Machine Learning Engineer

At Aether, we are building a full-stack machine learning system to predict the outcomes of high-throughput laboratory experiments. Our goal is to transform noisy, real-world biological data into reliable, auditable, and predictive systems that accelerate scientific discovery.As a Senior Machine Learning Engineer, manage and improve the end-to-end ML and data pipeline that connects automated laboratory systems to production-grade models. This is not a model-tuning role. You will design the infrastructure, signal processing systems, and model architectures that turn experimental chaos into structured insight.You’ll work at the intersection of software engineering, applied ML research, and computational science - partnering closely with lab engineers and scientists to ensure our systems are robust, interpretable, and scientifically grounded.What You’ll OwnEnd-to-End ML System ArchitectureDesign and maintain a full-stack ML system that predicts outcomes from high-throughput experimentsBuild data pipelines that ingest, validate, normalize, and version experimental dataEnsure full auditability and traceability across the data lifecycleData & Infrastructure EngineeringDevelop and maintain database schemas and views that power intuitive internal tools and lab-facing GUIsCapture experimental metadata in structured, reliable formatsApply best practices in database design, versioning, and interconnectivityCreate clear and actionable visualizations for scientific stakeholdersSignal Processing & Data IntegrityBuild signal processing pipelines for noisy, automated lab dataDevelop methods to detect anomalies and quarantine untrustworthy dataRecover signal from noisy inputs using statistical and algorithmic techniquesLeverage experimental controls to validate and cross-check outputsApplied ML Research & Model DevelopmentDesign, train, and improve neural network models to predict experimental outcomesEvaluate and compare model architectures (Transformers, CNNs, Graph Networks, etc.)Conduct scientific studies to validate modeling hypothesesImprove predictive accuracy through both modeling innovation and signal engineeringApply principles such as neural scaling laws to guide model developmentWhat You BringCore Technical SkillsPython expertise (PyTorch, NumPy, Pandas, multiprocessing, Plotly/Matplotlib)Experience developing ML systems in Linux and AWS environmentsStrong understanding of Git-based workflowsExperience with database design (Django, SQL)Deep grounding in algebra, statistics, and signal processingStrong experience training, testing, and evaluating neural network modelsMachine Learning DepthNeural Networks, Transformers, Convolutional Networks, Graph Neural NetworksModel training, evaluation frameworks, and performance comparisonComfort working in research-oriented, hypothesis-driven ML environmentsNice to HavePyTorch LightningExperience implementing or running bio-AI models (e.g., ESM, ESM-Fold, AlphaFold, Boltz)Molecular dynamics tools (ASE, GPAW, GROMACS)Cheminformatics tools (RDKit, SMILES, SMARTS)Sequence alignment tools (BLAST, MSA)Background in chemistry or physics Experience with LLM pretraining/fine-tuning, diffusion models, or reinforcement learningWhat Makes This Role DifferentYou will own real scientific systems - not just train models on curated datasetsYou’ll work directly with experimental data, not sanitized benchmarksYou’ll help define the infrastructure that future models depend onYou’ll operate with autonomy and technical depthYou’ll shape how machine learning integrates with real-world laboratory systemsNoteAether Biomachines is proud to be an Equal Opportunity Employer. We celebrate diversity and are committed to creating an inclusive environment for all employees. If you’re excited about this role but don’t meet every requirement, we encourage you to apply.The pay range for this role is $160,000 - $225,000 per year + equity, with final compensation based on skills and experience. Employment at Aether is at-will, and reasonable accommodations are available upon request. Applicants must be authorized to work in the U.S. At this time, Aether is not sponsoring visas for this position.