Machine Learning Application Engineer II

Maze Therapeutics applies precision medicine to address both common and rare diseases. The Machine Learning Application Engineer II role is based in South San Francisco and focuses on building and improving production-ready solutions that advance drug discovery efforts. Role overview This position centers on designing and developing data and machine learning…

About Us: Calico Life Sciences LLC, a pioneering research and development company founded by Alphabet, is dedicated to leveraging advanced technologies and modeling systems to deepen our understanding of the biology governing human aging. Our mission is to utilize this knowledge to create interventions that empower individuals to enjoy longer, healthier lives. With state-of-the-art technology labs, a firm commitment to curiosity-driven discovery science, and a dynamic drug-development pipeline in collaboration with academic and industry partners, Calico is an exhilarating environment for fostering medical breakthroughs. Role Overview: We are looking for a Senior / Staff Machine Learning Infrastructure Engineer to transform machine learning algorithms into practical applications and to construct a state-of-the-art computing and machine learning platform for analyzing biological datasets and modeling macromolecular sequences and structures. You will play a crucial role in a cross-functional initiative aimed at developing a premier computing and data analysis platform that underpins Calico's research endeavors through the following responsibilities: Develop and Optimize: Design and implement software infrastructure and tools that accelerate ML research, manage training and inference workflows, and streamline data ingestion and curation processes. Define Engineering Best Practices: Spearhead efforts to reorganize and refactor existing research codebases, enhancing code quality and reproducibility. Collaborate for Impact: Partner closely with our ML research scientists to deploy models that tackle critical questions in aging research and further Calico's mission. The ideal candidate will have extensive experience in designing, developing, and maintaining scalable and reliable ML infrastructure components, including data pipelines, model training and deployment systems, and monitoring tools. You should possess a proven track record of optimizing ML workflows for both performance and resource utilization, and remain updated on best practices in ML model management, versioning, and reproducibility. Effective communication and collaboration across functions are essential for executing complex projects successfully.

About ZiplineAre you ready to make a significant impact on the world? Zipline is on a transformative mission to revolutionize the logistics of goods distribution. We are dedicated to addressing the most pressing and intricate access challenges globally by developing the first instant delivery and logistics system that ensures equitable service for everyone, regardless of their location. We have powered Rwanda’s national blood delivery network, facilitated COVID-19 vaccine distribution in Ghana, provided on-demand home delivery for Walmart, and enabled healthcare providers to deliver care directly to homes in the U.S. Our innovative approach is reshaping how goods move for businesses, governments, and consumers alike.Our technology may be complex, but our vision is straightforward: a teleportation service that delivers essential items exactly when needed. Through the integration of robotics and autonomy, we are committed to decarbonizing the delivery process, minimizing road congestion, and lowering fossil fuel use and air pollution, all while ensuring equitable access for billions and fostering a more resilient global supply chain.Join Zipline and contribute to our mission of building an equitable and resilient global supply chain for billions across the globe.About You and The RoleAs the operator of the world’s largest autonomous logistics network, Zipline is delivering critical medical and commercial goods with unmatched precision and reliability. As we continue to expand into more complex and safety-critical environments, the systems underlying our autonomy stack must be robust, adaptable, and thoroughly integrated—particularly at the intersection of perception and deployment.We are seeking talented senior and staff perception engineers to join our dedicated Droid team, responsible for the autonomy that powers Zipline’s backyard delivery experience. This team manages the complete stack of onboard, offboard, and cloud-side perception systems that enable accurate and dependable delivery even in challenging customer environments. You will design real-time 3D perception models that capture geometry, scene semantics, and preferences for both delivery and package pickup. Your work will encompass the entire perception stack, optimizing onboard TensorRT engines and creating a data flywheel that identifies interesting samples from our diverse customer deliveries. Collaboration with the planner team will be essential to ensure we develop the right system, emphasizing practical implementation rather than merely creating the best perception model.This role is not focused on research; you will be expected to operate swiftly, deliver production-grade systems, and ingeniously apply cutting-edge techniques to solve high-impact challenges.

Join Calico Labs as a Machine Learning Scientist or Senior Machine Learning Scientist to drive advancements in artificial intelligence and machine learning research. In this role, you will collaborate with a talented team to develop innovative solutions that leverage cutting-edge technology to tackle complex biological questions.

Join Our TeamAt insitro, we are at the forefront of revolutionizing drug development through innovative imaging-based phenotyping of in-vitro biology. Our machine learning algorithms extract clinically significant insights from the extensive datasets we generate internally.As a Senior Machine Learning Scientist specializing in Imaging, you will craft advanced ML-driven computer vision pipelines to uncover insights regarding disease mechanisms from various microscopy techniques. Collaborating with a dynamic team of life scientists, software engineers, computational biologists, and fellow machine learning experts, your work will be pivotal in identifying therapeutic targets and creating highly effective, low-toxicity drugs.Joining our fast-growing biotech startup, you will have the opportunity to impact multiple promising pre-clinical drug targets, particularly in areas like ALS and metabolic diseases. This is an exciting time for insitro, offering numerous avenues for professional growth and influence. You will work closely with an exceptionally talented team, acquire diverse skills, and play a key role in shaping our culture, strategic focus, and outcomes.This position reports directly to the Director of Imaging, Cellular Machine Learning, and requires a hybrid work arrangement with at least three days per week in our South San Francisco headquarters. Be a part of our mission to make a meaningful difference in patients' lives!

At Atomic AI, we are at the forefront of innovation, utilizing artificial intelligence to revolutionize drug discovery. Our cutting-edge R&D platform, highlighted on the cover of Science, aims to tackle previously undruggable diseases through RNA targeting. We are continuously enhancing our platform by developing advanced machine learning techniques and unique foundational models, driven by our extensive in-house experimental data collection. Our diverse team of scientists and engineers is the cornerstone of our success.About the RoleAs a full-time Machine Learning Scientist, you will collaborate with engineers and experimental scientists to propel our technology platform for RNA structure prediction, target identification, and early drug discovery. You will co-lead the development and assessment of our machine learning pipeline, bringing innovative ideas to fruition within our continuously evolving state-of-the-art platform. Your proactive contributions will help shape the machine learning strategies and overall vision of the company.

Role overview insitro is hiring a Senior Machine Learning Scientist for its Computational Biology team in South San Francisco, CA. This group analyzes cellular aspects of in-vitro biology to support drug development. The work focuses on linking biological phenotypes to human diseases and translating those connections into insights for therapeutic discovery. What you will do Develop and improve machine learning methods for biological data analysis in areas such as network analysis, systems biology, graph-based modeling, causal structure learning, single cell omics, or imaging. Analyze high-throughput phenotypic screens and help create disease-relevant cell models. Work closely with experimental and computational biologists and other ML scientists to identify new phenotypes and design screening approaches. Integrate and interpret varied data types, including human cohort data, to uncover insights into disease mechanisms. Maintain high standards of scientific rigor and best practices in tool and analysis development. Report to the Head of Computational Biology and ML-Omics. Requirements Significant experience developing machine learning methods for biological data. Background in one or more of: network analysis, systems biology, graph-based modeling, causal structure learning, single cell omics, or imaging modalities. Strong analytical skills for complex, high-dimensional datasets. Ability to collaborate across scientific disciplines. Dedication to scientific rigor and high-quality research. Available to work on-site at least three days per week in South San Francisco. Why join insitro At insitro, team members work alongside talented colleagues in a biotech startup environment. The company values contributions that help shape both culture and strategic direction. This position offers the chance to expand skills and make a meaningful impact in drug discovery, with the potential to improve patient lives.

Join Tahoe Therapeutics as a Senior Machine Learning EngineerAt Tahoe Therapeutics, we are transforming drug discovery with our innovative approach that prioritizes the biology of real patients. Our groundbreaking Mosaic platform allows for scalable in vivo data generation at single-cell resolution, enabling us to understand how drugs impact patient-derived cells across diverse biological contexts. We are committed to constructing the world’s largest in vivo single-cell perturbation atlas and utilizing it to develop multimodal foundation models that elucidate the context-dependent dynamics of gene function, disease progression, and drug responses.Our mission is clear: to expedite the discovery of superior drugs and ensure they reach the patients who need them the most by leveraging advanced machine learning techniques alongside the most biologically pertinent datasets in drug discovery.Your ContributionsAs a Senior Machine Learning Engineer, you will lead the design of the next generation of foundation models for gene regulatory networks, drawing on Tahoe’s extensive single-cell datasets such as Tahoe-100M and beyond. This role is tailored for individuals with a robust background in machine learning and statistics, coupled with a passion for applying innovative ML developments to impactful challenges in drug discovery. We seek unconventional thinkers ready to advance the frontiers of possibility in our field.

Join Tahoe Therapeutics as a Senior Machine Learning Scientist!At Tahoe Therapeutics, we are at the forefront of revolutionizing drug discovery by leveraging real patient biology. Our innovative Mosaic platform enables scalable in vivo data generation at single-cell resolution, allowing for intricate mapping of drug effects on patient-derived cells across diverse biological contexts. As we develop the world’s most comprehensive in vivo single-cell perturbation atlas, we harness cutting-edge machine learning techniques combined with the richest biological datasets to accelerate the discovery of effective drugs for those who need them most.Your Role:As a Senior Machine Learning Scientist, you will be instrumental in designing the next generation of foundation models that elucidate gene regulatory networks, utilizing our extensive single-cell datasets such as Tahoe-100M. This position is ideal for individuals with a profound understanding of machine learning and statistics, eager to apply groundbreaking ML advancements to impactful challenges in drug discovery. We seek innovative thinkers who can contribute to the creation of models that will significantly influence the field of drug development.

The OpportunityAt insitro, machine learning is at the forefront of our innovative approach to drug development. Our unique TherML Platform harnesses AI to expedite therapeutic discovery across various modalities, from initial hit identification to lead optimization. This pioneering strategy allows us to swiftly design therapeutics targeting novel, internally discovered targets, utilizing extensive datasets recognized as some of the largest and most comprehensive in the industry.We are currently seeking a Machine Learning Scientist who will actively engage with our TherML platform to spearhead the design of multiple oligonucleotide therapeutic programs while directly influencing the enhancement of our platform and machine learning models. This position presents an exciting opportunity to translate state-of-the-art machine learning into tangible advancements in drug discovery. The role reports to the Senior Manager of Molecular Machine Learning and offers a flexible hybrid working model (2 days in-office per week) or remote work (one week on-site per quarter).

The OpportunityAt insitro, we are dedicated to harnessing the power of artificial intelligence and machine learning to pioneer the development of innovative medicines aimed at treating diseases that currently have limited or no effective therapies. The field of drug discovery has encountered significant challenges, including a sustained decline in productivity and high clinical failure rates, primarily due to inadequate understanding of the biological mechanisms underlying diseases. Despite substantial investments in building predictive biological models, the need for improved predictive frameworks remains critical.To address this challenge, insitro has successfully established a target and biology discovery engine that integrates high-throughput, multimodal cellular phenotyping and data generation with cutting-edge machine learning and AI methodologies. As the Head of CellML, you will lead a dynamic team of machine learning scientists and engineers focused on deriving biological insights from diverse data modalities collected at scale. This includes live and fixed microscopy imaging and various omics assays (such as scRNA, proteomics, and spatial). You will collaborate closely with our laboratory leaders to co-create the next generation of high-throughput perturbation cellular assays, including Optical Pooled Screening, live-cell staining imputation, Perturb-seq, and more. Additionally, you will work alongside our therapeutic area leaders to design impactful experiments and analyze data to enhance our therapeutic pipeline.Joining insitro means becoming part of a well-funded AI biotech company with a robust pipeline of therapeutic candidates and an expanding focus across various disease areas. We seek visionary leaders capable of fostering a culture that amalgamates science, machine learning, and engineering. This position reports to our Head of Compute and is a hybrid role, requiring presence at our South San Francisco headquarters at least three days a week.

Join Our MissionAt insitro, we are at the forefront of transforming drug development through the power of machine learning. Our pioneering ChemML Platform leverages advanced AI techniques to expedite small molecule discovery, from initial hit identification to lead optimization. By utilizing some of the most extensive datasets in the industry, we are able to design innovative drugs targeting novel AI-derived compounds swiftly.Billions of proprietary binding affinity measurementsHundreds of thousands of ADMET and In Vivo PK measurementsExperimental data generated through our AI-driven DMTL optimization cyclesWe are seeking an Applied Machine Learning Scientist who will actively engage with our ChemML platform to drive design across various therapeutic programs. This is a unique opportunity to apply cutting-edge machine learning techniques to make a tangible impact in drug discovery. The role reports to the Senior Manager, Molecular Machine Learning and offers a flexible hybrid work model (2 days in the office per week) or remote work arrangement (1 week in-office per quarter).

Join Our Innovative TeamAt insitro, we are on a mission to revolutionize drug development. With a notable decline in the productivity of global drug discovery, we harness advanced machine learning techniques alongside cutting-edge technologies to address complex diseases that impact millions annually. Our goal is to fundamentally change the pace and effectiveness of how new treatments are identified and developed.We invite passionate and driven interns to become a part of our computing team as Machine Learning Scientists for the Summer 2026 cohort. This opportunity allows you to collaborate closely with a mentor to develop and implement machine learning methods, all while analyzing extensive datasets from various biological modalities over an immersive 11-12 week program.Our headquarters are located in South San Francisco, offering a hybrid working schedule or the possibility to work remotely, depending on team needs. As part of a diverse team, you will engage across numerous fields, including imaging, omics, statistical genetics, pan-modality therapeutic discovery, clinical research, and research software engineering.Areas of FocusComputational Biology: Utilize publicly available single-cell transcriptomics resources to derive insights into the disease mechanisms pertinent to our therapeutic areas.Omics & Imaging Data Methods: Innovate and deploy state-of-the-art ML approaches to integrate large-scale multi-modal phenotypic datasets.Statistical and Translational Genetics: Create workflows for post-GWAS analyses, including fine-mapping and deep dives into translational genetics to enhance gene exploration from our discovery initiatives.Integrative Phenotyping: Design ML models to infer disease-relevant phenotypes from high-content clinical imaging datasets, such as MRI and PET-CT.

About Us Calico Life Sciences LLC, a pioneering research and development entity founded by Alphabet, is dedicated to unraveling the complex biology of human aging. Our mission is to leverage cutting-edge technologies and model systems to enhance our understanding of aging and develop transformative interventions that promote longer, healthier lives. With a vibrant pipeline of drug development in collaboration with academic and industry partners, Calico is a hub of curiosity-driven discovery and innovation, aiming to inspire groundbreaking medical advancements. Calico Postdoctoral Fellowship Program We invite passionate early-career scientists to join our quest to deepen the understanding of aging biology. This fellowship presents a distinctive opportunity for individuals to excel in aging research, refine their scientific acumen, and cultivate research independence. The Postdoctoral Fellowship is a fixed-term educational program lasting three years, with the possibility of a fourth-year extension and flexible start dates. As a Postdoctoral Fellow, you will be fully integrated into Calico's collaborative labs and community. The program aims to equip fellows with the skills necessary to become independent investigators in academia or industry upon successful completion. Expect regular mentorship feedback and participate in annual performance reviews to assess project progress and receive career guidance. Key Responsibilities Lead Independent Research: Drive your own project(s) focusing on innovative and potentially high-risk/high-reward research avenues. Contribute to Calico’s Core Mission: Enhance the understanding of aging and age-related diseases. Drive Scientific Progress: Conduct meticulous experiments, analyze data (including computational methods when applicable), and troubleshoot methodologies as necessary. Publish Work: Produce results that are expected to be submitted for publication promptly at the conclusion of the fellowship. Collaborate and Communicate: Work closely with diverse teams across Calico and present findings to audiences including computational scientists, lab scientists, and engineers. Professional Development: Engage with a community of fellow postdoctoral researchers.

Join AbbVie as a Senior Scientist I in our Machine Learning team dedicated to advancing Biologics Drug Substance Development and Cell Culture Development. In this key role, you will leverage your expertise in machine learning to drive innovations that enhance our drug development processes.

About Us: Calico Life Sciences LLC, a research and development organization backed by Alphabet, is dedicated to advancing our understanding of the biological mechanisms governing human aging. Our mission is to leverage cutting-edge technologies and sophisticated model systems to create interventions that promote longer, healthier lives. At Calico, we foster an environment of curiosity-driven scientific exploration, collaborating with academic and industry partners to accelerate medical breakthroughs. Position Overview: We are on the lookout for a Senior Machine Learning Scientist/Engineer to innovate and implement machine learning algorithms aimed at modeling and designing proteins. In this role, you will collaborate closely with a team of experienced experimental biologists to design experiments that test and refine our machine learning predictions iteratively. The ideal candidate will possess a deep understanding of contemporary machine learning methodologies, including language and sequence modeling, representation learning, generative models, and self-supervised learning techniques. You should have a proven track record in implementing, enhancing, and debugging advanced machine learning models, alongside expertise in building robust data infrastructures and tools. We seek a proactive, self-driven individual eager to explore the latest ML literature and apply innovative solutions to protein design challenges at Calico. Strong communication skills are essential, as you will need to effectively share your findings through publications and presentations and collaborate across teams to navigate complex projects.

About AKASAAt AKASA, we are on a mission to revolutionize healthcare through artificial intelligence. As the foremost provider of generative AI solutions for healthcare revenue cycles, we empower health systems to effectively capture and communicate the entire patient clinical journey. Our technology enables organizations to optimize their operations, allowing them to prioritize what truly matters: quality patient care. Our success is backed by over $205 million in funding from esteemed investors including Andreessen Horowitz, BOND, and Costanoa Ventures.This is an exhilarating time to join AKASA. Since the launch of our new AI-native product suite in 2024, revenue bookings have surged over 20 times. We have set records for our largest deals three times in a row, a testament to the significant improvements we are delivering in clinical quality and documentation accuracy—key concerns for healthcare leaders.Our deployments have garnered national recognition as one of the most comprehensive applications of GenAI in healthcare finance to date (link). Serving a client base that represents over $120 billion in net patient revenue, we partner with some of the most innovative health systems in the nation, including Cleveland Clinic, Duke, Stanford, and Johns Hopkins.Our accolades include being named one of America's Top Startup Employers 2026 by Forbes, the #1 most promising healthcare RCM startup of 2025 by Black Book Market Research, and one of the fastest-growing GenAI startups to watch by AIM Research. Our CEO has been recognized among the “Top 50 Healthcare Technology CEOs” by the Healthcare Technology Report, and we have proudly maintained our “Great Place to Work” certification for six consecutive years.We are leveraging this momentum to redefine possibilities in healthcare, and we are seeking exceptional individuals to help accelerate this vision.The OpportunityWe are in search of an experienced Senior Application Security Engineer who possesses a robust software engineering background coupled with a security-focused mindset. You will collaborate closely with our engineering teams to build secure systems from the ground up, rather than adding security measures as an afterthought. You will take ownership of our application security program, work in tandem with developers, and play a pivotal role in shaping our security framework.

About ZiplineAre you ready to make a difference? Zipline is dedicated to revolutionizing the logistics industry by addressing critical access challenges globally. Our mission is to create, manufacture, and operate an instant delivery system that provides equitable service to all individuals, regardless of their location. From facilitating Rwanda's blood delivery service to supporting Ghana's COVID-19 vaccine distribution, and even enabling Walmart's home delivery, we are reshaping how essential goods are transported.Our innovative technology simplifies a complex process: a teleportation service that ensures timely delivery of necessities. By leveraging robotics and autonomy, we aim to decarbonize deliveries, minimize road congestion, and reduce pollution while fostering equitable access for billions and strengthening the global supply chain.Join us at Zipline to contribute to building a more resilient and equitable global supply chain for millions.About You and the RoleAs the operator of the largest autonomous logistics network worldwide, Zipline reliably delivers critical medical and commercial goods. As we navigate increasingly sophisticated and safety-centric environments, our autonomy systems must be robust and intricately connected, particularly where perception and deployment converge.We are seeking a Senior Perception Engineer to join our Droid Team, responsible for the autonomy that enhances Zipline's delivery experience. This team oversees the complete stack of offboard and cloud-side perception systems that inform and enhance our onboard capabilities. Your work will include generating detailed 3D and semantic insights from aerial surveys, learning customer preferences, and analyzing terrain features, ensuring our aircraft are equipped for mission-critical deliveries in complex environments.This role emphasizes practical application; you will need to expedite the development of production-grade systems and creatively apply state-of-the-art techniques to address significant challenges.

Join the Revolution at ZiplineAre you ready to make a significant impact on the world? At Zipline, we're dedicated to revolutionizing the logistics and delivery landscape. Our mission is to tackle urgent access challenges globally by developing the world's first instant delivery system that serves all individuals equitably, no matter their location. From supporting Rwanda's national blood delivery system to facilitating the distribution of COVID-19 vaccines in Ghana, and enhancing home delivery services for Walmart, we are reshaping how goods move for businesses and governments alike.Our technology is intricate, yet our vision is straightforward: we aim to create a teleportation service that provides what you need, precisely when you need it. By leveraging cutting-edge robotics and autonomous systems, we are committed to decarbonizing delivery, alleviating road congestion, and minimizing air pollution while ensuring equitable access for billions and fortifying the global supply chain.Become a part of Zipline's mission to construct a more equitable and resilient global supply chain for billions of lives.About You and The RoleAt Zipline, we are at the forefront of enhancing airspace navigation safety and developing the largest autonomous delivery system in the world. We seek experienced machine learning and perception engineers to set new standards in aircraft detection and obstacle tracking. You will enable our drones to autonomously navigate through complex and dynamic environments safely.Your ResponsibilitiesPush the Boundaries of Perception: Create and implement innovative algorithms for detecting, localizing, and tracking aircraft and obstacles using advanced monocular and multi-view camera systems, integrating deep learning with geometric vision to achieve robust 3D situational awareness.Develop Reliable Vision Systems: Build scalable model training pipelines and rigorous evaluation frameworks that assess performance in real-world edge cases.Collaborate Across Teams: Work in tandem with systems, flight test, and validation teams to develop comprehensive test plans that push perception capabilities to their limits, adhering to Zipline's stringent safety standards.Enhance Operational Performance: Design powerful debugging, visualization, and analysis tools that derive insights from field data, facilitating rapid issue resolution and performance optimization.

About Xaira TherapeuticsXaira Therapeutics is a pioneering biotech startup dedicated to harnessing the power of artificial intelligence to revolutionize drug discovery and development. Our innovative team is at the forefront of creating generative AI models that facilitate the design of protein and antibody therapeutics, enabling the development of medications targeting historically challenging molecular entities. We are also working on foundational models that enhance our understanding of biology and disease, leading to improved target identification and patient stratification. Together, these advancements strive to continuously uncover novel therapies and enhance the efficiency of drug development processes. Headquartered in the vibrant tech hubs of the San Francisco Bay Area, Seattle, and London, Xaira is positioned to make a global impact in healthcare.About the RoleWe are on the lookout for a skilled AI Research Engineer to join our dynamic team. As an integral member of our interdisciplinary unit, you will work closely with AI scientists, engineers, and drug discovery specialists to develop and implement AI models aimed at expediting the discovery and development of innovative therapeutics. This position presents an exciting opportunity to apply state-of-the-art AI methodologies in practical settings to tackle critical healthcare challenges and contribute to enhancing global health outcomes.We seek candidates with a proven track record in building and deploying machine learning systems in industrial contexts, emphasizing rigor, scalability, and cross-functional collaboration. The ideal candidate will possess experience in transforming research concepts into robust, production-ready applications that deliver measurable results.