Graph ML Engineer (Drug Discovery)

Holisticon Connect is a division within NEXER GROUP - a custom software development company. We started in Poland in 2017 and are now a team of over 140 people with offices in Wrocław, Warsaw, and Cracow. We have the opportunity to work with world-renowned brands from Scandinavia, the UK, and Western Europe. Our goal is to grow stronger, in competence rather than in numbers. If you like what we do, check out our offer, maybe we will have the pleasure of meeting you! 😊  

We are looking for Graph Machine Learning Engineer with expertise in GNNs, structural biology, and computational drug discovery. You will work on protein and peptide structure modeling, developing graph-based molecular representation learning and improving AlphaFold-like models for binding site prediction. You will join innovative team focused on advancing AI-driven drug discovery. Your work will play a crucial role in accelerating drug discovery, target identification, and biomarker discovery. This is a unique opportunity to work in an emerging field at the core of pharmaceutical AI, where cutting-edge methods meet real-world biomedical challenges.

We offer a choice of employment form: B2B or Employment Contract 

• UoP: 17000 – 20000 PLN gross/month
• B2B: 140 – 170 PLN net/hour + VAT

You might be the perfect match if you are/have:

• Strong expertise in Graph Neural Networks (GNNs) – including PyTorch Geometric (PyG) and Deep Graph Library (DGL).
• Hands-on experience in structural biology and molecular representation learning, specifically working with machine learning models for proteins, peptide structures, or small molecule representations.
• Practical experience with AlphaFold or other geometric deep learning models.
• Experience in De novo design:
• Demonstrated success in projects involving metrics like binding affinity or synthesizability.
• Practical knowledge of generative models for molecule design (e.g., RL, VAE).
• Proficiency in Python and TensorFlow/ PyTorch.
• Deep understanding of link prediction, graph classification, and inductive learning.
• Experience in handling imbalanced biological data and bias correction.
• PhD in Computer Science, Machine Learning, Data Science, Applied Mathematics, Bioinformatics, or a related field.
• Strong problem-solving skills and the ability to work in an interdisciplinary environment.
• Experience collaborating with R&D teams.
• Excellent English communication skills, both written and spoken.
• Ability to work in cross-functional teams, bridging AI with biology and chemistry.

Moreover, we appreciate skills in these areas:

• Generative AI for molecule and peptide design.
• Multi-modal learning with heterogeneous graphs.
• OMICs data integration for drug discovery.
• Knowledge graphs in pharma (e.g., disease-gene, drug-target prediction).

By joining us, you gain the following: 

• Opportunity to work on exciting, international projects in cutting-edge industries like Automotive, Biotech, IoT; 
• Possibility to develop in cloud technologies. We are a certified AWS partner;
• Becoming part of a team that believes that the next step to a promising future is to put your heart into it and make it happen; 
• Respect for your private life so you don't have to work overtime or on weekends; 
• Team Events budget to socialize outside of work; 
• Company Events to celebrate smaller and bigger successes (Summer Party, Programmer's Day, and trips abroad – so far we've been in Cape Town, Are, and Barcelona). 

Perks and benefits: 

• Fully remote work or in our office in Wrocław, Warsaw or Cracow; 
• Free benefits such as Luxmed, Multisport, and life insurance in Nationale Nederlanden; 
• Attractive referral system (9,5k for senior, 6k for mid, 2,5k for junior); 
• Personal Training Budget with additional paid hours; 
• Passion Day - an extra day off for your hobby to spend as you please; 
• Flexible working hours with no micro-management approach. Our core hours are 9-15, the rest of the working time is up to you; 
• We provide high-quality work equipment + 2 additional monitors and accessories. 

If you apply for this position and match our expectations, then: 

1) You will be invited to an HR Screening with our IT Recruiter. 

2) You will have a technical interview. 

3) You will meet with a client. 

Submit your application online in one easy step! Apply now!