# Senior Director / Vice President, Machine Learning (Generative Chemistry)

**Company**: FL117, a venture-backed stealth AI x bio startup
**Location**: Cambridge, MA
**Experience**: senior
**Job type**: full-time
**Salary**: $279,000 - $412,500
**Category**: Engineering
**Industry**: Technology

**Apply**: https://job-boards.greenhouse.io/flagshippioneeringinc/jobs/8843608002?utm_source=yubhub.co&utm_medium=jobs_feed&utm_campaign=apply
**Canonical**: https://yubhub.co/jobs/job_96a35192-c16

## Description

FL117, a venture-backed stealth AI x bio startup, is seeking a highly skilled Sr. Director/VP ML, Generative Chemistry. You will lead AI/ML and cheminformatics projects building the next-gen multi-modal generative models for biomolecular design. You will define and deliver pragmatic AI strategies, oversee method and platform development, and ensure rigor in model development, benchmarking, and scaling.

Responsibilities:

- Program Leadership: Lead development, implementation, control, and reporting of several AI/ML or computational projects within assigned ventures in line with broader strategic plans of PI and Flagship, budgets, and timelines.

- Technical Ownership: Take a specialized technical role on project teams to oversee method development, pipeline development, and LLM based agent/workflow design; drive benchmarking, scaling, and implementation into production grade systems.

- Best Practices: Promote operational excellence in AI projects by educating cross-functional collaborators.

- Team Leadership: Manage and/or coordinate internal scientists and engineers and cross functional project teams as applicable; mentor early hires; support recruiting and interview.

- Planning & Resourcing: Contribute to project planning, including budgets, resources, and timelines; surface risks and tradeoffs early with clear options.

- Landscape & Strategy: Independently scout emerging literature and the AI/ML landscape; synthesize concepts to propose new development strategies and identify opportunities for PI and venture portfolios.

Must-have Qualifications:

- MSc or PhD in Computer Science, AI/ML, Physics, Biophysics, or a related field

- 7+ years of experience scientific/engineering/computational in Pharma or Biotech settings; industry AI/ML experience preferred

- Experience driving results directly or indirectly through teams of engineers/scientists in dynamic, fast paced, entrepreneurial, and technical environments.

- Clear evidence of sustained independent thought and creativity driving high impact, across drug development and chemistry AI/ML projects.

- Successful track record of leadership and contribution to decision making on progression of AI/ML models within projects or programs.

- Depth across multiple core tools and concepts, including Python; modern ML frameworks (PyTorch or JAX/TensorFlow); version control; databases; deep learning architectures; and relevant informatics software.

- Consistent record of outstanding performance reflected in publications, patents, or high impact internal reports where applicable

Preferred Experience:

- Breadth across domains such as protein modeling/design, cheminformatics/docking/ADMET, biophysics/MD, and LLM/agentic automation.

- Strong presence in the ML community through publications and conference proceedings.

- MLOps expertise: data contracts and lineage (e.g., DVC/LakeFS), experiment tracking (MLflow/W&B), secure AWS infrastructure (S3, Batch/ECS/EKS, SageMaker), Docker, IaC (Terraform/CDK), and CI/CD (GitHub Actions).

- Generative modeling (diffusion/flow/VAEs) for sequences, graphs, or 3D structures; docking rescoring (e.g., gnina, DiffDock) and pose quality metrics.

- Workflow orchestration (Airflow/Prefect/Argo), data warehouses (Redshift/Snowflake), vector search (FAISS/pgvector), and lightweight internal tools (FastAPI, Streamlit/Gradio).

- Familiarity with ML software development and cloud services (Docker, AWS Batch, Step Functions, EKS, AWS ParallelCluster, etc.)

- Experience with libraries like: rdkit, rosetta, prody, biopython, pymol, openmm, dagster, prefect, etc.

- Experience mentoring early hires, acting as interim Head of ML, and contributing to hiring plans and interview processes at startups.

The salary range for this role is $279,000 - $412,500. FL117 currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits.

## Skills

### Required
- Python
- modern ML frameworks (PyTorch or JAX/TensorFlow)
- version control
- databases
- deep learning architectures
- informatics software

### Nice to have
- breadth across domains such as protein modeling/design, cheminformatics/docking/ADMET, biophysics/MD, and LLM/agentic automation
- strong presence in the ML community through publications and conference proceedings
- MLOps expertise
- generative modeling
- workflow orchestration
- data warehouses
- vector search
- lightweight internal tools
- familiarity with ML software development and cloud services
- experience with libraries like: rdkit, rosetta, prody, biopython, pymol, openmm, dagster, prefect

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