Senior Machine Learning Scientist, Multimodal & Relational Foundation Models

What You Will Contribute To Altos

As part of our team, you will help to accelerate and optimize our progress in developing unified, multi-modal generative foundation models for multiscale biology. You will be an integral part of our multidisciplinary teams building the computational platforms that will enable Altos to achieve its mission.

In this role, you will partner and collaborate with other multidisciplinary Scientists and Engineers across the Institute of Computation to design, build, and scale state-of-the-art foundation models that tackle biological questions and aid in the discovery of novel interventions for aging and disease. You will focus on the synthesis of unstructured multimodal signals with the structured relational data and knowledge graphs that represent biological reality.

The successful candidate will thrive in a fast-paced environment that stresses teamwork, transparency, scientific excellence, originality, and integrity.

Responsibilities

As a Staff Machine Learning Scientist, you will use your experience to focus on designing, developing, and evaluating state-of-the-art foundation models, at scale, to benefit the research.

• Pre-train and fine-tune large-scale machine learning systems using multimodal biological data, natural language, and structured relational inputs.   
• Architect and implement novel hybrid models that integrate Large Language Models (LLMs) with Graph Neural Networks (GNNs) for multi-hop reasoning over biological knowledge graphs .
• Develop Relational Foundation Models (RFMs) that enable zero-shot predictive tasks over heterogeneous, multi-table biological datasets.   
• Lead the design of efficient data loading strategies and distributed training recipes (e.g., FSDP, DeepSpeed) to train models across multiple GPU nodes.   
• Gain insights into model performance based on theory, deep research, and the mathematical underpinnings of set-invariant and graph-structured architectures .
• Apply strong coding experience to model development and deployment, ensuring research prototypes transition into reliable, scalable production systems.
• Stay up-to-date on the latest developments in deep learning—including native early-fusion and Mixture-of-Experts (MoE) architectures—and apply this knowledge to Altos' research .
• Mentor junior staff while maintaining a high individual technical contribution to the core research ecosystem and peer-reviewed publications.

Who You Are  

We are looking for someone who is:

• Excited about the Altos mission of restoring cell health and resilience to reverse disease, injury, and age-related disabilities.
• Highly collaborative in mindset and ways of working across research and engineering boundaries.
• Self-motivated to drive and deliver on long-term technical projects and scientific goals.
• Demonstrates the desire to grow professionally and expand their skillset in biology, machine learning, and/or drug development.
• Able to communicate and explain the design, results, and impact of complex AI architectures to both scientific and non-scientific staff.
• Keen to contribute to seminars and scientific initiatives within Altos and the broader AI research community.

Minimum Qualifications

• PhD in Computer Science, Machine Learning, or a similar quantitative field with 5+ years of relevant work experience in academic or industry settings.
• Prior experience in developing and implementing novel generative AI models, specifically in multimodal integration, GraphRAG, or relational deep learning .
• Deep understanding of Machine Learning principles and how they apply to diverse architectures like Transformers, GNNs, and diffusion models .
• Very strong programming skills in Python and deep learning libraries (e.g., PyTorch, JAX, Hugging Face Transformers/Accelerate).   
• Proven experience with multi-GPU and distributed training at scale (e.g., DDP, FSDP, DeepSpeed, Megatron, or Ray).   
• Strong track record of published, peer-reviewed innovative AI/ML research at top-tier conferences (NeurIPS, ICML, ICLR, CVPR).

Preferred Qualifications

• Familiarity with tabular foundation models (e.g., TabPFN) and in-context learning strategies for structured data .
• Specific experience in native multimodal modeling (early-fusion) or the synthesis of LLMs and Knowledge Graphs .
• Track record of ML applied to biological data, such as NGS data (RNA-seq, ATAC-seq), biological imaging (microscopy, IF), or spatial transcriptomics.
• Experience in optimizing large-scale inference via quantization, distillation, or memory-efficient attention mechanisms.

The salary range for Redwood City, CA:

• Senior Scientist I, Machine Learning: $270,600 - $330,000

The salary range for San Diego, CA:

• Senior Scientist I, Machine Learning: $251,700 - $307,000

Exact compensation may vary based on skills, experience, and location.

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- Please click here to read the Altos Labs EU and UK Applicant Privacy Notice (bit.ly/eu_uk_privacy_notice)
- This Privacy Notice is not a contract, express or implied and it does not set terms or conditions of employment.