Hey! I'm Ali 👋

I'm a Researcher at MAGICS Lab, building cross-domain representation learning methods for robotics and computational biology.

If you're working on interesting ML, robotics, or biology problems and want to trade ideas or collaborate, please feel free to reach out.


About Me

Often, we try to improve model performance by building domain-specific methods tuned to particular modalities or benchmarks. I'm interested in building cross-domain methods along two axes: learning stable noise-invariant latent representations and designing model architectures that support reliable long-horizon inference in noisy environments. I develop these methods in both robotics and computational biology. In both settings, I work on self-supervised objectives that learn robust latents and on reward-guided inference methods that correct long-horizon trajectory drift.

I work on these problems at Northwestern University and am fortunate to be advised by Prof. Han Liu and Prof. Zhaoran Wang. My work on virtual cell models and cellular reprogramming is conducted in collaboration with the Chan Zuckerberg Biohub. I like to understand the systems that my methods interact with, so I build accessible robotics hardware. Outside of research, I enjoy mountain biking and swimming.


Publications & Projects


Publications & Preprints

Humanity's Last Exam

Long Phan et al.

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ML
A large-scale benchmark that stress-tests multimodal foundation models on PhD-level questions across science, engineering, and the humanities.

SSD Duality

Jerry Yao-Chieh Hu, Xiwen Zhang, Ali ElSheikh, Weimin Wu, Han Liu

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ML
Extends structured state-space duality to diagonal SSMs and characterizes when an SSM admits a 1-semiseparable masked attention dual.

Cell-JEPA: Latent Representation Learning for Single-Cell Transcriptomics

Ali ElSheikh, Rui-Xi Wang, Weimin Wu, Yibo Wen, et al.

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BIO
Latent representation learning for single-cell transcriptomics with a JEPA-style objective trained on 5.8M scRNA-seq cells to learn robust cell embeddings.

Virtual Cells Need Context, Not Just Scale

Payam Dibaeinia, Sudarshan Babu, Mei Knudson, Ali ElSheikh, et al.

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BIO
Position paper arguing virtual cell models need broader biological context coverage and causal transportability, not just larger model capacity.
Manuscripts in Progress

RewardDiffusion

ROBOT
Reward-augmented diffusion policy for LeRobot that jointly predicts actions and dense rewards during inference.

cell-bench

BIO
Unified training and evaluation suite for single-cell models supporting scVI-based models, CPA, and GEARS with twelve standardized evaluation metrics.

Harnessing PRDM1-PGC1α Axis to Enhance CAR T Cell Therapy

BIO
PRDM1 knockout boosts CD19 CAR T expansion and persistence via PGC1α-driven mitochondrial fitness.
Projects & Software

aArm & SO-100

ROBOT
Built and upgraded the SO-100 platform with new electronics and four additional camera feeds. Designing aArm, a 7-DoF robot arm with QDD actuators, and building its control stack.

QDD Actuator

ROBOT
Inspired by OpenQDD v1; reworked electronics and added a 10:1 helical reducer producing ~20 Nm peak holding torque with a lower-cost FOC driver and magnetic encoder.

Tool-Using Agents

ML
Adapted the VeRL framework to optimize LLM agents for tool-use behavior and strict output formatting via RL post-training.

Options & Portfolio Lab

ML
Toolkit for constructing option spreads and approximating risk-neutral distributions with an ML pipeline for portfolio imputation and hierarchical risk parity.