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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 develop and advance foundation models that capture biological networks driving cellular dysfunction and integrate diverse perturbation modalities to accelerate drug discovery. This role involves hands-on development of large-scale models for high-dimensional biological data, with a focus on perturbation modeling.

The work requires strong expertise across deep learning, cell biology and computational biology. 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

  • Design and implement novel algorithms and architectures for large-scale foundation models (e.g. Diffusion models, Transformers, VAEs) using single-cell RNA-seq and other modalities.
  • Develop mechanistic interpretability methods to infer gene networks and regulatory mechanisms via attention, graph-based, and/or causal representation methods.
  • Build state-of-the-art perturbation models using multi-modal perturbation (small molecules, CRISPR, cytokines) and phenotypic data.
  • Pre-train, post-train and deploy generative AI models using proprietary datasets, and distributed training and inference on cloud platforms.
  • Establish clinically relevant benchmarking and evaluation frameworks to assess context generalization and guide model improvements.
  • Stay current with the latest research in foundation models, representation learning (across biology, NLP, vision, and audio), and perturbation modeling.

  Scientific Collaboration

  • Collaborate with interdisciplinary scientists from biology, chemistry, and technology teams to translate research questions into cutting-edge ML solutions.
  • Communicate technical concepts clearly to diverse scientific audiences.
  • Contribute to strategic roadmap planning and technical decisions.

What experiences will you need:

• PhD in Computer Science, Computational Biology, or related field, OR Master's degree with 3+ years of relevant ML research or industry experience.
• Strong foundation in statistics, deep learning and generative AI.
• Proficient in Python and scalable ML frameworks (e.g. PyTorch, Hugging Face)
• 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 (eg: Perturb-seq).
• Experience developing deep generative models for representation learning.
• Excellent communication skills and ability to work in interdisciplinary teams.

What sets you apart:

• Experience efficiently training and fine-tuning foundation models on omics data.
• Experience with cloud computing (AWS/GCP) and MLOps best practices.
• Experience with self-supervised learning, contrastive learning, domain adaptation and/or reinforcement learning.
• Knowledge of ML algorithms for network inference.
• Ability to work in a fast-paced, multidisciplinary, biotech environment.

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’s mission is to fundamentally redesign the way drugs are created for the sake of bringing new hope to patients.  By shifting the focus from a single target to the underlying cellular dysfunction, we unravel the complexity of disease biology and create medicines that were never before possible. The company has developed unique capabilities that link biology and chemistry with high dimensional -omic data from which we design medicines against the cellular signature of disease. The Cellarity platform allows us to uncover new biology in diseases even in the absence of known causal targets. 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. 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.