arXiv subjects

Zhijian Wei

Publications and source records attributed to Zhijian Wei.

3 recordsLinked to original sources

arXiv2026

Does Learning Protein Folding Generalize to Broader Reasoning?

Large language models rely heavily on human text, which often conveys surface answers rather than the spatial and structural logic behind them. Protein folding is a natural testbed, because one solved structure yields thousands of exactly checkable spatial and topological statements. We ask: can learning to fold proteins teach general models reusable reasoning capabilities? To answer this, we build FoldingCorpus, a protein-derived question-answer dataset, and Fold2Reason, a recipe that post-trains on it through two complementary signals: discrete structural answers predicted via the model's native language head, and continuous 3D geometry decoded from the same shared representations. On FoldBench, Fold2Reason achieves structure prediction scores 2.7 to 3.5 times those of Qwen3.5-9B. Beyond protein structure prediction, it improves performance on all 10 benchmarks spanning spatial, graph, scientific, and general reasoning, raising macro-average accuracy from 45.09% to 48.33% (+3.23 pp), with positive gains on all 10 benchmarks, while matched controls built from random, synthetic, and shuffled structure yield substantially smaller or negative gains. Our work shows that non-linguistic, structure-dense scientific data can systematically improve broad reasoning in language models, making a solved scientific problem a practical source of post-training supervision.

cs.LG↗

arXiv2026

VCWorld: A Biological World Model for Virtual Cell Simulation

Virtual cell modeling aims to predict cellular responses to perturbations. Existing virtual cell models rely heavily on large-scale single-cell datasets, learning explicit mappings between gene expression and perturbations. Although recent models attempt to incorporate multi-source biological information, their generalization remains constrained by data quality, coverage, and batch effects. More critically, these models often function as black boxes, offering predictions without interpretability or consistency with biological principles, which undermines their credibility in scientific research. To address these challenges, we present VCWorld, a cell-level white-box simulator that integrates structured biological knowledge with the iterative reasoning capabilities of large language models to instantiate a biological world model. VCWorld operates in a data-efficient manner to reproduce perturbation-induced signaling cascades and generates interpretable, stepwise predictions alongside explicit mechanistic hypotheses. In drug perturbation benchmarks, VCWorld achieves state-of-the-art predictive performance, and the inferred mechanistic pathways are consistent with publicly available biological evidence.

q-bio.CB↗

arXiv2024

Photonics for Neuromorphic Computing: Fundamentals, Devices, and Opportunities

In the dynamic landscape of Artificial Intelligence (AI), two notable phenomena are becoming predominant: the exponential growth of large AI model sizes and the explosion of massive amount of data. Meanwhile, scientific research such as quantum computing and protein synthesis increasingly demand higher computing capacities. Neuromorphic computing, inspired by the mechanism and functionality of human brains, uses physical artificial neurons to do computations and is drawing widespread attention. Conventional electronic computing has experienced certain difficulties, particularly concerning the latency, crosstalk, and energy consumption of digital processors. As the Moore's law approaches its terminus, there is a urgent need for alternative computing architectures that can satisfy this growing computing demand and break through the von Neumann model. Recently, the expansion of optoelectronic devices on photonic integration platforms has led to significant growth in photonic computing, where photonic integrated circuits (PICs) have enabled ultrafast artificial neural networks (ANN) with sub-nanosecond latencies, low heat dissipation, and high parallelism. Such non-von Neumann photonic computing systems hold the promise to cater to the escalating requirements of AI and scientific computing. In this review, we study recent advancements in integrated photonic neuromorphic systems, and from the perspective of materials and device engineering, we lay out the scientific and technological breakthroughs necessary to advance the state-of-the-art. In particular, we examine various technologies and devices employed in neuromorphic photonic AI accelerators, spanning from traditional optics to PICs. We evaluate the performances of different designs by energy efficiency in operations per joule (OP/J) and compute density in operations per squared millimeter per ...

physics.optics↗