Senior Principal / Associate Director, Scientific ML for Drug Discovery jobs in United States
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Lila Sciences · 22 hours ago

Senior Principal / Associate Director, Scientific ML for Drug Discovery

positionCambridge, MA
timeFull-time
remoteOnsite
senioritySenior Level, Lead/Staff, Director/Executive
date8+ years exp

Lila Sciences is pioneering a new age of boundless discovery by building capabilities to apply AI to scientific methods. The role involves leading a cross-functional Scientific ML team to deliver impactful programs, setting technical direction, and ensuring high standards for scientific rigor and collaboration.

Artificial Intelligence (AI)Life ScienceSoftware
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H1B Sponsor Likelynote

Responsibilities

Define the technical vision and quarterly milestones for SBDD, ligand-based QSAR/ADMET, synthesis planning, and physics-ML; prioritize along live program needs and compute budget
Hire, mentor, and develop a 6+ person team spanning AI scientists and an ML platform engineer; establish high standards for scientific rigor, code quality, and collaboration
Orchestrate a synthesis-aware, MPO-constrained, uncertainty-calibrated design workflow that fuses assay-driven ligand models with structure/physics signals and ADMET/PK constraints
Institute leakage-safe datasets and splits (scaffold/time/series), prospective validations, OOD tests, and model gating; publish model cards and decision logs for auditability
Co-design schemas, ontologies, and provenance with Assay Informatics, Structural Biology, and Data Platform; ensure reliable ETL from ELN/LIMS, structure, and simulation
Partner with ML Engineering to deliver reproducible training, scalable serving (APIs/batch), monitoring, and incident response for scientific services on cloud + HPC
Coordinate with partner teams internal and external to Lila for assay QC, structural prep, and data platform SLAs; evaluate vendors and open-source where it accelerates impact
Set a high bar for clarity, integrity, and humility; communicate uncertainty and trade-offs to technical and executive stakeholders

Qualification

AI SBDDLigand-based QSAR/ADMETSynthesis planningML engineering excellenceStatistical mechanicsMedicinal chemistryLeadershipOpen-source leadershipHTS/DEL analyticsStructural bioinformatics

Required

8+ years (post-PhD or equivalent) building and shipping ML for drug discovery or closely related domains; demonstrated impact on live programs
Technical depth and breadth: Expertise in at least two of the following and fluency across the rest: AI SBDD (equivariant/3D graph models for pose/affinity, pocket embeddings), Ligand-based QSAR/ADMET and active learning for hit-to-lead/lead opt, Synthesis planning and reaction/condition/yield modeling, ADMET/PK/PD (IVIVE, PBPK/QSP) and uncertainty/calibration, ML-for-simulation/free energy (Δ-learning surrogates, learned force fields)
ML engineering excellence: PyTorch/JAX, geometric learning, generative modeling, experiment tracking, model/data versioning, serving; comfort with hybrid cloud + HPC
Scientific rigor: Statistical mechanics and thermodynamics basics, medicinal chemistry and DMPK fundamentals, assay QC and leakage control; designs prospective, decision-grade evaluations
Leadership: Hires and grows high-performing teams; sets crisp priorities; aligns diverse stakeholders; communicates clearly at both the whiteboard and the exec table

Preferred

PhD in CS, Computational Chemistry, Chemoinformatics, Biophysics, or related field with publications in top ML/drug discovery venues
Delivered unified design loops that improved hit rate/MPO and reduced cycle time; experience integrating retrosynthesis and PBPK into optimization
Open-source leadership (e.g., RDKit/Chemprop/DeepChem, PyTorch Geometric/e3nn, OpenMM) or vendor evaluation/deployment experience
Experience with HTS/DEL analytics, structural bioinformatics (AlphaFold/ensembles), or regulated documentation (model qualification)

Company

Lila Sciences

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Lila Sciences creates a scientific superintelligence platform and autonomous labs for life sciences, chemistry, and materials science. It is a sub-organization of Flagship Pioneering.
dateFounded in 2023
location
Cambridge, Massachusetts, USA
people-size201-500 employees
web-link
https://www.lila.ai

H1B Sponsorship

Lila Sciences has a track record of offering H1B sponsorships. Please note that this does not guarantee sponsorship for this specific role. Below presents additional info for your reference. (Data Powered by US Department of Labor)
Distribution of Different Job Fields Receiving Sponsorship
Represents job field similar to this job
Trends of Total Sponsorships
2025 (8)

Funding

Current Stage
Growth Stage
Total Funding
$550M
Key Investors
NVenturesFlagship Pioneering
2025-10-14Series A· $115M
2025-09-14Series A· $235M
2025-03-10Seed· $200M

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Company data provided by crunchbase