Schedule#

Final project presentation and report#

Each study group will propose a final project that is related to the course material and discuss it with the instructor for approval. The goal of the discussion is to ensure that the project is neither too easy nor too difficult and that it is feasible within the time frame of the course. After the discussion, the study group should start working on the project.

Each study group will give a presentation of the final project during the lecture time on April 24. Each group will have 20 minutes to present the project and 4 minutes for Q&A. Every group member should participate in the presentation. The presentation should be in the form of slides and the slides need to be submitted to the instructor by April 23 11:59 PM.

Besides the presentation, each group should submit a report of the project. The report is due on April 30 11:59 PM. The report should be in the form of a PDF file and should be submitted to the instructor. The report should be no more than 5 pages long and the page limit does not include the references.

Both the presentation and the report should include the following points:

  • What is the problem the project is trying to solve or the question it is trying to answer?

  • What are the key ideas and techniques used in the project?

  • What are the results?

  • What are the strengths and weaknesses of the ideas and techniques used in the project?

  • What are possible future directions for the project?

The report should include the following sections:

  • Title: The title of the project.

  • Abstract: A brief summary of the project (no more than 200 words).

  • Introduction: A brief introduction to the problem and the project.

  • Methods: A description of the methods used in the project.

  • Results: A description of the results.

  • Discussion: A discussion of the results and the strengths and weaknesses of the methods used in the project.

  • Author contributions: A detailed description of the contributions of each group member to the project.

  • References (as needed): A list of references used in the project.

Lecture schedule#

Journal club presentation#

The journal club presentation will be during the lecture time on March 11. Each study group need to select a research article and submit the title and authors of the article to the instructor by February 28. Each study group will have 20 minutes to present the research article and 4 minutes for Q&A. Every groupe member should participate in the presentation. The presentation should at least cover the following points:

  • What is the problem the paper is trying to solve or the question it is trying to answer?

  • What are the key ideas and techniques used in the paper?

  • What is the main contribution or result of the paper?

  • What are the strengths and weaknesses of the paper?

The objective of the presentation is to let the audience understand these points without reading the paper. The presentation should be clear, concise, and engaging. The presentation should be in the form of slides. The slides should be submitted to the instructor by March 10.

The research article should be in the field of using ML/MD to study biophysical problems, broadly defined. It could be an application of ML/MD to a biophysical problem and a methodological paper that develops new ML/MD methods. The article should be published in a peer-reviewed journal or conference proceedings such as:

  • General journals: Nature, Science, Nature Methods, Nature Biotechnology, Nature Communications, PNAS

  • General chemistry/physics journals: Journal of American Chemical Society, Angewandte Chemie International Edition, ACS Central Science, Physical Review Letters, Physical Review X

  • Specialized chemistry/physics/biophysical journals: Journal of Chemical Theory and Computation, Journal of Chemical Information and Modeling, Journal of Physical Chemistry Letters, Journal of Physical Chemistry B, Journal of Chemical Physics, PLOS Computational Biology, Biophysical Journal

  • ML Conference proceedings: NeurIPS, ICML, ICLR, AISTATS, UAI