Jiajun Wu

Ridvan Yesiloglu, Sakib Mostafa, James Zou et al.

Most single-cell foundation models are adapted from language models, representing each cell as a sequence of gene tokens. This discards the relationships among genes and often the magnitude of their expression. We present scVision, a vision foundation model that instead renders each cell as a continuous image. Using optimal transport, it places genes at fixed positions on a single shared, pan-tissue layout so that co-expressed genes become spatial neighbours, turning a transcriptome into an image in which gene programs appear as local texture. We pretrain a vision transformer by masked image modelling on 72 million human cells and use the frozen encoder with no fine-tuning. In zero-shot evaluations on six independent, held-out studies, scVision is the most accurate cell-type annotator and recovers gene programs without supervision, ahead of existing foundation models and classical baselines; on multi-study integration it matches the strongest token-based model while conserving the most biological structure, without ever seeing a batch label. Permuting the gene layout with the network fixed sharply lowers accuracy, more than removing the vision transformer itself, showing that biologically meaningful position, not the network, carries the signal. By preserving expression magnitude and gene relationships, scVision reframes single-cell representation learning as a vision problem, connecting it to the mature methods of computer vision.

Qiang Zhu, Jiajun Wu

Reinforcement learning for multi-turn search reasoning typically relies on terminal outcome rewards, which cannot distinguish useful, redundant, and harmful intermediate interactions. We propose LAPO, a self-generated process-supervision method based on backward leave-one-turn attribution. For each search turn, LAPO replaces the turn and its retrieval observation with a fixed [DELETE] placeholder and measures the resulting change in the current policy's mean log-likelihood of the gold answer. This Answer-Likelihood Gain estimates the turn's contribution while preserving all downstream interactions, allowing early evidence to be evaluated in the complete reasoning context. LAPO further applies sign-consistency gating, retaining only normalized process advantages whose directions agree with their raw attribution scores. The method requires no additional reward model, teacher, verifier, or LLM-as-a-Judge. Across seven knowledge-intensive question-answering datasets with local retrieval, LAPO achieves an average exact-match score of 0.326, outperforming the strongest step-reward baseline, IGPO, by 0.053. Ablations show complementary benefits from backward attribution and sign-consistency gating, demonstrating that policy-derived retrospective attribution can provide effective process supervision for multi-turn search agents.