Machine Learning Scientist

Flagship Pioneering Co-Op Program; Somerville (MA); On-site; USD 132,000 - 209,000; Full time

Job summary

Cellarity seeks a Machine Learning Scientist to join our ML team and lead efforts in applying proprietary foundation models to enable predictive drug discovery. The role involves hands‑on modeling of high‑dimensional biological data and fine‑tuning state‑of‑the‑art models to support early drug discovery.

You will collaborate with biology, chemistry, and omics researchers in a highly interdisciplinary environment to drive AI-powered interventions and targets identification.

Qualifications

• PhD in Computer Science, Computational Biology, or related field, OR Master’s degree with 3+ years or Master’s or Bachelor’s degree with 6+ years of relevant ML research experience for drug discovery.
• Strong foundation in statistics, deep learning and generative AI.
• Experience with high-dimensional biological data analysis (bulk/single-cell RNA-seq, gene regulatory networks, PPI networks, multi-omics integration).
• Experience with chemical / CRISPR perturbation screen data (e.g., Perturb-seq), including analysis and modeling.
• Familiarity with single-cell foundation models (e.g., Geneformer, scGPT, scFoundation) and their downstream applications.
• Experience applying or fine‑tuning pretrained foundation models or deep generative models for downstream biological tasks.
• Experience with cloud computing (AWS/GCP) and MLOps best practices.
• Excellent communication skills and ability to work in interdisciplinary teams.

Responsibilities

• Model Development

Skills

Statistics foundation

Deep learning

Generative AI

Cloud computing

MLOps

Communication skills

Interdisciplinary teamwork

Education

PhD in Computer Science or Computational Biology

Tools

Geneformer

scGPT

scFoundation

Perturb-seq

Job description

What if you could join a rapidly growing company and play a critical role in bringing new medicines to patients through looking at and treating disease in a revolutionary way.

What this position is all about

We seek a Machine Learning Scientist to join our ML team and lead focused efforts in applying and adapting proprietary foundation models to enable Cellarity’s predictive drug discovery platform. As a lead ML Scientist the candidate will develop and apply AI methods to identify novel interventions and targets to accelerate early drug discovery.

This role involves hands‑on modeling of high‑dimensional biological data, leveraging and fine‑tuning state‑of‑the‑art foundation models, while enabling interpretability and biological reasoning. Ideal candidate will have demonstrated application of deep learning and computational biology to biological problems.

The successful candidate will work closely with researchers in biology, chemistry, and omics technology in a collaborative environment.

What you would be responsible for

• Model Development

What experiences will you need

• PhD in Computer Science, Computational Biology, or related field, OR Master’s degree with 3+ years or Master’s or Bachelor’s degree with 6+ years of relevant ML research experience for drug discovery.
• Strong foundation in statistics, deep learning and generative AI.
• Experience with high-dimensional biological data analysis (bulk/single-cell RNA-seq, gene regulatory networks, PPI networks, multi-omics integration).
• Experience with chemical / CRISPR perturbation screen data (e.g., Perturb-seq), including analysis and modeling.
• Familiarity with single-cell foundation models (e.g., Geneformer, scGPT, scFoundation) and their downstream applications.
• Experience applying or fine‑tuning pretrained foundation models or deep generative models for downstream biological tasks.
• Experience with cloud computing (AWS/GCP) and MLOps best practices.
• Excellent communication skills and ability to work in interdisciplinary teams.

What sets you apart

• Experience building agentic AI systems (e.g., LLM-based agents, tool use, multi‑step reasoning workflows) for scientific discovery or data analysis.
• Familiarity with target identification and prioritization in drug discovery.

What it’s like to work at Cellarity

At Cellarity, we

• Push Boundaries: We create a legacy with breakthrough science in service of patients.
• Inject Energy: We build strengths from different perspectives and tell it like it is
• Own it: We transcend our job descriptions and relentlessly follow through on our commitments.
• Go all out: We work quickly and with conviction.

Company Summary

Cellarity is a privately held, clinical‑phase drug discovery startup using AI and single‑cell omics to develop life‑changing medicines that are unreachable by traditional methods of drug discovery. Our pipeline spans multiple exploratory programs across different indications, offering broad opportunities to apply machine learning to diverse disease areas. Cellarity is a product of Flagship Pioneering’s venture creation engine, which has conceived and created companies such as Moderna (NASDAQ: MRNA), Generate:Biomedicines, and Lila Sciences.

Cellarity is 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.

Recruitment & Staffing Agencies : Cellarity does not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to Cellarity or its employees is strictly prohibited unless contacted directly by Cellarity’s internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of Cellarity, and Cellarity will not owe any referral or other fees with respect thereto.

Privacy Notice for Applicants

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The salary range for this role is $132,000 - $209,000. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. Cellarity currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Cellarity’s good faith estimate as of the date of publication and may be modified in the future.