit: Tara Winstead