Postdoctoral researcher in Machine Learning applied to simulations in biomedicine (R2)

Job Reference

135_20_LS_CB_R2

Position

Postdoctoral researcher in Machine Learning applied to simulations in biomedicine (R2)

Closing Date

Friday, 31 July, 2020
Reference: 135_20_LS_CB_R2
Job title: Postdoctoral researcher in Machine Learning applied to simulations in biomedicine (R2)

About BSC

The Barcelona Supercomputing Center - Centro Nacional de Supercomputación (BSC-CNS) is the leading supercomputing center in Spain. It houses MareNostrum, one of the most powerful supercomputers in Europe, and is a hosting member of the PRACE European distributed supercomputing infrastructure. The mission of BSC is to research, develop and manage information technologies in order to facilitate scientific progress. BSC combines HPC service provision and R&D into both computer and computational science (life, earth and engineering sciences) under one roof, and currently has over 650 staff from 49 countries.

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Context And Mission

The Computational Biology group, led by ICREA professor Alfonso Valencia, is looking for a Postdoctoral Researcher to work in the context of a recently granted European project that aims at the refactoring of system biology simulation tools for HPC and exascale architectures.
The Life Sciences Department at the BSC integrates the independent research of senior scientists that work on various aspects of computational biology, ranging from bioinformatics for genomics to computational biochemistry and text mining. The Computational Biology group (http://life.bsc.es/compbio) is involved in multiple projects covering a wide range of topics including multilayer network modeling, epigenomics and computations systems biology. Recently the Computational Biology group has been granted with the HPC/Exascale Centre of Excellence in Personalised Medicine (PerMedCoE). The goal of the PerMedCoE is to provide an efficient and sustainable entry point to the HPC/Exascale-upgraded methodology to translate omics analyses into actionable models of cellular functions of medical relevance.
Personalised Medicine opens unexplored frontiers to treat diseases at the individual level combining clinical and omics information. However, the performances of the current simulation software are still insufficient to tackle medical problems such as tumour evolution or patient-specific treatments. The challenge is to develop a sustainable roadmap to scale-up the essential software for the cell-level simulation to the new European HPC/Exascale systems. Simulation of cellular mechanistic models are essential for the translation of omic data to medical relevant actions and these should be accessible to the end-users in the appropriate environment of the PerMed-specific big confidential data.
The candidate will work in collaboration with senior researchers Miguel Ponce-de-León and Arnau Montagud in the Computational Biology Group of the Life Sciences Department as well as other departments at the BSC, especially Computer Science (with Workflows and Distributed Computing group and Performance Tools group) and Operations Department (with High-Level Support Team). The work is in the framework of the research lines of the group, involving in personalized medicine, and the use and expansion of multiscale simulation tools.
The Researcher will work in a highly sophisticated HPC environment, will have access to state-of-the-art systems and computational infrastructures, and will establish collaborations with experts in different areas both at international and local levels, in particular. The Researcher’s tasks will involve the development and application of AI/ML approaches for the analysis and optimization of biological multiscale simulations with the aim of predicting the impact of alterations such as mutations as well as medical interventions in the dynamics of the system.

Key Duties

  • Development of AI/ML novel approaches for adaptive parameter space search for extreme model exploration.
  • Optimization-based approaches for robust parameter estimation, model calibration and uncertainty quantification.
  • Use predictive computational methods based on statistical and inference approaches to model complex biological processes.
  • Integration of heterogeneous data sources using advanced data mining techniques.
  • Preparation and presentation of scientific articles.
  • Collaborate in the preparation and presentation of scientific projects.
  • Establish and maintain collaborations with international researchers.

Requirements

  • Education
    • PhD in computer science, bioinformatics or similar with a strong background in AI/ML.
    • Alternatively, an MSc on AI or Bioinformatics, with a strong computer science background, or background on applied mathematics/physics with demonstrated experience in AI methods.
  • Essential Knowledge and Professional Experience
    • Experience in AI methodologies
    • Interest in the life sciences area
  • Additional Knowledge and Professional Experience
    • Knowledge and experience in life sciences research
    • Knowledge and experience in AI methodologies:
      ▪ Data pre/post-processing (feature selection, feature reduction, plotting and visualization)
      ▪ Supervised and unsupervised learning (classification, clustering, regression)
      ▪ Knowledge representation
      ▪ Complex networks (graph-based representation, graph analytics)
      ▪ Deep learning (TensorFlow, PyTorch, Caffe, word embeddings)
    • Programming: Python (scikit-learn, numpy, matplotlib), Matlab, R, Java, C, C++, Git
  • Competences
    • Fluency in spoken and written English, while fluency in other European languages will be also valued
    • Capacity to explore new research lines
    • Good communication and presentation skills
    • Ability to work both independently and within a team

Conditions

  • The position will be located at BSC within the Life Sciences Department
  • We offer a full-time contract, a good working environment, a highly stimulating environment with state-of-the-art infrastructure, flexible working hours, extensive training plan, tickets restaurant, private health insurance, fully support to the relocation procedures
  • Duration: Temporary - 1 year renewable renewable
  • Salary: we offer a competitive salary commensurate with the qualifications and experience of the candidate and according to the cost of living in Barcelona
  • Starting date: September/October 2020

Applications Procedure

All applications must include:

  • A Cover Letter with a statement of interest in English, including two contacts for further references - Applications without this document will not be considered

  • A full CV in English including contact details


Deadline

The vacancy will remain open until suitable candidate has been hired. Applications will be regularly reviewed and potential candidates will be contacted.

Diversity and Equal Opportunity Employment

BSC-CNS is an equal opportunity employer committed to diversity and inclusion. We are pleased to consider all qualified applicants for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, age, disability or any other basis protected by applicable state or local law.

Application Form

Please, upload your CV document using the following name structure: Name_Surname_CV
Files must be less than 3 MB.
Allowed file types: txt rtf pdf doc docx.
Please, upload your CV document using the following name structure: Name_Surname_CoverLetter
Files must be less than 3 MB.
Allowed file types: txt rtf pdf doc docx zip.
Please, upload your CV document using the following name structure: Name_Surname_OtherDocument
Files must be less than 10 MB.
Allowed file types: txt rtf pdf doc docx rar tar zip.
** Consider that the information provided in relation to gender and nationality will be used solely for statistical purposes.