(Senior) Scientist, Multimodal Biological Reasoning

About Pioneering Intelligence Pioneering Intelligence builds on Flagship Pioneering’s legacy of founding cutting-edge science and computational ventures, harnessing recent advances in AI, machine learning, and data to accelerate fundamental research and create a portfolio of AI-first companies. As part of Flagship’s integrated model of science, entrepreneurship, and capital, it transforms breakthrough ideas into world-changing companies, elevating the AI advances happening across the ecosystem in human health, sustainability, and beyond. The Role Pioneering Intelligence is seeking a Senior Scientist for Flagship’s ambitious efforts to build polyintelligent AI systems that unify human scientific expertise, machine intelligence, and nature’s biological signals into multi-modal, multi-scale reasoning engines for biology. As a Senior Scientist, you will have the unique opportunity to shape our biological reasoning efforts on both the technical and application levels. You will be a key contributor on a team innovating on machine learning model architectures that will create best-in-class biological reasoning engines that tackle the unconventional life sciences problems that Flagship pursues. You will work with teams in Pioneering Intelligence and Flagship-at-large to apply our reasoning engines to discover new biology and engineer new biological solutions through massively parallel in-silico reasoning. Key Responsibilities Design technical architecture, training strategies, and evaluations for a multi-modal, multi-scale biological reasoning model. Train and validate large-scale biological reasoning models. Development and curation of novel biological datasets. Construct new datasets and benchmarks to empirically evaluate biological validity and generalization. Translate biological questions into well-defined ML problems, build and scale training data pipelines and model benchmarks for downstream applications. Contribute to the technical and product roadmap, data strategy and research priorities. Qualifications PhD in Computer Science, Machine Learning, Computational Biology, Systems Biology or related quantitative field (or Master’s with equivalent research experience). Strong machine learning and software engineering fundamentals. Experience handling and processing large scale biological datasets. Ability to work independently in an ambiguous environment, foster cross-team collaborations, and communicate externally. Demonstrated ability to work in cross-functional settings with scientists or biotech teams to bridge needs and technical implementation. Preferred Qualifications Experience pre-training, fine-tuning and/or post-training large foundation models (e.g. billion+ parameter LLMs or VLMs) or foundation models in biology (e.g. ESM, Evo2, Carbon, Nucleotide Transformer, UCE, CellFM, TranscriptFormer, etc.) Experience with multi-modal machine learning, particularly non-text modalities. High impact contributions in relevant venues, such as major product releases within a company, publications (NeurIPS, ICML, ICLR, Nature, Science, Cell, etc.), or open-source contributions in AI for Science. Experience with causal reasoning, especially as relevant to perturbation biology, pathways, and/or mechanism-of-action reasoning Fluency in at least one life science domain (molecular biology, genetics, biochemistry, cell biology, structural biology, biophysics, bioengineering, or related) Experience deploying AI/ML into scientific workflows at enterprise scale. Familiarity with distributed training infrastructure

ABOUT FLAGSHIP PIONEERING:

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. 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 At Flagship, we accept impossible missions to enable bigger leaps. Our core values guide us through uncertainty and toward lasting impact. We are an equal opportunity employer . 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. We recognize that great candidates often bring unique strengths without fulfilling every qualification . 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 and interest in Flagship. Recruitment & 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.

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The salary range for this role is $136,000 - $264,000. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. Pioneering Intelligence currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Pioneering Intelligence’s good faith estimate as of the date of publication and may be modified in the future. Privacy 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 your 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 View email address on click.appcast.io. #J-18808-Ljbffr Flagship Pioneering Co-Op Program