ML Engineer - Large Molecules at Apheris

Seniority in posting: experienced

Language

Location: Berlin
Type: Full-time
Level: not_specified
Posted: Oct 1, 2026

Description

Apheris is hiring an ML Engineer to build, train, evaluate, and release large biomolecular models for antibody modeling, co-folding, binder prediction, and developability. The role involves adapting research prototypes and open-source models such as OpenFold, Boltz-2, and ESM into reliable components for federated training and evaluation pipelines, designing benchmarks, and delivering model work to pharmaceutical R&D teams. Candidates should have an MSc, PhD, or equivalent experience in machine learning, computational biology, bioinformatics, physics, or a related field, along with strong Python, PyTorch, and biomolecular deep-learning experience.

Required Skills

Python
PyTorch
Deep learning
Co-folding
Protein language models
Federated learning
Kubernetes
MLOps

Additional Information

Minimum Education: MSc, PhD, or equivalent experience in machine learning, computational biology, bioinformatics, physics, or a related field
Required Previous Experiences: Training and evaluating models on biological data
Training or fine-tuning deep learning models on biomolecular data
Hands-on experience with co-folding or protein language models beyond inference
Preferred Qualifications: Kubernetes-based training, evaluation, or deployment
Federated learning, privacy-preserving ML, or distributed and multi-GPU training
Experience in pharmaceutical, biotechnology, or regulated environments
Publications in machine learning, computational biology, or structural biology venues
Translation Company Name: Apheris