The Department of Bioinformatics at Semmelweis University is announcing a competition for the classification of breast cancer patients. The goal is to select patients who respond to chemotherapy and/or hormonal therapy based on bioinformatic evaluation of clinical data.
The dataset attached to the task contains breast cancer cases from public data portals. Analyze the available data and identify a set of clinical features that influences the efficacy of different therapeutic options. Based on the identified correlations, develop an algorithm for the classification of the cases according to the significant differences in the benefit of adjuvant chemotherapy and endocrine therapy where applicable. Document your work: briefly describe the applied methods and justify your choice. Check for the conditions. Analyze the effectiveness of the application.
Accepted methods and tools:
- statistical methods or artificial intelligence algorithms
- MS Excel
- Galaxy platform
- R software packages
Notes to the solution:
- The input of the algorithm is a set of clinical data arbitrarily selected from the training dataset.
- The expected output of the algorithm is a classification of the cases.
The solution should also include the estimated therapeutic effect in the identified classes at one or more arbitrarily selected endpoints. - It is not mandatory to include all cases in the classification. Document all exclusion criteria.
- The application can apply different algorithms to different classes.
- The purpose of the documentation is to make the application fully reproducible for the evaluator. During external validation, we perform the same steps as the submitted work on an independent data set.
Registration:
You can apply for the competition by sending your name and NEPTUN code to bioinformatika@med.semmelweis-univ.hu. Applicants will receive the input data via e-mail.
Application deadline: 31/03/2021.
The submitted work must contain:
- source code or algorithm
- documentation (up to four A4 pages)
Deadline for submission: 30/04/2021.
Evaluation:
We test the solutions on an independent data set. During external validation, the most effective prediction wins.
Contact: dr. Nikoletta Vas
e-mail: vas.nikoletta@med.semmelweis-univ.hu
Prizes:
- The winner can choose and participate in an international bioinformatics course or conference in a member state of the European Union between 01.09.2021 and 31.12.2021. List of international events on the Elixir Europe website:
https://tess.elixir-europe.org/events
- The maximum duration of the chosen course or conference is six days.
- The prize covers the registration fee and the cost of travel and accommodation (in a hotel of up to three stars).
- We offer excellent grade for the practical exam for current or future students of the Bioinformatics course if their application can classify at least 60% of cases with a significant difference in treatment-dependent outcomes during external validation.
We wish success for all applicants!
Dr. Nikoletta Vas and Dr. Balázs Győrffy