--- title: 'ML Research Engineer, Foundation Models (Senior / Staff / Principal) at Genesis Molecular AI' canonical: 'https://feeny.ai/job/ml-research-engineer-foundation-models-senior-staff-principal-genesis-molecular-7ky449yvkh2y' type: 'job' last_seen: '2026-09-07' --- # ML Research Engineer, Foundation Models (Senior / Staff / Principal) at Genesis Molecular AI - **Company:** Genesis Molecular AI - **Location:** San Mateo, CA - **Employment:** full-time - **Work type:** hybrid - **Posted:** 2025-07-30 - **Last confirmed live:** 2026-09-07 - **Apply:** https://jobs.ashbyhq.com/genesis-molecular-ai/fbca4380-dc17-4b90-acf3-cf4b105cbc0d ## Job description ML Research Engineer, Foundation Models ## About the Team Join a world-class team at the forefront of AI and biochemistry. At Genesis Molecular AI, we’re a tight-knit team of proven deep learning researchers, software engineers, and drug discovery pioneers. Our shared mission is nothing short of revolutionary: to forge the next generation of AI foundation models that unlock new therapies for patients with severe diseases. We conduct fundamental research at the intersection of machine learning, physics, and computational chemistry, pushing the boundaries of each field. The Genesis AI team is building the engine for this revolution. We develop large-scale generative models trained across the full spectrum of molecular data, supported by extensive compute infrastructure and simulation pipelines. The work sits at the intersection of machine learning research, structural biology, and computational chemistry, requiring deep technical rigor and strong interdisciplinary collaboration. ## About the Role This role is for a highly skilled ML Research Engineer who thrives at the intersection of fundamental research and production-grade engineering. As a core member of the Genesis AI team, you will serve as the engineering pillar for inventing, scaling, and shipping our next generation of foundation models for molecular science. You will partner closely with ML researchers, computational chemists, and drug discovery scientists to translate cutting-edge model ideas into systems that power real drug discovery programs. Your work may involve: - Scaling model pretraining pipelines - Advancing reinforcement learning or post-training systems - Optimizing performance of large molecular models - Bringing structure prediction models like Pearl into production environments used by chemists and drug programs This role requires someone who can bridge ML and computational chemistry, translating between disciplines and helping teams move quickly from research insight to deployed capability. We are looking for someone who can own problems end-to-end, in a fast-moving research environment, translating novel ML ideas into systems that scientists can use in active discovery programs. Positions are available at various levels of seniority: Senior, Staff, and Principal. You Will - Drive the R&D and scaling of our foundation models, taking ownership of the engineering and experimentation for key research initiatives. - Make cutting-edge foundation model research a reality at scale. Implement, optimize, and build novel foundation models from the initial research prototypes to high-performance production models. - Optimize performance of large-scale ML systems, including distributed training, inference efficiency, and GPU-level optimizations where necessary. - Constantly engage with deep learning literature, building upon novel architectures and training methods to create new capabilities. - Bridge machine learning research and computational chemistry workflows, working closely with computational chemists, structural biologists, and medicinal chemists to ensure models translate effectively into real drug discovery programs. - Help productionize Pearl and related structure prediction models, enabling reliable deployment and integration into Genesis’ internal and partner drug discovery pipelines. - Own the experimental lifecycle with scientific rigor. You'll design experimental plans, own their execution on our large-scale compute infrastructure, and drive the deep analysis of results to inform the next research cycle and to validate most promising approaches. - Ship state-of-the-art models to production, - Collaborate intensely. Work closely with the broader team to integrate your models into our drug discovery platform. - Mentor and guide other researchers and engineers, fostering a culture of high-quality code, rigorous experimentation, and continuous innovation. - Contribute to the global research community by publishing some of your work and representing Genesis at top tier AI/ML conferences and workshops. ## Who You Are - 2+ years industry experience of building complex ML systems. - A research engineer with deep ML rigor. You have deep expertise in building scalable, high-performance foundation models, pretraining, and posttraining methods, and systems around them. - A builder who ships. You write clean, high-performance code and are comfortable working across the ML stack (Python, PyTorch, distributed training systems). You have demonstrated experience translating research into working systems quickly. - An expert in modern ML engineering. You understand the mathematics and systems behind modern ML methods. You can design, optimize, and implement novel modeling approaches. - Experienced in training models at scale. You understand distributed training, large-scale datasets, and performance optimization across GPU clusters. You thrive in environments where models move rapidly from prototype to production. - Experience with GPU systems programming Hands-on experience writing CUDA kernels or optimizing GPU workloads beyond standard frameworks. - Hands-on experience with our core libraries: PyTorch, PyTorch Lightning, and Ray Distributed Training, PyTorch Geometric, etc. - Comfortable in research ambiguity. You can iterate on novel architectures, training pipelines, and experimental ideas while maintaining rigorous engineering discipline. - A first-principles thinker. You approach problems from fundamentals and take pride in building robust systems from conceptual design to state-of-the-art implementation. - A curious mind, excited to dive into the emerging field at the intersection of AI, physics, chemistry, and biology and make foundational contributions and discoveries. Inspired by our culture of intellectual curiosity and the shared belief that breakthroughs happen when diverse perspectives and minds unite. - A strong cross-functional collaborator. You communicate effectively with scientists across disciplines including computational chemistry, structural biology, and medicinal chemistry. - No prior biology or chemistry experience is required, though curiosity and willingness to learn are essential. Nice to haves - Experience with novel research in one or more of the following domains: LLMs, diffusion, reinforcement learning or other cutting edge generative or predictive machine learning models. - Computational chemistry or drug discovery systems Especially experience related to protein-ligand structure prediction, small-molecule modeling, or computational drug discovery workflows. - Generative modeling methods Diffusion models or other generative architectures applied to scientific or molecular problems. - LLM post-training techniques Experience with SFT, RLHF, synthetic data pipelines, or other post-training systems. - Performance engineering Experience with Triton kernels, TensorRT, quantization, or large-scale model serving. - Publications in top-tier ML venues NeurIPS, ICML, ICLR, or similar. - Experience with ML frameworks used at Genesis PyTorch, PyTorch Lightning, Ray Distributed Training, PyTorch Geometric, or related systems. - Advanced degree MS or PhD in machine learning, computer science, computational science, or equivalent research/engineering experience. ## What we offer - Competitive compensation package that includes salary and equity. - Comprehensive health benefits: Medical, Dental, and Vision (covered 100% for the employees). - 401(k) plan. - Open (unlimited) PTO policy. - Free lunches and dinners at our offices. - Paid family leave (maternity and paternity). - Life and long- and short-term disability insurance. ## About Genesis Molecular AI Genesis Molecular AI http://genesis.ml is pioneering foundation models for molecular AI to unlock a new era of drug design and development. Our generative and predictive AI platform, GEMS (Genesis Exploration of Molecular Space), integrates AI and physics into industry-leading models to generate and optimize drug molecules, including the breakthrough generative diffusion model Pearl https://www.businesswire.com/news/home/20251028030745/en/Genesis-Molecular-AI-Unveils-Pearl-a-Field-Leading-Foundation-Model-that-Achieves-Unprecedented-Performance-in-Drug-Protein-Structure-Prediction for structure prediction. Genesis is backed by premier AI and life science investors, including a16z, NVIDIA, Rock Springs Capital, Menlo Ventures, T. Rowe Price, Fidelity, and Radical Ventures. Genesis has also signed category-leading AI-pharma deals, the most recent of which was a significant expansion with Incyte (see coverage in Forbes https://www.forbes.com/sites/innovationrx/2026/05/20/inside-incytes-120-million-ai-for-drug-development-deal/ and GEN https://www.genengnews.com/topics/artificial-intelligence/small-molecules-to-big-partnership-incyte-genesis-expand-ai-collaboration-to-1b/) with a total potential deal value of several billion dollars. Genesis is headquartered in San Mateo, CA, with a fully integrated laboratory in San Diego. We are proud to be an inclusive workplace and an Equal Opportunity Employer. ## About Genesis Molecular AI ## Company Overview - **One-liner**: Genesis Molecular AI combines frontier AI research with deep drug discovery expertise to develop a proprietary platform (GEMS) that accelerates the design and optimization of small molecule medicines. - **Entity Type**: Private (Series B; raised over $300M in total funding) - **Headquarters**: Burlingame, California, United States (with a fully integrated laboratory in San Diego and offices in New York) - **Founded**: Not publicly disclosed (first major funding round – $200M Series B – closed in 2023) - **Founders**: Evan Feinberg Ph.D. (CEO, Co-founder) and Sergey Edunov (Co-founder); other key leaders include Will McCarthy (CTO) and Shifeng Pan Ph.D. (COO) ## Core Business - **Primary Industry**: Biotechnology – AI-powered small molecule drug discovery. - **Target Customers**: Large pharmaceutical partners (B2B) via platform collaborations, plus an internal pipeline of wholly owned drug programs. - **Mission/Purpose**: “Solving the hardest problems in drug discovery to change the landscape of medicine” by creating and scaling domain-specific AI models that integrate physics, chemistry, biology, and software. ## Products & Services - **[GEMS Platform](https://www.genesis.ml/)**: An AI operating system for molecular design. GEMS (Genesis Exploration of Molecular Space) integrates generative and predictive models to accelerate hit identification, lead optimization, and candidate selection. It is deployed for internal pipeline programs and major pharma collaborations. - **[Pearl Foundation Model](https://www.genesis.ml/about)**: A generative foundation model for biomolecular structure prediction (protein-ligand) that demonstrated field-leading performance. Built in collaboration with NVIDIA and trained on large-scale synthetic data. - **Internal Drug Pipeline**: Small molecule inhibitors targeting oncology (e.g., pan-mutant allosteric PIK3CA inhibitors) and immunology (e.g., inflammatory signaling pathways). Programs are in discovery stage approaching development candidate nomination. - **Platform Partnership Model**: “Forward-deployed engineers and scientists” work alongside pharma partners (Gilead, Incyte) to apply GEMS to their targets, with deal structures that include upfront payments, milestones, and data sharing that feeds back into model training. ## Market Standing - **Valuation/Market Cap**: Not disclosed. - **Key Metric**: Total funding raised >$300M (including $200M Series B in 2023 co-led by a16z, with participation from Fidelity, BlackRock, NVIDIA’s NVentures, Rock Springs Capital, T. Rowe Price, Radical Ventures, Menlo Ventures). - **Notable Investors/Partners**: Andreessen Horowitz, Fidelity, BlackRock, NVIDIA (NVentures), Rock Springs Capital, T. Rowe Price, Radical Ventures, Menlo Ventures. Pharma partners: Gilead ($35M upfront, 2024), Incyte ($150M total upfront including equity investment, 2025–2026). - **Growth Signals**: 125 employees (+26.4% YoY); operates in 7 countries; LinkedIn following grew 41.9% in the past year; Pearl model launched to strong benchmarking results; Incyte expanded collaboration with at least 5 additional targets and data for model training. ## Competitive Advantages - **Integration of disciplines**: The company pairs leading AI researchers with world-class drug hunters, co-creating models and medicines in iterative loops. - **Wet-lab flywheel**: In-house lab in San Diego generates experimental data that closes the loop for model training, prediction, and validation – a virtuous cycle that strengthens the platform with every program. - **Partnership data advantage**: Deals with Gilead and Incyte provide significant proprietary experimental data (e.g., Incyte data for training GEMS), creating a moat that is hard for pure-play AI companies to replicate. - **Domain-specific foundation models**: Models like Pearl are purpose-built for small molecule drug discovery, unlike general-purpose generative AI. ## Strategic Focus - **Advancing internal pipeline**: Moving lead programs in oncology (PIK3CA, apoptosis) and immunology toward development candidate nomination. - **Scaling platform partnerships**: Expanding existing collaborations and signing new ones to broaden the impact of GEMS and generate more training data. - **Continuous model improvement**: Investing in next-generation foundation models (e.g., Pearl) and leveraging partner data to stay at the frontier of molecular AI. - **Hiring across AI and drug discovery**: Open roles for machine learning research scientists, software engineers, computational chemists, medicinal chemists, and biologists indicate a focus on scaling both the tech and biology teams. ## Why Work Here - **Culture**: Described as a “meritocracy of ideas” where the strongest ideas win through evidence and reasoning, not hierarchy. Values include ownership, experimentation, candor with kindness, curiosity, and collaboration across disciplines. - **Work Environment**: Flexible work environment with offices in Burlingame, San Diego, and New York. Daily meals and snacks provided in the office. Ergonomic consulting and equipment available. - **Compensation & Benefits**: Highly competitive compensation including base salary, bonus, and equity. Comprehensive health, dental, and vision insurance. Open PTO policy, parental leave, 401(k) retirement savings, financial planning resources. - **Impact**: Employees work on some of the hardest problems in drug discovery – applying cutting-edge AI to targets that are canonically undruggable, with the potential to create new treatment options for severe diseases. - **Team Composition**: The company actively hires across AI research, software engineering, molecular simulation, and drug discovery disciplines, fostering an interdisciplinary environment where researchers and drug hunters co-create daily. ## Sources 1. [genesis.ml](https://www.genesis.ml/) 2. [genesis.ml/about](https://www.genesis.ml/about) 3. [genesis.ml/careers](https://www.genesis.ml/careers) 4. [genesis.ml/partners-pipeline](https://www.genesis.ml/partners-pipeline) 5. [LinkedIn - Genesis Molecular AI](https://www.linkedin.com/company/genesis-molecular-ai) ## Other roles at Genesis Molecular AI - [Contract Recruiting Coordinator](https://feeny.ai/job/contract-recruiting-coordinator-genesis-molecular-ai-new-york-jp3t2jz8ff95) — New York, NY / San Francisco, CA - [Manager, New Product Planning](https://feeny.ai/job/manager-new-product-planning-genesis-molecular-ai-san-diego-s9gybtg3hfg8) — San Diego, CA - [ML & Molecular Simulation Scientist](https://feeny.ai/job/ml-molecular-simulation-scientist-genesis-molecular-ai-san-mateo-z7qx94p0vrzb) — San Mateo, CA - [Applied ML Scientist (Staff / Principal)](https://feeny.ai/job/applied-ml-scientist-staff-principal-genesis-molecular-ai-san-mateo-ypytjf6pxab2) — San Mateo, CA - [Staff Technical Recruiter](https://feeny.ai/job/staff-technical-recruiter-genesis-molecular-ai-san-mateo-t76m4py49wex) — San Mateo, CA - [Fullstack Software Engineer (Senior / Staff)](https://feeny.ai/job/fullstack-software-engineer-senior-staff-genesis-molecular-ai-san-mateo-pap6516adm11) — San Mateo, CA - [Software Engineer - Core Infrastructure](https://feeny.ai/job/software-engineer-core-infrastructure-genesis-molecular-ai-san-mateo-sgbtcj4j76d4) — San Mateo, CA - [Machine Learning Infrastructure Engineer](https://feeny.ai/job/machine-learning-infrastructure-engineer-genesis-molecular-ai-san-mateo-a012z1zdp33y) — San Mateo, CA - [Product Management Lead](https://feeny.ai/job/product-management-lead-genesis-molecular-ai-san-mateo-qv16q5s8c4q2) — San Mateo, CA - [ML Research Scientist, Foundation Models (Senior / Staff / Principal)](https://feeny.ai/job/ml-research-scientist-foundation-models-senior-staff-principal-genesis-gnpr61e1bf7n) — San Mateo, CA