Job Title: Machine Learning Engineer
Job Duties: Analyze NGS and genomic datasets, including metagenomic sequences, amplicon sequencing, RNA-seq, scRNAseq, and Perturb-seq, to generate new biological discoveries and insights. Design and implement bespoke analysis pipelines of genomic and NGS data. Develop, test, and maintain modular software pipelines to answer biological questions and evaluate new bioengineering tools. Build and curate large databases of relevant biological sequence data. Document code and processes using tools like Jupyter/RMarkdown notebooks, Python/R packages, Nextflow pipelines, and git/GitHub. Communicate analysis results to both experimental scientists and computational scientists effectively. Design and apply bioinformatics algorithms including unsupervised and supervised machine learning, dynamic programming, or graphic algorithms. Actively participate in the design, implementation, and refinement of state-of-the-art foundation models developed in collaboration with other ML researchers and scientists at Arc with the goal of understanding and designing complex biological systems. Engineer large-scale distributed model pretraining and pipelines for efficient model inference. Provide statistical and computational tools for biologically based activities, such as genetic analysis, measurement of gene expression, or gene function determination. Enable robust systematic evaluation of trained models. Stay up-to-date with the latest advancements in technologies for large-scale sequence modeling and alignment, and implement the most promising strategies to ensure the underlying models remain state-of-the-art. Manipulate publicly accessible, commercial, or proprietary genomic, proteomic, or post-genomic databases. Work with experimental biologists to ensure that the developed models are grounded in biologically meaningful problems and evaluations. Develop new software applications or customize existing applications to meet specific scientific project needs. Publish findings through journal publications, white papers, and presentations (both internal and external). Consult with researchers to analyze problems, recommend technology-based solutions, or determine computational strategies. Foster internal and external collaborations centered on generative design of biological systems at Arc Institute. Communicate research results through conference presentations, scientific publications, or project reports. Commit to a collaborative and inclusive team environment, sharing expertise and mentoring others. 
Minimum Requirements: Master’s degree or foreign degree equivalent in Biology, Computational Biology, Computer Science, Machine Learning, or a related field and three years of experience in machine learning research or machine learning engineering in an academic or industry research lab. Experience must include experience in each of the following:
•    Three (3) years of experience in machine learning frameworks such as PyTorch or JAX.
•    Three (3) years of experience with developing machine learning models, leveraging tools such as distributed training, DDP, FSDP, DeepSpeed or Megatron-LM.
•    Three (3) years of experience communicating and collaborating with biologists and software/infrastructure engineers.
•    Three (3) years of experience working in a fast-paced, multi-disciplinary, and highly collaborative research environment.

In the alternative, employer will accept a bachelor’s degree or foreign degree equivalent in Biology, Computational Biology, Computer Science, Machine Learning, or a related field and five (5) years of experience in machine learning research or machine learning engineering in an academic or industry research lab., including experience in each of the following: 
•    Three (3) years of experience in machine learning frameworks such as PyTorch or JAX.
•    Three (3) years of experience with developing machine learning models, leveraging tools such as distributed training, DDP, FSDP, DeepSpeed or Megatron-LM.
•    Three (3) years of experience communicating and collaborating with biologists and software/infrastructure engineers.
•    Three (3) years of experience working in a fast-paced, multi-disciplinary, and highly collaborative research environment.
 Experience may be gained concurrently.

Position full-time, 40 hours per week, with Arc Research Institute dba Arc Institute, located in Palo Alto, CA.  Hybrid worksite/may telecommute part of week.
Apply by emailing resume to jobs@arcinstitute.org.  Must reference Job#: 492026

SALARY: Base salary range for this position is $214,000 - $262,000. These amounts reflect the range of base salary that the Institute reasonably would expect to pay a new hire or internal candidate for this position. The actual base compensation paid to any individual for this position may vary depending on factors such as experience, market conditions, education/training, skill level, and whether the compensation is internally equitable, and does not include bonuses, commissions, differential pay, other forms of compensation, or benefits. This position is also eligible to receive an annual discretionary bonus, with the amount dependent on individual and institute performance factors.

Posted: 05/14/2026