ML Scientist, Biomolecular Foundation Models

<p><strong>THE ROLE</strong></p> <p>FL117, a venture-back stealth AI x bio startup, is seeking a highly skilled <strong>ML Scientist.</strong> Here you will build out the architectures, training pipelines and overall development of next-gen multi-modal generative models for biomolecular design. We are looking for those excited to work on ambitious projects in a fast-paced environment to push the frontier of AI-powered drug discovery.</p> <p><strong>KEY RESPONSIBILITIES</strong></p> <ul> <li>Spearhead the design and development of cutting-edge deep learning models aimed at advancing generative biomolecular design.</li> <li>Design novel representation and tokenization of biomolecules to enable more efficient transfer learning</li> <li><strong>Own and establish a robust research infrastructure.</strong></li> </ul> <p><strong>PROFESSIONAL EXPERIENCE &amp; QUALIFICATIONS</strong></p> <ul> <li>MSc or PhD in Computer Science, AI/ML, Physics, Biophysics, or a related field</li> <li>2+ years of internship/full-time industry or postdoctoral ML research experience</li> <li>2+ years of experience developing production-grade machine learning solutions</li> <li>Experience training large-scale generative (transformer/diffusion) models on HPC or multi-GPU, multi-node distributed systems</li> <li>Proficiency in Python and relevant ML libraries (PyTorch or TensorFlow)</li> <li>Proven ability to lead technical initiatives, communicate progress, and drive innovation in generative biomolecular design</li> </ul> <p><strong>Preferred Experience:</strong></p> <ul> <li>Contributed to open-source data projects in biology/chemistry. Please send us your GitHub, if applicable.</li> <li>Strong presence in the ML community through publications and conference proceedings. Please send a list of publications, if applicable.</li> <li>Knowledge of biological data formats (FASTA, SDF, PDBx/mmCIF) and domain-specific ontologies/metadata standards</li> <li>Experience with models like ESM, DiffDock, ProteinMPNN, OpenFold, etc.</li> <li>Familiarity with ML software development and cloud services (Docker, AWS Batch, Step Functions, EKS, AWS ParallelCluster, etc.)</li> <li>Experience with librariers like: rdkit, rosetta, prody, biopython, pymol, openmm, dagster, prefect, etc.</li> </ul> <p><strong>ABOUT FLAGSHIP PIONEERING</strong></p> <p>Flagship Pioneering invents and builds platform companies, each with the potential for multiple products that transform human health, sustainability and beyond. Since its launch in 2000, Flagship has originated more than 100 companies. Many of these companies have addressed humanity’s most urgent challenges: vaccinating billions of people against COVID-19, curing intractable diseases, improving human health, preempting illness, and feeding the world by improving the resiliency and sustainability of agriculture.&nbsp;&nbsp;</p> <p>Flagship has been recognized twice on FORTUNE’s “Change the World” list, an annual ranking of companies that have made a positive social and environmental impact through activities that are part of their core business strategies and has been twice named to Fast Company’s annual list of the World’s Most Innovative Companies. Learn more about Flagship at&nbsp;<a href="https://nam12.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.flagshippioneering.com%2F&amp;data=05%7C02%7Cemccurdy%40flagshippioneering.com%7C8e54295c994c4d440a7b08ddc94a4a72%7Cd00b8682fc8b4548b82dda0524788e9b%7C0%7C0%7C638888043086011906%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C0%7C%7C%7C&amp;sdata=gknIK%2BmYfQpsSi0%2FyQmhzNBo4DurYfmbUQpruIKf6Mc%3D&amp;reserved=0">www.flagshippioneering.com</a>.</p> <p>At Flagship, we accept impossible missions to enable bigger leaps. Our <a href="https://www.flagshippioneering.com/values">core values</a> guide us through uncertainty and toward lasting impact.</p> <p>&nbsp;</p> <p><strong>We are an equal opportunity employer</strong>. All qualified applicants will be considered for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, protected veteran status, or any other characteristic protected by law.</p> <p>We recognize that great candidates often bring unique strengths <strong>without fulfilling every qualification</strong>. If you have some of the experience listed above but not all, please apply anyway. We are dedicated to building diverse and inclusive teams and look forward to learning more about your background<strong> and interest in Flagship.</strong></p> <p><strong><em>Recruitment &amp; Staffing Agencies</em></strong><em>: Flagship Pioneering and its affiliated Flagship Lab companies (collectively, “FSP”) do not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to FSP or its employees is strictly prohibited unless contacted directly by Flagship Pioneering’s internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of FSP, and FSP will not owe any referral or other fees with respect thereto.</em></p> <p>#LI-MB1</p>