arXiv subjects

Handong Wang

Publications and source records attributed to Handong Wang.

3 recordsLinked to original sources

arXiv2026

SymFold: Synergizing Evolutionary and Structural Priors for Accurate Protein Inverse Folding

Protein inverse folding aims to recover amino acid sequences for a given 3D protein structure, underpinning broad applications such as enzyme engineering and drug discovery.Current methods often follow a serial pipeline, in which a structure encoder predicts a coarse sequence, which is then refined by protein language models (PLMs). However, because PLMs only perform post-hoc sequence edits, the refinement is bounded by the quality of upstream predictions.Thanks to recent multimodal protein language models (MPLMs), we could directly encode structure to generate sequences with pretrained structural knowledge, but we observe that they are not effective for inverse folding. Therefore, we introduce a symmetric dual-path architecture that both leverages PLMs for pretrained sequence evolution knowledge and MPLMs for pretrained structural knowledge to iteratively guide protein sequence generation.Through extensive experiments across standard protein inverse folding benchmarks, our method achieves state-of-the-art performance, surpassing prior approaches, and ablation studies validate the rationale of our symmetric design, revealing a promising direction for the community.

cs.AI↗

arXiv2026

PopPert: Population-level Joint-Distribution Modeling for Single-Cell Perturbation Prediction

Predicting transcriptional responses to specific perturbations is critical for understanding cellular regulatory mechanisms and accelerating drug discovery. Single-cell RNA sequencing destroys each measured cell, yielding only unpaired populations of control and perturbed cells. However, existing methods typically model perturbation prediction at the single-cell level and assume cell-to-cell correspondence, which conflicts with the unpaired nature of the observed data. To address this challenge, we propose PopPert, a framework that explicitly parameterizes population-level joint gene expression distributions for collective transcriptional state modeling. Given a control population distribution and a perturbation condition, PopPert predicts perturbation-induced changes in distribution parameters, eliminating the need for cell-level correspondence and reducing sensitivity to single-cell noise. To effectively capture gene co-expression patterns, PopPert leverages a low-rank Gaussian Copula to model cross-gene statistical dependencies and construct the joint gene expression distribution, additionally allowing sampling of synthetic perturbed single-cell profiles. Across multiple single-cell benchmarks spanning both genetic and chemical perturbations, PopPert achieves superior overall performance in differential expression recovery, perturbation effect estimation, and population-level distribution matching. These results establish population-level joint distribution learning as an effective paradigm for predicting transcriptional responses from unpaired single-cell populations. Code for PopPert is publicly available at https://github.com/whd1125/PopPert.

q-bio.GN↗

arXiv2026

TRIG: Trajectory-Rig Decoupled Metric Geometry Learning

Vision-centric autonomous driving requires accurate metric geometry and ego-motion estimation from synchronized multi-camera observations. Recent visual geometry models show strong performance in pose estimation, depth prediction, and 3D reconstruction, but are not tailored to rigid multi-camera driving systems. They often encode camera poses as entangled representations, in which time-varying ego-motion and static camera-rig geometry are jointly modeled, limiting the utilization of vehicle-side geometric priors. We propose Trajectory-Rig Decoupled Metric Geometry Learning (TRIG), a geometry perception framework for autonomous driving. TRIG factorizes camera poses into ego-trajectory and camera-rig components, enabling separate modeling of ego-motion and static multi-camera topology. We introduce decoupled pose encoding and supervision, which separately constrain trajectory evolution and rig geometry for metric-consistent learning. Moreover, sparse Temporal--Spatial attention separates cross-camera interaction from temporal aggregation, reducing global attention cost while preserving geometric reasoning. Experiments on five autonomous driving benchmarks show that TRIG achieves state-of-the-art performance in pose estimation, metric depth prediction, and 3D reconstruction.

cs.CV↗