Applied ML Scientist, Cheminformatics ( Staff / Principal)

Genesis Therapeutics; Burlingame (CA); On-site; USD 120,000 - 160,000; Full time

Job summary

A leading company in AI-driven drug discovery seeks a skilled professional to bridge AI research and experimental teams. The role involves leveraging AI techniques for drug discovery, collaborating with various stakeholders, and requires strong data science and software engineering skills.

Benefits

Competitive compensation package

Comprehensive health benefits

401(k) plan

Open (unlimited) PTO policy

Free lunches and dinners

Paid family leave

Life and disability insurance

Qualifications

• Experience in drug discovery settings.
• Excellent data science and software engineering skills.

Responsibilities

• Work with project teams to assess model performance.
• Evaluate model quality against project data.

Skills

Data Science

Applied ML

Software Engineering

Cheminformatics

Education

PhD in cheminformatics

Tools

Python

Numpy

Matplotlib

RDKit

OpenEye

scikit-learn

PyTorch

Job description

About The Team

We’re a tight-knit team of proven drug hunters, deep learning researchers, and software engineers united by a common mission — drive AI innovation in biochemistry, discovering and developing groundbreaking therapies for patients suffering from severe disorders.

Genesis AI team is focused on developing foundation models for drug discovery by conducting fundamental research at the intersection of machine learning, physics, and computational chemistry, as well as engineering robust software systems that enable running large-scale simulations and training generative and predictive AI models designed to learn from all kinds of molecular data, leveraging our cluster with thousands of GPUs and CPUs.

About The Role

This unique role serves as a critical bridge between our AI research and experimental drug discovery teams. You will collaborate closely with both groups, leveraging cutting-edge AI techniques to evaluate, analyze, and deploy models to maximize the impact of our industry-leading AI platform on drug discovery programs.

The ideal candidate will be comfortable in experimental and engineering contexts and skilled at communicating with stakeholders from both domains. Their day-to-day responsibilities will require basic familiarity with experimental techniques, excellent data science skills, and demonstrated ability in applied ML.

Positions are available at various levels of seniority: Senior, Staff, and Principal.

You will

1. Work directly with project teams to assess model performance and utility, including applicability to current project needs, and collaborate with ML and engineering teams to resolve issues or add new functionality
2. Assist experimental colleagues with use and interpretation of model predictions by providing context about model quality and prediction uncertainty
3. Evaluate model quality by validating predictions against project data and internal or external benchmarks
4. Curate internal and external datasets for model training and validation (in collaboration with experimental teams)
5. Contribute to design and analysis of experiments on model changes and alternative architectures

You are

1. Experience working with chemistry project teams in an industrial or academic drug discovery setting
2. Experience with modeling and analysis of small molecule datasets
3. Familiarity with common experiment types (biochemical/binding/cell-based assays, in vivo studies, etc.) and CADD workflows (docking, virtual screening, ADME prediction, etc.)
4. Excellent data science skills, including exploratory data analysis and statistical methods for model comparison and evaluation
5. Strong software engineering skills, including experience with Python, Numpy, and Matplotlib
6. Strong cheminformatics skills, including experience with RDKit or OpenEye
7. Strong applied ML background, including familiarity with deep neural networks and experience with scikit-learn and PyTorch

Nice to have's

1. Publications in peer-reviewed journals or conferences describing ML applications in drug discovery or related areas
2. PhD or equivalent in cheminformatics, computer-aided drug design, or a related field
3. Experience with graph neural networks, multitask modeling, active learning, Bayesian optimization, model uncertainty, and multi-objective optimization
4. Experience with implementation of ML model architectures in PyTorch
5. Experience in a collaborative software engineering environment, including code reviews and pull request workflows
6. Experience with SQL and database management
7. Strong opinions on molecule featurization and model validation

Compensation, Benefits, And Perks

1. Competitive compensation package that includes salary and equity
2. Comprehensive health benefits: Medical, Dental, and Vision (covered 100% for the employees)
3. 401(k) plan
4. Open (unlimited) PTO policy
5. Free lunches and dinners at our offices
6. Paid family leave (maternity and paternity)
7. Life and long- and short-term disability insurance

About Genesis Therapeutics

Genesis Therapeutics is unifying AI and biotech to discover novel and breakthrough treatments for patients with severe and devastating conditions. Founded on groundbreaking molecular ML research, Genesis has established itself as an industry leader in AI for small molecule drug discovery. Our team has created the industry's most advanced molecular AI platform, GEMS (Genesis Exploration of Molecular Space), to accelerate and optimize small molecule drug discovery and enable the discovery of novel first-in-class and best-in-class drugs for challenging targets.

We have built an internal pipeline with multiple programs against high-value, data-poor, and undruggable targets, where GEMS provides a distinct advantage. Genesis has signed AI-focused platform collaborations with major pharmaceutical companies, including Incyte Corporation (Feb 2025) and Gilead Sciences (Sept 2024).

We raised a $200M Series B in August 2023 and over $300M from top investors, including Andreessen Horowitz, Rock Springs Capital, T. Rowe Price, Fidelity, Radical Ventures, NVentures, BlackRock, and Menlo Ventures.

Genesis is headquartered in Burlingame, CA, with a fully integrated laboratory in San Diego. We are committed to an inclusive workplace and are an Equal Opportunity Employer.