Title of research project

B650 Contrat Public ANS MM DUCLOS LIMICS

Research Engineer

Contract type Contrat (CDD) Category Workload Fulltime

Scientific field Informatique
Santé, médecine humaine, vétérinaire
Science de la donnée (stockage, sécurité, mesure, analyse)

WorklJob Descriptionoad

Description of the offer Context LIMICS develops innovative approaches to predict antibiotic resistance in pathogenic bacteria by exploiting whole genome sequencing (WGS) data. The candidate will join a multidisciplinary team composed of computer scientists, biologists, pharmacists, physicians, and data science specialists. He/she will participate in the development of a neural network dedicated to predicting antibiotic resistance phenotypes from bacterial genomic data, with a focus on translational research and clinical application. Main tasks • Design, develop, and optimize a neural network model for predicting antibiotic resistance from whole genome sequencing data; • Set up analysis pipelines for the pre-processing of genomic data (quality control, assembly, annotation, extraction of variants or relevant genomic features); • Develop analytical tools and modules in Python for training, evaluating, and interpreting deep learning models; • Compare different modeling strategies (convolutional networks, hybrid architectures, k-mer-based approaches, genomic embeddings, etc.) and evaluate their performance (AUC, sensitivity, and specificity); • Ensure the reproducibility and robustness of analyses: version management, documentation, implementation of tests; • Participate in scientific promotion: preparation of figures, drafting of technical reports, and contribution to scientific publications.

Field of research Artificial intelligence applied to healthcare

Skills Linux environment, Slurm-type computing cluster, Python programming (PyTorch, TensorFlow/Keras, deep learning, neural networks, model interpretability, model optimization, model evaluation.

Knowledge Knowledge of biology is desirable but not a prerequisite, Bacterial genomics, public health,

Work environment

Location Bobigny

Laboratory Laboratoire d'Informatique Médicale et d'Ingénieurie des Connaissances en e- Santé

Degree level

Degree required PhD

Experience required Use of deep learning methods on bacterial genome sequencing and antibiotic resistance data, experience with antibiotic resistance databases, use of computing clusters

Additionnal information

Start date 04 01 26

Job Type Contrat (CDD)

Salary 2464 € per month

Contract duration 6 mois

Composition of the selection jury

Application deadline 03 01 26

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