Flagshippioneeringinc

Principal ML Scientist, Multimodal Biological Reasoning

Cambridge, MA USA · Principal

Sponsorship not specified$216k-$297kDetected 7 days ago

Machine LearningData ScienceLLMsComplianceRecruitingBioinformaticsResearch

About the role

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.

Responsibilities

Own the roadmap: lead the project from architecture and data exploration through model readiness, benchmarking, refinement, and agentic integration.
Guide technical architecture through a biological lens: guide multi-modal, multi-scale model design and ensure the system can ingest and reason over modalities relevant to mechanism-of-action reasoning, target discovery, perturbation biology, pathway reasoning, protein function, and autonomous discovery workflows.
Build the engine for a novel science platform: develop and integrate reasoning engines into Pioneering Intelligence's AI Scientist platform for autonomous science.
Source and shape portfolio use cases: interface with Flagship teams and portfolio company end-users to identify use cases, source data assets, define success criteria, and create end-user feedback loops for reasoning engines that are scientifically meaningful, tractable, and answer high-value questions with real world application.
lead the project from architecture and data exploration through model readiness, benchmarking, refinement, and agentic integration.
guide multi-modal, multi-scale model design and ensure the system can ingest and reason over modalities relevant to mechanism-of-action reasoning, target discovery, perturbation biology, pathway reasoning, protein function, and autonomous discovery workflows.
develop and integrate reasoning engines into Pioneering Intelligence's AI Scientist platform for autonomous science.
As Lead, you will have the unique opportunity to shape our biological reasoning efforts on both the technical and application levels.
You will have the opportunity to originate and lead multiple projects in this space over time.

Requirements

Experience in biotech, pharma, AI-for-science, AI drug discovery, venture creation, or a platform organization serving multiple scientific programs.
Experience deploying AI/ML for biology systems into scientific workflows at enterprise scale.
Experience with LLMs, biological foundation models, protein language models, genomic foundation models, scientific agents, or AI discovery platforms.
If you have some of the experience listed above but not all, please apply anyway.
Deep experience in computational biology, AI-for-biology, AI-enabled drug discovery, translational data science, biological foundation models, or scientific discovery platforms.
Demonstrated ability to work with scientists or biotech teams to scope high-value use cases, identify data assets, define success criteria, and translate discovery needs into technical execution plans.
Working knowledge of biological data modalities such as genomics, transcriptomics, perturbation data, protein sequence, protein structure, pathways, imaging, pathology, or time-series biological data.
Experience leading small, high-caliber technical teams through ambiguous scientific or product problems.
Ability to communicate clearly with ML researchers, data engineers, portfolio-company scientists, executives, and venture creation leaders.
Industry-leading expertise in modern LLMs, multimodal modeling, representation learning, fine-tuning, post-training, benchmarking, and ML systems.
Strong judgment around mechanism-of-action reasoning, target discovery, perturbation biology, scientific credibility, model limitations, hallucination risk, interpretability, and validation.
Comfort operating in an entrepreneurial environment where the goal is not only to build a model, but to create a new capability that can reshape company creation and scientific discovery.

Compensation

Pioneering Intelligence currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits.

Benefits

You will be a hands-on lead for a team of talented machine learning scientists innovating on model architectures that will create best-in-class biological reasoning engines.
Flagship Pioneering invents and builds platform companies, each with the potential for multiple products that transform human health, sustainability and beyond.
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.

Company info

interface with Flagship teams and portfolio company end-users to identify use cases, source data assets, define success criteria, and create end-user feedback loops for reasoning engines that are scientifically meaningful, tractable, and answer high-value questions with real world application.

Visa & Work Authorization

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