{"id":227953,"url":"https://alion.io/job/flagship-pioneering-senior-scientist-machine-learning","title":"Senior Scientist, Machine Learning","company":{"id":8393,"name":"Flagship Pioneering","domain":"flagshippioneering.com","url":"https://alion.io/company/flagshippioneering","size_band":"1001-5000","is_staffing_agency":false,"employer_type":"direct","is_intermediary":true,"listed_via":null,"ats_vendor":"Greenhouse","truth_index":{"grade":"B","score":79,"open_postings":10,"ghost_share":0,"stale_share":0.8,"repost_share":0.1,"time_to_fill_p50_days":50,"computed_at":"2026-10-29T05:49:05Z"}},"role":"Science & Research","role_family":"Science & Research","seniority":"senior","employment_type":null,"work_mode":"on_site","remote_scope":null,"remote_scope_basis":null,"remote_working_hours":null,"hiring_geo_confidence":"explicit","locations":["Cambridge, United States"],"countries":["US"],"hiring_countries":[],"hiring_countries_total":0,"salary":{"min":168000,"max":258500,"currency":"USD","period":"year","gross":null,"usd_annual":258500},"salary_estimate":null,"experience_years_min":5,"visa_sponsorship":false,"relocation_package":false,"has_equity":false,"technologies":[{"name":"Machine Learning","optional":false},{"name":"Fine-tuning","optional":true},{"name":"HPC","optional":true},{"name":"Python","optional":true}],"status":"live","first_seen_at":"2026-07-24T14:39:17Z","employer_posted_date":"2026-10-05","last_verified_at":"2026-10-29T11:17:22Z","board_verified":true,"closed_at":null,"days_open":97,"trust":{"level":"ok","repost_count":null,"flags":[],"days_open":97},"description":"What if… you could join an organization that creates, resources, and builds life sciences companies that invent breakthrough technologies in order to transform health care and sustainability? \nFlagship Labs 129 (FL129) is an early-stage biotechnology startup with an ambitious and exciting mission: to unlock the future of small molecule drug discovery. FL129 is developing a revolutionary approach to this challenge and is recruiting a team of top-tier scientists to build this powerful and first-in-category platform. This is a unique opportunity to be one of the first employees of a biotech startup that combines an innovative mindset with the resources and know-how of Flagship Pioneering. This is a hands-on role with substantial ownership for a scientist who is excited to set technical direction from day one and, over time, help build the team. \nPosition Summary: \nWe are seeking a motivated and highly collaborative Senior Scientist to join FL129’s growing team of experimental and computational scientists to build a novel platform technology. The successful candidate will have a strong track record of scientific and technical innovation in machine learning for molecular modeling, with hands-on experience across both proteins and small molecule ligands. Additional experience with computational docking methods is preferred. The ideal teammate will be highly adaptable, have strong organizational and communication skills, and will thrive in a highly collaborative and multidisciplinary environment. \nKey Responsibilities: \nTechnology development, aligned with FL129’s core strategic goals. This role is among the first hires, and we’re looking for someone who thinks critically and will influence the company’s scientific direction. \nDevelopment, training, validation, and application of novel molecular models \nCurate training and benchmark datasets, and design and implement rigorous benchmarks to assess model performance. \nOptimize existing workflows and establish best experimental and documentation practices to enable platform excellence. \nClose collaboration with wet lab scientific team to drive achievement of key project goals. \nTranslate experimental data into meaningful insights and present results at team meetings. \nPreferred Qualifications: \nPh.D. in machine learning, computational biology, or a similar field with 5+ years of industry or postdoctoral experience. \nFamiliarity with SOTA models such as Boltz-2, ESM-2, Chai-2 and related. \nExperience training and fine-tuning molecular models for tasks such as: protein language modeling, protein structure prediction, binder prediction, protein design, protein engineering, small molecule pose prediction, and related. \nExperience curating and harmonizing publicly available protein and small molecule datasets. \nExpertise with a high-level programming language such as Python and modern HPC and cloud compute workflows. \nNice to have: deep structural understanding of proteins and protein-ligand complexes, including holo (ligand-bound) conformations rather than apo structures alone. \nMotivated team-player and independent force-of-nature with strong organizational and written/verbal communication skills. \nWhat we can offer you: \nOpportunity to lay the scientific foundation of a transformative platform company as an early employee. \nCustom-tailored role to maximize impactful contributions, professional growth, and scientific interests. \nWeekly lunches, monthly social events, and community lunchroom with free snacks, coffee, all embedded in a vibrant community of scientists and entrepreneurs across multiple Flagship Pioneering portfolio companies. \nWe are seeking individuals with an entrepreneurial spirit, strong communication skills, and comfort in working in and contributing to a dynamic and cross-functional team environment. The level of the role will be commensurate with the education and years of experience of the identified candidates. \nFlagship Pioneering and our ecosystem companies are committed to equal employment opportunity regardless of race, color, ancestry, religion, sex, national origin, sexual orientation, age, citizenship, marital status, disability, gender identity or Veteran status. \nRecruitment & Staffing Agencies: 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\nPrivacy Notice for Applicants: When you apply for a role at Flagship Pioneering or one of its portfolio companies, we collect and use personal information you provide (such as your name, contact details, work history, and application materials) to evaluate your application, communicate with you, and comply with legal obligations. Your application data is processed through Greenhouse, our applicant tracking system, and may also be reviewed using AI-assisted screening tools. We do not sell your personal information. California residents have rights under the CCPA/CPRA including to know, delete, and opt out of the sharing of their personal information. If you are located in the EU or UK, we process your data under GDPR and you have rights to access, rectify, and erase your data. To exercise your rights or for questions, contact . \nThe salary range for this role is $168,000 - $258,500. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. FL129 currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on FL129's good faith estimate as of the date of publication and may be modified in the future.\nPrivacy Notice for Applicants: When you apply for a role at Flagship Pioneering or one of its portfolio companies, we collect and use personal information you provide (such as your name, contact details, work history, and application materials) to evaluate your application, communicate with you, and comply with legal obligations. Your application data is processed through Greenhouse, our applicant tracking system, and may also be reviewed using AI-assisted screening tools. We do not sell your personal information. California residents have rights under the CCPA/CPRA including to know, delete, and opt out of the sharing of their personal information. If you are located in the EU or UK, we process your data under GDPR and you have rights to access, rectify, and erase your data. To exercise your rights or for questions, contact .","description_format":"text","description_chars":6995,"description_truncated":false,"requirements":{"experience_years_min":5,"management_years_min":null,"team_size_min":null,"manages_managers":false,"education":{"level":"phd","optional":false},"security_clearance":false,"languages":[]},"benefits":[],"hiring_locations":[{"name":"United Kingdom","iso":"GB","kind":"country"}],"hiring_excludes":[],"relocation_offered":false,"industries":["Bioinformatics","Venture Capital"],"lifecycle":[{"event":"open","at":"2026-09-05T09:30:20Z"}],"visa":[{"country":"US","licensed_sponsor":true,"evidence":"H-1B filings in 12 months: 10 · green card filings: 2","filings_12m":10,"filings_prev_12m":3,"green_card_filings_12m":2,"median_offered_wage_usd":150833,"route":null,"cap_exempt":false,"checked_at":"2026-10-15T11:24:14+00:00","sources":["US Department of Labor: LCA disclosure data (H-1B, H-1B1, E-3)","US Department of Labor: PERM disclosure data (green cards)"],"filings_for_role_12m":0}],"liveness":{"score":17,"band":"cold","label":"Long shot","p_open":1,"p_active":0.468,"p_room":0.36,"age_days":96,"expected_fill_days":50,"reasons":["conf:3","stale_co","velocity","win:tail","crowd:"],"computed_at":"2026-10-29T05:49:05Z"},"pay":{"stated_usd_annual":258500,"is_top_pay":true},"html_url":"https://alion.io/job/flagship-pioneering-senior-scientist-machine-learning","json_url":"https://alion.io/job/flagship-pioneering-senior-scientist-machine-learning.json","meta":{"generated_at":"2026-10-29T15:24:43Z","cache_seconds":300,"methodology":"https://alion.io/methodology","terms":"https://alion.io/terms","contact":"https://alion.io/contact","api":"https://alion.io/developers","about":"Alion is a live layer of people, companies and AI agents: who they are, whether they are real and active right now, what they do and how to work with them, readable by people and by agents and paid per call.","catalog":"https://alion.io/catalog.json","usage":{"tier":"crawler_verified","counted_by":"address","units_charged":1,"used_today":23106,"day_limit":null,"remaining_today":null,"minute_limit":300,"resets_at":"2026-10-30T00:00:00Z"}},"offers":[{"id":"company.slices","title":"One company in depth, by slice","status":"live","price":{"credits":0.02,"usd":0.002,"plus_per_slice":{"credits":0.05,"usd":0.005}},"unit":"per company, plus each slice with data","note":"the employer in depth","call":{"mcp_tool":"get_company","arguments":{"id":8393},"rest":"https://alion.io/mcp/rest/get_company?id=8393"},"human":"https://alion.io/catalog?offer=company.slices&for=job%2Fflagship-pioneering-senior-scientist-machine-learning"},{"id":"market.stats","title":"A market slice: pay, demand and time to fill","status":"live","price":{"credits":1,"usd":0.1},"unit":"per slice","note":"pay, demand and time to fill for this role and place","call":{"mcp_tool":"market_stats"},"human":"https://alion.io/catalog?offer=market.stats&for=job%2Fflagship-pioneering-senior-scientist-machine-learning"},{"id":"job.search","title":"Open jobs by role, technology, place, pay and visa","status":"live","price":{"credits":0.02,"usd":0.002},"unit":"per posting in a list","note":"similar open postings","call":{"mcp_tool":"search_jobs"},"human":"https://alion.io/catalog?offer=job.search&for=job%2Fflagship-pioneering-senior-scientist-machine-learning"},{"id":"company.verify","title":"Is this company real and active right now","status":"pilot","price":null,"unit":"per company","request":{"url":"https://alion.io/catalog/request","method":"POST","body":"{\"offer\": \"company.verify\", \"for\": \"job/flagship-pioneering-senior-scientist-machine-learning\", \"note\": \"what you need it for\"}"},"human":"https://alion.io/catalog?offer=company.verify&for=job%2Fflagship-pioneering-senior-scientist-machine-learning"}],"agent":{"mcp":"https://alion.io/mcp/jobs","mcp_open":"https://alion.io/mcp/open","next":[{"tool":"get_job","arguments":{"id":227953}},{"tool":"search_jobs","arguments":{"company":"flagshippioneering.com","detail":"compact"}},{"tool":"match_people","arguments":{"job_id":227953},"note":"people open to offers who fit this vacancy"}],"note":"The same data through MCP tools: https://alion.io/mcp/open needs no sign-in (compact searches, postings, people); https://alion.io/mcp with an Alion account has everything. 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