Postdoctoral Fellow, Multimodal Modeling

The Team

Our decoding inflammation team builds tools to enable precise molecular-level measurements of inflammation within human tissues in real time, and develop proactive, early interventions that can be deployed when inflammation — which underlies the most significant causes of death worldwide — first flares in the body. You can learn more about our work here. 

Our team collaborates with three powerhouse universities - Northwestern University, the University of Chicago, and the University of Illinois Urbana-Champaign - to develop first-in-class technologies and make breakthroughs.

Our Vision

• Pursue large scientific challenges that cannot be pursued in conventional environments
• Enable individual investigators to pursue their riskiest and most innovative ideas
• Facilitate research by scientists and clinicians at our home institutions and beyond

We are a team of passionate individuals powered by technology, guided by scientific research, and driven by collaboration, working toward a mission to cure or prevent all disease. 

The Opportunity

The Chan Zuckerberg Biohub Chicago is seeking outstanding early-career scientists to join and participate in the launch of the Proteoform Spatial Biology Group by continuing their training as a Postdoctoral Fellow in Multimodal Modeling. The Proteoform Spatial Biology Group aims to uncover the spatiotemporal regulation of proteins and their unique molecular forms, proteoforms, in inflammation and autoimmunity. For this position, the ideal candidate is expected to have experience in working with multimodal and multiscale modeling of diverse datatypes across confocal microscopy images, mass spectrometry-based proteomics, phosphoproteomics, and/or interactomics.

What You'll Do

• Design and train self-supervised multimodal models that fuse confocal protein imaging, single-cell protein proximity networks, and mass spectrometry-based phosphoproteomics into shared representations, using objectives such as reconstruction and contrastive alignment (e.g., CLIP)
• Work with graph-structured proximity-network data, collaborating on graph- and topology-aware modeling approaches, and 
• Leverage existing high-performing imaging models for feature extraction and inference, adapting them for co-embedding and building new image models where needed
• Develop cross-modal alignment strategies relating surface organization to signaling and localization, and use the learned representations to model continuous cell-state structure and the features driving state transitions
• Present findings internally and externally, and co-author publications

What You'll Bring

• Essential:
  • PhD in machine learning, computational biology, bioengineering, biophysics, or a related field
  • Experience applying deep learning to images, including use of pretrained vision models
  • Demonstrated experience building both supervised and unsupervised models
  • Experience with multimodal modeling or data fusion across heterogeneous data types
  • Experience with graph neural networks or other graph/network representation learning
  • Proficiency in Python and modern deep learning frameworks (e.g., PyTorch, JAX, or TensorFlow)
•  Nice to Have: 
  • Experience with contrastive or self-supervised learning (e.g., CLIP) for multimodal data
  • Familiarity with topology-aware or higher-order modeling (e.g., simplicial or motif-based methods)
  • Background in proteomics or mass spectrometry data analysis
  • Experience with sequencing-based or single-cell omics data analysis
  • Experience with microscopy or spatial imaging analysis in a biological setting
  • Fluency with immunology or single-cell state modeling
  • Experience building reproducible analysis pipelines and contributing to shared or open-source codebases

Compensation

The Chicago, IL base pay for a new hire in this role is $84,150. New hires are typically hired into the lower portion of the range, enabling employee growth in the range over time. Actual placement in range is based on job-related skills and experience, as evaluated throughout the interview process. 

This position may be eligible to participate in our discretionary annual performance bonus program. Bonus eligibility and targets are determined in accordance with our total rewards philosophy and may vary by role.

Benefits for the Whole You 

We’re thankful to have an incredible team behind our work. To honor their commitment, we offer a wide range of benefits to support the people who make all we do possible. 

• Provides a generous employer match on employee 401(k) contributions to support planning for the future.
• Paid time off to volunteer at an organization of your choice. 
• Funding for select family-forming benefits. 
• Relocation support for employees who need assistance moving

If you’re interested in a role but your previous experience doesn’t perfectly align with each qualification in the job description, we still encourage you to apply as you may be the perfect fit for this or another role.

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