Jacob Levine

Jacob Levine, Miguel Aenlle, Craig Zilles et al.

Automated grading systems have enabled scalable assessment for many response types, but handwritten mathematics remains a barrier due to the complexity of multi-step solutions. Vision-capable large language models (LLMs) offer new opportunities here, yet their reliability in authentic instructional settings remains poorly understood. We present an empirical evaluation of an LLM-based grader for handwritten mathematical work using instructor-defined rubrics. Extending a prior pipeline for typed responses, we integrate transcription and rubric-based evaluation of photographic submissions within a single LLM call, evaluating on student work from two university STEM courses. Comparing AI grading decisions against human-assigned ground truth at the rubric-item level, we observe high overall accuracy, with most errors -- 87\% in the best model -- attributable to transcription failures rather than rubric misapplication. We categorize common error modes, including image quality issues, hallucinated content, and incorrect handling of equivalent expressions. These findings highlight both the promise and limitations of LLM-based grading for handwritten mathematics, providing guidance for system design, prompt refinement, and deployment in educational settings.

Menghua Wu, Russell Littman, Jacob Levine et al.

High-content perturbation experiments allow scientists to probe biomolecular systems at unprecedented resolution, but experimental and analysis costs pose significant barriers to widespread adoption. Machine learning has the potential to guide efficient exploration of the perturbation space and extract novel insights from these data. However, current approaches neglect the semantic richness of the relevant biology, and their objectives are misaligned with downstream biological analyses. In this paper, we hypothesize that large language models (LLMs) present a natural medium for representing complex biological relationships and rationalizing experimental outcomes. We propose PerturbQA, a benchmark for structured reasoning over perturbation experiments. Unlike current benchmarks that primarily interrogate existing knowledge, PerturbQA is inspired by open problems in perturbation modeling: prediction of differential expression and change of direction for unseen perturbations, and gene set enrichment. We evaluate state-of-the-art machine learning and statistical approaches for modeling perturbations, as well as standard LLM reasoning strategies, and we find that current methods perform poorly on PerturbQA. As a proof of feasibility, we introduce Summer (SUMMarize, retrievE, and answeR, a simple, domain-informed LLM framework that matches or exceeds the current state-of-the-art. Our code and data are publicly available at https://github.com/genentech/PerturbQA.