Machine Learning Engineer Visa Sponsorship Jobs in Colorado
Colorado's machine learning engineer job market centers on Denver, Boulder, and the Front Range tech corridor, with employers like Google, Palantir, and Lockheed Martin regularly hiring for ML roles. The state's aerospace, defense, and enterprise software industries drive consistent demand, and several companies have established H-1B visa sponsorship track records for machine learning positions.
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Get Access To All JobsCOMPANY DESCRIPTION
Flagship Pioneering is a bioplatform innovation company that invents and builds companies that change the world. We bring together the greatest scientific minds with entrepreneurial company builders and assemble the capital to allow them to take courageous leaps. Those big leaps in human health, sustainability and beyond exponentially accelerate scientific progress in areas ranging from disease detection and treatment and nature-positive agriculture to novel applications of AI that are driving the creation of new technologies. What sets Flagship apart is our ability to advance science and technology by uniting innovation, company creation, and capital investment under one roof in a way that is largely without precedent. Our scientific founders, entrepreneurial leaders, and professional capital managers are each aligned around an institutionalized process that enables us to innovate and transform for the benefit of people and planet. Many of the companies Flagship has founded have addressed humanity’s most urgent challenges: vaccinating billions of people against COVID-19, curing intractable diseases, improving human health, preempting illness, and feeding the world by improving the resiliency and sustainability of agriculture. Flagship has been recognized twice on FORTUNE’s “Change the World” list, an annual ranking of companies that have made a positive social and environmental impact through activities that are part of their core business strategies, and has been twice named to Fast Company’s annual list of the World’s Most Innovative Companies.
THE ROLE
We are seeking a Senior Machine Learning Scientist, Climate and Hydrology to lead the scientific direction and machine learning development for hydrology-aware climate modeling within our broader environmental modeling platform. This role sits at the intersection of hydrology, weather and climate science, and large-scale machine learning. The Sr. Scientist will help shape how hydrologic process understanding, climate data, and modern ML methods are brought together in next-generation prediction systems, with emphasis on scientifically grounded model development and evaluation. The individual in this role will work across science, ML, engineering, and data teams to define research priorities, guide model training and benchmarking, build reproducible workflows, and translate scientific insight into scalable model development. This is a cross-functional role requiring strong technical depth, structured scientific thinking, and the ability to move between foundational research and applied execution.
KEY RESPONSIBILITIES
- Lead scientific and technical efforts at the intersection of hydrology, climate science, and machine learning.
- Help define research priorities, modeling directions, and evaluation strategies for next-generation climate and environmental prediction systems.
- Contribute to the development and improvement of ML-based modeling approaches informed by physical and Earth system science.
- Work with large-scale climate, weather, hydrology, and remote sensing datasets to support model development and scientific analysis.
- Build and oversee reproducible workflows for data processing, model training, benchmarking, and validation.
- Collaborate closely with research, engineering, and data teams to translate scientific goals into scalable technical execution.
- Guide assessment of model performance, uncertainty, and scientific robustness across a range of environmental conditions and applications.
- Communicate findings through internal reviews, external collaborations, publications, and technical presentations.
- Help shape the broader scientific roadmap and contribute to team growth and cross-functional leadership.
PROFESSIONAL EXPERIENCE & QUALIFICATIONS
- PhD in machine learning, computational science, Earth science, atmospheric science, hydrology, AI, computer science, or a related quantitative discipline.
- 5+ years of postdoctoral, industry, or applied research experience in climate ML, weather ML, hydrologic modeling, Earth system modeling, or a closely related field.
- Demonstrated experience with ML-accelerated weather, climate, or hydrology models, with a strong publication track record in the area.
- Experience working with large climate datasets, including reanalysis products, remote sensing datasets, observational datasets, and model output.
- Experience with the computational infrastructure required to manage, preprocess, and train on large-scale climate datasets, preferably in the AWS ecosystem.
- Strong programming skills in Python and experience with modern ML frameworks such as PyTorch.
- Background in scientific ML, spatiotemporal modeling, data assimilation, hybrid physics-ML methods, or related approaches is strongly preferred.
- Ability to design rigorous evaluation frameworks, performance metrics, and benchmarking approaches for environmental prediction systems.
- Strong technical writing and communication skills, including reports, presentations, and peer-reviewed publications.
- Demonstrated ability to work independently in fast-paced, ambiguous environments while collaborating effectively across disciplines.
- Experience leading cross-functional scientific efforts, mentoring researchers, or helping define research roadmaps is preferred.
LOCATION: Cambridge, MA or Boulder, CO (some travel to Cambridge, MA based headquarters if working from Colorado)
ABOUT FLAGSHIP PIONEERING:
Flagship Pioneering invents and builds platform companies, each with the potential for multiple products that transform human health, sustainability and beyond. Since its launch in 2000, Flagship has originated more than 100 companies. Many of these companies have addressed humanity’s most urgent challenges: vaccinating billions of people against COVID-19, curing intractable diseases, improving human health, preempting illness, and feeding the world by improving the resiliency and sustainability of agriculture. Flagship has been recognized twice on FORTUNE’s “Change the World” list, an annual ranking of companies that have made a positive social and environmental impact through activities that are part of their core business strategies and has been twice named to Fast Company’s annual list of the World’s Most Innovative Companies. At Flagship, we accept impossible missions to enable bigger leaps. Our core values guide us through uncertainty and toward lasting impact.
We are an equal opportunity employer
All qualified applicants will be considered for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, protected veteran status, or any other characteristic protected by law. We recognize that great candidates often bring unique strengths without fulfilling every qualification. If you have some of the experience listed above but not all, please apply anyway. We are dedicated to building diverse and inclusive teams and look forward to learning more about your background and interest in Flagship.
Recruitment & Staffing Agencies:
Flagship Pioneering and its affiliated Flagship Lab companies (collectively, “FSP”) do not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to FSP or its employees is strictly prohibited unless contacted directly by Flagship Pioneering’s internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of FSP, and FSP will not owe any referral or other fees with respect thereto.
The salary ranges for this role are $127,000 - $205,900 (Colorado) and $168,000 - $231,000 (Massachusetts). Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. Protocos currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Protoco's good faith estimate as of the date of publication and may be modified in the future.
Privacy Notice for Applicants:
When you apply for a role at Flagship Pioneering or one of its portfolio companies, we collect and use personal information you provide (such as your name, contact details, work history, and application materials) to evaluate your application, communicate with you, and comply with legal obligations. Your application data is processed through Greenhouse, our applicant tracking system, and may also be reviewed using AI-assisted screening tools. We do not sell your personal information. California residents have rights under the CCPA/CPRA including to know, delete, and opt out of the sharing of their personal information. If you are located in the EU or UK, we process your data under GDPR and you have rights to access, rectify, and erase your data. To exercise your rights or for questions, contact privacy@flagshippioneering.com.
COMPANY DESCRIPTION
Flagship Pioneering is a bioplatform innovation company that invents and builds companies that change the world. We bring together the greatest scientific minds with entrepreneurial company builders and assemble the capital to allow them to take courageous leaps. Those big leaps in human health, sustainability and beyond exponentially accelerate scientific progress in areas ranging from disease detection and treatment and nature-positive agriculture to novel applications of AI that are driving the creation of new technologies. What sets Flagship apart is our ability to advance science and technology by uniting innovation, company creation, and capital investment under one roof in a way that is largely without precedent. Our scientific founders, entrepreneurial leaders, and professional capital managers are each aligned around an institutionalized process that enables us to innovate and transform for the benefit of people and planet. Many of the companies Flagship has founded have addressed humanity’s most urgent challenges: vaccinating billions of people against COVID-19, curing intractable diseases, improving human health, preempting illness, and feeding the world by improving the resiliency and sustainability of agriculture. Flagship has been recognized twice on FORTUNE’s “Change the World” list, an annual ranking of companies that have made a positive social and environmental impact through activities that are part of their core business strategies, and has been twice named to Fast Company’s annual list of the World’s Most Innovative Companies.
THE ROLE
We are seeking a Senior Machine Learning Scientist, Climate and Hydrology to lead the scientific direction and machine learning development for hydrology-aware climate modeling within our broader environmental modeling platform. This role sits at the intersection of hydrology, weather and climate science, and large-scale machine learning. The Sr. Scientist will help shape how hydrologic process understanding, climate data, and modern ML methods are brought together in next-generation prediction systems, with emphasis on scientifically grounded model development and evaluation. The individual in this role will work across science, ML, engineering, and data teams to define research priorities, guide model training and benchmarking, build reproducible workflows, and translate scientific insight into scalable model development. This is a cross-functional role requiring strong technical depth, structured scientific thinking, and the ability to move between foundational research and applied execution.
KEY RESPONSIBILITIES
- Lead scientific and technical efforts at the intersection of hydrology, climate science, and machine learning.
- Help define research priorities, modeling directions, and evaluation strategies for next-generation climate and environmental prediction systems.
- Contribute to the development and improvement of ML-based modeling approaches informed by physical and Earth system science.
- Work with large-scale climate, weather, hydrology, and remote sensing datasets to support model development and scientific analysis.
- Build and oversee reproducible workflows for data processing, model training, benchmarking, and validation.
- Collaborate closely with research, engineering, and data teams to translate scientific goals into scalable technical execution.
- Guide assessment of model performance, uncertainty, and scientific robustness across a range of environmental conditions and applications.
- Communicate findings through internal reviews, external collaborations, publications, and technical presentations.
- Help shape the broader scientific roadmap and contribute to team growth and cross-functional leadership.
PROFESSIONAL EXPERIENCE & QUALIFICATIONS
- PhD in machine learning, computational science, Earth science, atmospheric science, hydrology, AI, computer science, or a related quantitative discipline.
- 5+ years of postdoctoral, industry, or applied research experience in climate ML, weather ML, hydrologic modeling, Earth system modeling, or a closely related field.
- Demonstrated experience with ML-accelerated weather, climate, or hydrology models, with a strong publication track record in the area.
- Experience working with large climate datasets, including reanalysis products, remote sensing datasets, observational datasets, and model output.
- Experience with the computational infrastructure required to manage, preprocess, and train on large-scale climate datasets, preferably in the AWS ecosystem.
- Strong programming skills in Python and experience with modern ML frameworks such as PyTorch.
- Background in scientific ML, spatiotemporal modeling, data assimilation, hybrid physics-ML methods, or related approaches is strongly preferred.
- Ability to design rigorous evaluation frameworks, performance metrics, and benchmarking approaches for environmental prediction systems.
- Strong technical writing and communication skills, including reports, presentations, and peer-reviewed publications.
- Demonstrated ability to work independently in fast-paced, ambiguous environments while collaborating effectively across disciplines.
- Experience leading cross-functional scientific efforts, mentoring researchers, or helping define research roadmaps is preferred.
LOCATION: Cambridge, MA or Boulder, CO (some travel to Cambridge, MA based headquarters if working from Colorado)
ABOUT FLAGSHIP PIONEERING:
Flagship Pioneering invents and builds platform companies, each with the potential for multiple products that transform human health, sustainability and beyond. Since its launch in 2000, Flagship has originated more than 100 companies. Many of these companies have addressed humanity’s most urgent challenges: vaccinating billions of people against COVID-19, curing intractable diseases, improving human health, preempting illness, and feeding the world by improving the resiliency and sustainability of agriculture. Flagship has been recognized twice on FORTUNE’s “Change the World” list, an annual ranking of companies that have made a positive social and environmental impact through activities that are part of their core business strategies and has been twice named to Fast Company’s annual list of the World’s Most Innovative Companies. At Flagship, we accept impossible missions to enable bigger leaps. Our core values guide us through uncertainty and toward lasting impact.
We are an equal opportunity employer
All qualified applicants will be considered for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, protected veteran status, or any other characteristic protected by law. We recognize that great candidates often bring unique strengths without fulfilling every qualification. If you have some of the experience listed above but not all, please apply anyway. We are dedicated to building diverse and inclusive teams and look forward to learning more about your background and interest in Flagship.
Recruitment & Staffing Agencies:
Flagship Pioneering and its affiliated Flagship Lab companies (collectively, “FSP”) do not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to FSP or its employees is strictly prohibited unless contacted directly by Flagship Pioneering’s internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of FSP, and FSP will not owe any referral or other fees with respect thereto.
The salary ranges for this role are $127,000 - $205,900 (Colorado) and $168,000 - $231,000 (Massachusetts). Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. Protocos currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Protoco's good faith estimate as of the date of publication and may be modified in the future.
Privacy Notice for Applicants:
When you apply for a role at Flagship Pioneering or one of its portfolio companies, we collect and use personal information you provide (such as your name, contact details, work history, and application materials) to evaluate your application, communicate with you, and comply with legal obligations. Your application data is processed through Greenhouse, our applicant tracking system, and may also be reviewed using AI-assisted screening tools. We do not sell your personal information. California residents have rights under the CCPA/CPRA including to know, delete, and opt out of the sharing of their personal information. If you are located in the EU or UK, we process your data under GDPR and you have rights to access, rectify, and erase your data. To exercise your rights or for questions, contact privacy@flagshippioneering.com.
Machine Learning Engineer Job Roles in Colorado
See all Machine Learning Engineer Jobs in Colorado
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Search Machine Learning Engineer Jobs in ColoradoMachine Learning Engineer Jobs in Colorado: Frequently Asked Questions
Which companies sponsor visas for machine learning engineers in Colorado?
Google's Boulder engineering office, Palantir Technologies in Denver, Lockheed Martin Space in Littleton, and Arrow Electronics have all filed H-1B Labor Condition Applications for machine learning and related roles. Colorado also has a growing cluster of enterprise software and aerospace companies that sponsor ML engineers, including Trimble, DISH Network, and various Series B and later-stage startups headquartered in the Denver metro.
Which visa types are most common for machine learning engineer roles in Colorado?
The H-1B is the most common visa for machine learning engineers in Colorado, as ML roles typically meet the specialty occupation requirement given the degree-specific nature of the work. Candidates with an advanced degree may also be considered for the EB-2 or EB-2 NIW immigrant visa pathway. Australians may qualify for the E-3 visa, and Canadians and Mexicans may qualify for the TN visa under the USMCA's engineer and computer systems analyst categories.
Which cities in Colorado have the most machine learning engineer sponsorship jobs?
Denver and Boulder account for the largest share of machine learning engineer sponsorship activity in Colorado. Denver is home to Palantir, DISH Network, and a concentration of enterprise tech employers, while Boulder hosts Google, several biotech firms, and university-affiliated research spinoffs. The broader Front Range corridor, including Broomfield, Loveland, and Fort Collins, also sees ML hiring driven by aerospace, defense contractors, and Colorado State University research partnerships.
How to find machine learning engineer visa sponsorship jobs in Colorado?
Migrate Mate filters machine learning engineer jobs specifically by visa sponsorship willingness and state, making it straightforward to browse Colorado-based ML roles without sorting through positions that don't sponsor. You can search for machine learning engineer openings in Denver, Boulder, and surrounding cities, and review employer sponsorship history before applying. Creating a profile on Migrate Mate also helps you track new Colorado ML postings as they appear.
Are there any Colorado-specific factors that affect visa sponsorship for machine learning engineers?
Colorado's prevailing wage requirements apply to H-1B petitions filed in the state, and ML engineer roles in Denver and Boulder often fall into higher DOL wage tiers given the technical specialization involved. The University of Colorado and Colorado State University supply a steady pipeline of international graduate students in ML and data science, which means some Colorado employers already have H-1B sponsorship infrastructure in place. Colorado's aerospace and defense sector adds a consideration: some roles require security clearances, which international visa holders generally cannot obtain.
What is the prevailing wage for sponsored machine learning engineer jobs in Colorado?
U.S. employers sponsoring a visa must pay at least the prevailing wage, which is what workers in the same role, area, and experience level typically earn. The Department of Labor sets this rate to make sure companies aren't hiring foreign workers simply because they'd accept lower pay than a U.S. worker. It varies by job title, location, and experience. You can look up current prevailing wage rates for any occupation and location using the OFLC Wage Search page.