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Added 5 months ago
AA
Python Backend Engineer (AI & Scalable Systems)
Apex Align Agency
Remote, Canada
- $110,000 to $145,000 CAD / year
- Full-time
- Remote
We are looking for a strong Python Backend Engineer who can design and build scalable, production-grade backend systems across AI, automation, and cloud-native environments.
Added 5 months ago
A
Full-Stack Engineer - Production Planning
Afresh
Ontario
- $114,000 to $174,000 CAD / year
- Full-time
Partner with product managers, designers, and our users to deliver a great product experience.
Added 2 months ago
R&D Project Manager
Cyclic Materials Inc.
Kingston, ON
This position is ideal for a metallurgist or chemical/process engineer who has moved beyond purely technical execution and can lead multidisciplinary R&D workstreams with clear scope,…
Added 3 months ago
CI
Lead Engineer, Total Fund Management Financing, Public Markets Technology
CPP Investments | Investissements RPC
Toronto, ON
- Full-time
With a long-term horizon and global reach, we deploy capital at scale across public and private markets. Our size, stability, and disciplined investment philosophy allow us to pursue…
Added 3 months ago
S
Senior ML Research Engineer, Virtual Cell
SandboxAQ
Remote, Canada
- $125,800 to $222,000 CAD / year
- Full-time
- Remote
Software Engineering: Strong Python programming skills and experience with modern ML frameworks (e.g. PyTorch, JAX) and experiment tracking/data versioning tools (e.g. Weights & Biases).
Added 2 months ago
AI Engineer
Guidepoint
Toronto, ON
Integrate Intelligent Systems: Engineer solutions that seamlessly combine LLMs with our proprietary knowledge repositories, external APIs, and real-time data streams to create powerful…
Added 1 month ago
W
Staff Systems Engineer - Safety Methodologies
Waabi
Toronto, ON
- $200,000 to $256,000 USD / year
- Full-time
…are seeking a passionate and experienced safety or systems engineer to spearhead the development and implementation of critical safety framework methods that underpin our driverless…
Added 1 month ago
M
Senior Software Engineer
Mastercard
Vancouver, BC
- Full-time
The Business Rules Engineering & Strategy team is looking for a Senior Software Engineer to drive forth our mission of building robust IBM ODM Rule solutions that provide transaction-level…
Added 1 month ago
W
Senior / Staff Software Engineer, AI Tech Strike Team
Waabi
Toronto, ON
- $165,000 to $265,000 USD / year
- Full-time
…Strike Team to establish centralized best practices for working with AI across Waabi with the aim of maximizing productivity. We are looking for hands-on senior software engineers to build…
Added 1 month ago
TR
Forward Deployed Engineering Intern / Co-op Winter 2027
Trexo Robotics
Remote, Canada
- Full-time
- Remote
We're looking for a Forward Deployed Engineer intern to embed with our internal teams - sales, ops, customer success, RA/QA, finance - figure out where work actually breaks, and build the…
Added 5 months ago
T
Data Engineer
Tactable
Toronto, Ontario
- Full-time
At Tactable, this is what drives us. We’re building a world-class cloud, data, and API engineering firm with a mission to power the most influential tech of tomorrow, through expert-led…
Added 2 months ago
Q
DSP Application Engineer, Principal
Qualcomm
Ottawa, ON
- Full-time
…connected future for all. As a Qualcomm Hardware Application Engineer, you will provide technical expertise of hardware through trainings, product demonstrations, and the design, debug,…
Added 2 months ago
Senior Security Engineer, AI & DevSecOps
Atlas HXM
Canada
…how to engage each member of their workforce and then execute with accountability built in - direct Employer of Record (EOR), Agent of Record (AOR), payroll, and compliance capabilities…
Added 1 month ago
E
Production Engineer
Evertz
Burlington, ON
- Full-time
Python certification with experience is an asset
Added 1 month ago
MC
Senior Machine Learning Engineer Specialist – AI Centre of Excellence (35668)
Myticas Consulting
Canada
- Contract
The successful candidate will bring expert-level Python and SQL skills, combined with deep hands-on experience with Azure Machine Learning, Databricks, MLflow, CI/CD, MLOps, model…
Added 1 month ago
Senior Backend Product Engineer, Menu Operations
HelloFresh
Toronto, ON
…preparing for expansion, we are looking for a Senior Software Engineer with strong backend experience, a talent for turning complex logic into clean, reliable systems, and enough full-stack…
Added 1 month ago
E
BI Dev/Ops Engineer, Sys Admin/Architect
eBay
Toronto, ON
- Full-time
The BI Platforms - Dev/Ops Engineer, System Admin, Systems Architect will be part of the Data Services team under the Information Technology Services and Solutions group that will design…
Added 1 month ago
MI
Deployment Engineer
Magna International
Aurora, ON
- Full-time
The Deployment Engineer will implement the AMR solution as per the contract established between Magna’s Customers and the New Mobility Pre-Sales / Solution Engineering Team across various…
Added 1 month ago
N
Firmware Engineer
Nokia
Canada
- Full-time
As an Early Career Firmware Engineer, you’ll be part of an agile Scrum team developing software that controls and monitors next‑generation optical network equipment. You’ll be writing…
Added 5 months ago
TA
Forward Deployment Engineer (Generative AI)
Tiger Analytics
Canada
- Full-time
Tiger Analytics is looking for experienced Forward Deployment Engineer (Generative AI) with Gen AI experience to join our fast-growing advanced analytics consulting firm. Our employees…
Added 5 months ago
SI
Staff Validation/Verification Engineer - 17399
Synopsys Inc
Nepean, Ontario
- Full-time
…analysis solutions, and design services. We partner closely with our customers across a wide range of industries to maximize their R&D capability and productivity, powering innovation today…
Added 5 months ago
E
Embedded Software Engineer
evertz.io
Burlington, Ontario
- $60,000 to $90,000 CAD / year
- Internship
We're looking for a passionate Embedded Software Engineer to join our development team, where you'll play a key role in designing, implementing, and maintaining embedded software for…
Added 5 months ago
E
DSP Engineer (Markham)
EvertzAV
Markham, Ontario
- Internship
Experience with real-time systems design on FPGA, CPU and GPU based platforms
Added 5 months ago
E
Embedded Software Engineer
EvertzAV
Burlington, Ontario
- $60,000 to $90,000 CAD / year
- Internship
We're looking for a passionate Embedded Software Engineer to join our development team, where you'll play a key role in designing, implementing, and maintaining embedded software for…
Added 5 months ago
C
System Engineer-EN
CAE
Montreal, Quebec
- Full-time
As a member of the Hardware Engineering team, the Systems Engineer will contribute to the qualification, delivery, and integration of the MAD‑XR (Magnetic Anomaly Detection) avionics system…

SandboxAQ

Senior ML Research Engineer, Virtual Cell

Remote, Canada

Remote

$125,800 to $222,000 CAD / year · Full-time

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Job details

Pay: $125,800 to $222,000 CAD / year
Job type: Full-time
Workplace: Remote
Posting language: English
Posted: Jul 17, 2026

Original job description

About SandboxAQ

SandboxAQ is a high-growth company delivering AI solutions that address some of the world's greatest challenges. The company’s Large Quantitative Models (LQMs) power advances in life sciences, financial services, navigation, cybersecurity, and other sectors.

We are a global team that is tech-focused and includes experts in AI, chemistry, cybersecurity, physics, mathematics, medicine, engineering, and other specialties. The company emerged from Alphabet Inc. as an independent, growth capital-backed company in 2022, funded by leading investors and supported by a braintrust of industry leaders.

At SandboxAQ, we’ve cultivated an environment that encourages creativity, collaboration, and impact. By investing deeply in our people, we’re building a thriving, global workforce poised to tackle the world's epic challenges. Join us to advance your career in pursuit of an inspiring mission, in a community of like-minded people who value entrepreneurialism, ownership, and transformative impact.

The Opportunity

The AI Sim R&D team builds leading-edge ML and physics-based models ("LQMs") to advance drug discovery. Within this team, AQCell is our virtual cell platform: it takes a cell representation (e.g. basal gene expression) and a perturbation descriptor (e.g. SMILES, dose, and time), predicts the resulting transcriptomic response, and maps that response through pathway activity to functional endpoints such as cell viability, IC50, and toxicity dose-response - helping drug discovery scientists understand the biological repercussions of a compound across the cell, not just whether it binds its target.

As a Machine Learning Engineer on AQCell, you will build and maintain the models and data infrastructure that power this pipeline. You will work across large, heterogeneous transcriptomic and functional-endpoint datasets (e.g. LINCS L1000, GDSC, Tahoe-100M, and DILImap), train and evaluate expression-perturbation and cell-viability prediction models over them, and help harden our evaluation pipeline and baselines so we can trust and improve model performance over time. This role sits at the intersection of machine learning and biology, and offers the opportunity to shape how virtual cell models are trained, validated, and scaled toward real drug discovery decisions.

Key Responsibilities

Model Development: Build, train, and maintain machine learning models for expression-perturbation prediction (e.g. transcriptomic response to a drug perturbation) and downstream functional-endpoint prediction (e.g. cell viability, IC50, toxicity dose-response).
Large-Scale Dataset Management: Acquire, harmonize, and manage large-scale biological datasets (e.g. LINCS L1000, GDSC, Tahoe-100M, DILImap) - including schema harmonization, normalization, and de-duplication across cell, drug, and assay identifiers - and manage model training pipelines over these pooled datasets.
Evaluation & Baselines: Contribute to automating and hardening the end-to-end evaluation pipeline, including implementing robust statistical baselines (e.g. cell- and drug-conditioned mean baselines) to rigorously benchmark model performance.
Research Translation: Translate ideas from the scientific literature (e.g. transformer-based perturbation models, knowledge graph and GNN-based embeddings) into working, well-tested code integrated into our modeling framework.
Cross-Functional Collaboration: Partner with computational biologists, software engineers, and product stakeholders to ensure models are grounded in sound biology and are usable in real drug discovery workflows.
Communication: Clearly document methods, assumptions, and results, and communicate findings to both technical and non-technical stakeholders.

Essential Skills & Experience

Academic Foundation: Bachelor's degree in a scientific or quantitative field (Computer Science, Physics, Mathematics, Biology, Chemistry, or related); an advanced degree (MS or PhD) is preferred.
Applied ML in Science: Demonstrated experience building and maintaining machine learning models in a scientific discipline in an industry setting, including taking models from prototype through validation and maintenance; experience in a life sciences setting is preferred.
Large-Scale Data Management: Required experience managing large-scale datasets and managing the training of models over them, including data ingestion, cleaning, versioning, and pipeline maintenance at scale.
Software Engineering: Strong Python programming skills and experience with modern ML frameworks (e.g. PyTorch, JAX) and experiment tracking/data versioning tools (e.g. Weights & Biases).
Scientific Rigor: Ability to design sound evaluation methodology (e.g. train/test splitting strategies, held-out generalization tests) and to critically interpret model performance against meaningful baselines.

Highly Desired Skills & Experience

Bioinformatics & Computational Biology: Experience with bioinformatics and computational biology data analysis tools, particularly transcriptomics harmonization and normalization tools (e.g. batch correction, pseudobulking, gene ID mapping/standardization).
Domain Datasets: Familiarity with public perturbation or drug-sensitivity datasets such as LINCS L1000, GDSC, DepMap, or single-cell perturbation atlases.
Knowledge Graphs & GNNs: Experience with knowledge graph embeddings or graph neural networks applied to drugs, targets, or cells.
Cheminformatics: Familiarity with cheminformatics representations (SMILES, InChI keys, PubChem/Cellosaurus identifiers) used to harmonize drug and cell metadata across datasets.
Collaborative Innovation: Experience working in interdisciplinary environments where AI intersects with the biological sciences.

Why Join Us?

We offer competitive compensation, a comprehensive benefits package, and opportunities for professional growth.

Compensation: Competitive base salary, performance-based incentives or bonuses (where applicable), and equity participation.
Benefits: Comprehensive medical, dental, and vision coverage for employees and dependents with generous employer premium contributions, retirement savings with company matching, paid parental leave, and inclusive family-building benefits.
Work-Life Balance: Flexible paid time off, company-wide seasonal breaks, and support for flexible work arrangements that enable sustainable performance.
Career Development: Opportunities for continuous learning and growth through on-the-job development, cross-functional collaboration, and access to internal learning and development programs.

SandboxAQ Welcomes All

We are committed to fostering a culture of belonging and respect, where diverse perspectives are actively sought and valued. Our multidisciplinary environment provides ample opportunity for continuous growth - working alongside humble, empowered, and ambitious colleagues ready to tackle epic challenges.

Equal Employment Opportunity: All qualified applicants will receive consideration regardless of race, color, ancestry, religion, sex, national origin, sexual orientation, age, citizenship, marital status, disability, gender identity, or Veteran status.

Accommodations: We provide reasonable accommodations for individuals with disabilities in job application procedures for open roles. If you need such an accommodation, please let a member of our Recruiting team know.

Read: Guidance for candidates on using AI Tools in interviews

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More about this job

Responsibilities

Architect, scale, and optimize scientific codebases to power Large Quantitative Models for drug and materials discovery. Transition high-impact research prototypes into robust, production-grade software and orchestrate distributed training pipelines.

Requirements

Requires a PhD or research-focused MSc in a quantitative field and at least 5 years of industry experience in production software development. Candidates must have expertise in translating research papers into ML artifacts and experience with structural biology data science.

Skills

Machine Learning Engineering
Structural Biology
Computational Chemistry
MLOps
Distributed Training Pipelines
GPU Optimization
Research Translation
Product Lifecycle Management
Generative Chemistry Models
Structure Prediction
Cloud Platforms

Benefits

Medical coverage
Dental coverage
Vision coverage
Retirement savings with company matching
Paid parental leave
Family-building benefits
Flexible paid time off
Company-wide seasonal breaks
Equity participation
Performance-based incentives

Remote locations

Canada

Remote locations (standardized)

Canada

Visa sponsorship

Not detected in the job text

Keywords

Large Quantitative Models
LQM
AI for Life Sciences
Drug Discovery
Materials Discovery
In Silico Design
Computational Chemistry
Structural Biology
MLOps
GPU Infrastructure
Biopharma
Generative Chemistry
Affinity Models
Structure Prediction
Distributed Training
Production Code
Cloud Computing
AI Simulation
BioSim

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