Scientist /Senior Scientist, Multimodal & Relational Machine Learning Foundation Models

Altos Labs; San Francisco (CA); On-site; USD 200,900 - 257,500; Full time

Job summary

Altos Labs in San Francisco is seeking a Machine Learning Scientist to develop innovative AI models for biological data integration. The position involves working with multidisciplinary teams to pre-train systems and architect hybrid models. Candidates should hold a PhD and possess extensive experience in machine learning, particularly with deep learning frameworks like PyTorch. A collaborative mindset and a self-motivated approach to problem-solving are essential. Competitive salary range reflects expertise in the field.

Qualifications

• 5+ years of relevant work experience in academic or industry settings.
• Experience in developing AI models, specifically in multimodal integration.
• Strong understanding of diverse architectures like Transformers and GNNs.

Responsibilities

• Pre-train and fine-tune large-scale machine learning systems.
• Architect novel hybrid models for multi-hop reasoning.
• Develop Relational Foundation Models for predictive tasks.

Skills

Machine Learning

Python programming

Deep learning libraries

Collaborative mindset

Education

PhD in Computer Science or Machine Learning

Tools

PyTorch

JAX

Job description

Our Mission

Our mission is to restore cell health and resilience through cell rejuvenation to reverse disease, injury, and the disabilities that can occur throughout life.

Our Value

Our Single Altos Value: Everyone Owns Achieving Our Inspiring Mission.

Diversity at Altos

Altos Labs has been named one of the Top 3 Biotech Companies and ranked for the second year on the Forbes 2026 Best Startups in America list. At Altos, exceptional scientists and industry leaders from around the world work together to advance a shared mission. Our intentional focus is on Belonging, so that all employees know that they are valued for their unique perspectives. We are all accountable for sustaining a diverse and inclusive environment.

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

• 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

• 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:

• Scientist I, Machine Learning: $200,900 - $257,500
• Scientist II, Machine Learning: $226,200 - $290,000
• Senior Scientist I, Machine Learning: $257,400 - $330,000

The salary range for San Diego, CA:

• Scientist I, Machine Learning: $179,400 - $230,000
• Scientist II, Machine Learning: $212,900 - $273,000
• Senior Scientist I, Machine Learning: $239,500 - $307,000

For UK applicants, before submitting your application:

• 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.

Equal Opportunity Employment

We value collaboration and scientific excellence.

We believe that a culture of belonging are foundational to scientific innovation and inquiry. At Altos Labs, exceptional scientists and industry leaders from around the world work together to advance a shared mission. Our intentional focus is on Belonging, so that all employees know that they are valued for their unique perspectives. We are all accountable for sustaining an inclusive environment.

Altos Labs provides equal employment opportunities to all employees and applicants for employment, without regard to race, color, religion, age, sex, national origin, disability status, genetics, protected veteran status, sexual orientation, gender identity or expression, or any other characteristic protected by federal, state or local laws. Altos prohibits unlawful discrimination and harassment. This policy applies to all terms and conditions of employment, including recruiting, hiring, placement, promotion, termination, layoff, recall, transfer, leaves of absence, compensation and training.

Thank you for your interest in Altos Labs where we strive for a culture of scientific excellence, learning, and belonging.

Note: Altos Labs will not ask you to download a messaging app for an interview or outlay your own money to get started as an employee. If this sounds like your interaction with people claiming to be with Altos, it is not legitimate and has nothing to do with Altos. Learn more about a common job scam at https://www.linkedin.com/pulse/how-spot-avoid-online-job-scams-biron-clark/