arXiv subjects

Zhuoran Qiao

Publications and source records attributed to Zhuoran Qiao.

11 recordsLinked to original sources

arXiv2026

DynamicWAM: Dual-Path Motion Conditioning for World-Action Models in Dynamic Manipulation

Dynamic manipulation requires robots to infer target motion and respond promptly, yet existing World-Action Models (WAMs) typically condition only on the current frame and execute large backbones synchronously, limiting motion awareness and responsive control in dynamic scenes. We propose DynamicWAM, a compact WAM for dynamic object manipulation with dual-path motion conditioning. DynamicWAM introduces history-flow conditioning, encoding temporally aligned optical-flow frames alongside the current observation through a frozen pretrained video VAE to preserve spatial motion structure, while injecting kinematic descriptors of displacement, duration, velocity, and acceleration into the action expert to provide motion magnitude and timing. The two complementary paths are fused through joint world-action attention. A distilled compact backbone and real-time chunking (RTC)-based asynchronous execution further enable responsive control. On DOMINO, DynamicWAM achieves a 38.2% success rate and a 53.2 manipulation score, outperforming all evaluated baselines. Across 12 real-world tasks spanning linear, circular, and compound target motion, it achieves a 46.7% average success rate, exceeding the strongest baseline by 22.9 percentage points.

cs.RO↗

arXiv2026

Multi-Agent Off-World Exploration for Sparse Evidence Discovery via Gaussian Belief Mapping and Dual-Domain Coverage

Off-world multi-robot exploration is challenged by sparse targets, limited sensing, hazardous terrain, and restricted communication. Many scientifically valuable clues are visually ambiguous and often require close-range observations, making efficient and safe informative path planning essential. Existing methods often rely on predefined areas of interest (AOIs), which may be incomplete or biased, and typically handle terrain risk only through soft penalties, which are insufficient for avoiding non-recoverable regions. To address these issues, we propose a multi-agent informative path planning framework for sparse evidence discovery based on Gaussian belief mapping and dual-domain coverage. The method maintains Gaussian-process-based interest and risk beliefs and combines them with trajectory-intent representations to support coordinated sequential decision-making among multiple agents. It further prioritizes search inside the AOI while preserving limited exploration outside it, thereby improving robustness to AOI bias. In addition, the risk-aware design helps agents balance information gain and operational safety in hazardous environments. Experimental results in simulated lunar environments show that the proposed method consistently outperforms sampling-based and greedy baselines under different budgets and communication ranges. In particular, it achieves lower final uncertainty in risk-aware settings and remains robust under limited communication, demonstrating its effectiveness for cooperative off-world robotic exploration.

cs.RO↗

arXiv2024

NeuralPLexer3: Accurate Biomolecular Complex Structure Prediction with Flow Models

Structure determination is essential to a mechanistic understanding of diseases and the development of novel therapeutics. Machine-learning-based structure prediction methods have made significant advancements by computationally predicting protein and bioassembly structures from sequences and molecular topology alone. Despite substantial progress in the field, challenges remain to deliver structure prediction models to real-world drug discovery. Here, we present NeuralPLexer3 -- a physics-inspired flow-based generative model that achieves state-of-the-art prediction accuracy on key biomolecular interaction types and improves training and sampling efficiency compared to its predecessors and alternative methodologies. Examined through newly developed benchmarking strategies, NeuralPLexer3 excels in vital areas that are crucial to structure-based drug design, such as physical validity and ligand-induced conformational changes.

cs.LG↗

arXiv2024

Polaritons in non-fullerene acceptors for high responsivity angle-independent organic narrowband infrared photodiodes

Narrowband infrared organic photodetectors are in great demand for sensing, imaging, and spectroscopy applications. However, most existing strategies for narrowband detection depend on spectral filtering either through saturable absorption, which requires active layers exceeding 500 nm, restricting the choice of materials for producing high-quality films, or cavity effects, which inherently introduce strong angular dispersion. Microcavity exciton-polariton (polariton) modes, which emerge from strong exciton-photon coupling, have recently been explored as an angular dispersion suppression strategy for organic optoelectronics. In this work, we present the first narrowband infrared polariton organic photodiode that combines angle-independent response with a record-high responsivity of 0.24 A/W at 965 nm and -2 V. This device, featuring a 100-nm-thin active layer comprising a non-fullerene acceptor, exhibits a detection mode with a full-width at half maximum of less than 30 nm and a marginal angular dispersion of under 15 nm across $\pm$$45^\circ$. This study highlights the potential of polaritons as an innovative platform for developing next-generation optoelectronic devices that achieve simultaneous enhancements in optical and electronic performance.

physics.optics↗

arXiv2024

Multi-modal Molecule Structure-text Model for Text-based Retrieval and Editing

There is increasing adoption of artificial intelligence in drug discovery. However, existing studies use machine learning to mainly utilize the chemical structures of molecules but ignore the vast textual knowledge available in chemistry. Incorporating textual knowledge enables us to realize new drug design objectives, adapt to text-based instructions and predict complex biological activities. Here we present a multi-modal molecule structure-text model, MoleculeSTM, by jointly learning molecules' chemical structures and textual descriptions via a contrastive learning strategy. To train MoleculeSTM, we construct a large multi-modal dataset, namely, PubChemSTM, with over 280,000 chemical structure-text pairs. To demonstrate the effectiveness and utility of MoleculeSTM, we design two challenging zero-shot tasks based on text instructions, including structure-text retrieval and molecule editing. MoleculeSTM has two main properties: open vocabulary and compositionality via natural language. In experiments, MoleculeSTM obtains the state-of-the-art generalization ability to novel biochemical concepts across various benchmarks.

cs.LG↗

arXiv2023

Retrieval-based Controllable Molecule Generation

Generating new molecules with specified chemical and biological properties via generative models has emerged as a promising direction for drug discovery. However, existing methods require extensive training/fine-tuning with a large dataset, often unavailable in real-world generation tasks. In this work, we propose a new retrieval-based framework for controllable molecule generation. We use a small set of exemplar molecules, i.e., those that (partially) satisfy the design criteria, to steer the pre-trained generative model towards synthesizing molecules that satisfy the given design criteria. We design a retrieval mechanism that retrieves and fuses the exemplar molecules with the input molecule, which is trained by a new self-supervised objective that predicts the nearest neighbor of the input molecule. We also propose an iterative refinement process to dynamically update the generated molecules and retrieval database for better generalization. Our approach is agnostic to the choice of generative models and requires no task-specific fine-tuning. On various tasks ranging from simple design criteria to a challenging real-world scenario for designing lead compounds that bind to the SARS-CoV-2 main protease, we demonstrate our approach extrapolates well beyond the retrieval database, and achieves better performance and wider applicability than previous methods. Code is available at https://github.com/NVlabs/RetMol.

q-bio.QM↗

arXiv2023

State-specific protein-ligand complex structure prediction with a multi-scale deep generative model

The binding complexes formed by proteins and small molecule ligands are ubiquitous and critical to life. Despite recent advancements in protein structure prediction, existing algorithms are so far unable to systematically predict the binding ligand structures along with their regulatory effects on protein folding. To address this discrepancy, we present NeuralPLexer, a computational approach that can directly predict protein-ligand complex structures solely using protein sequence and ligand molecular graph inputs. NeuralPLexer adopts a deep generative model to sample the 3D structures of the binding complex and their conformational changes at an atomistic resolution. The model is based on a diffusion process that incorporates essential biophysical constraints and a multi-scale geometric deep learning system to iteratively sample residue-level contact maps and all heavy-atom coordinates in a hierarchical manner. NeuralPLexer achieves state-of-the-art performance compared to all existing methods on benchmarks for both protein-ligand blind docking and flexible binding site structure recovery. Moreover, owing to its specificity in sampling both ligand-free-state and ligand-bound-state ensembles, NeuralPLexer consistently outperforms AlphaFold2 in terms of global protein structure accuracy on both representative structure pairs with large conformational changes (average TM-score=0.93) and recently determined ligand-binding proteins (average TM-score=0.89). Case studies reveal that the predicted conformational variations are consistent with structure determination experiments for important targets, including human KRAS$^\textrm{G12C}$, ketol-acid reductoisomerase, and purine GPCRs. Our study suggests that a data-driven approach can capture the structural cooperativity between proteins and small molecules, showing promise in accelerating the design of enzymes, drug molecules, and beyond.

q-bio.QM↗

arXiv2022

Informing Geometric Deep Learning with Electronic Interactions to Accelerate Quantum Chemistry

Predicting electronic energies, densities, and related chemical properties can facilitate the discovery of novel catalysts, medicines, and battery materials. By developing a physics-inspired equivariant neural network, we introduce a method to learn molecular representations based on the electronic interactions among atomic orbitals. Our method, OrbNet-Equi, leverages efficient tight-binding simulations and learned mappings to recover high fidelity quantum chemical properties. OrbNet-Equi models a wide spectrum of target properties with an accuracy consistently better than standard machine learning methods and a speed orders of magnitude greater than density functional theory. Despite only using training samples collected from readily available small-molecule libraries, OrbNet-Equi outperforms traditional methods on comprehensive downstream benchmarks that encompass diverse main-group chemical processes. Our method also describes interactions in challenging charge-transfer complexes and open-shell systems. We anticipate that the strategy presented here will help to expand opportunities for studies in chemistry and materials science, where the acquisition of experimental or reference training data is costly.

cs.LG↗

arXiv2022

OrbNet: Deep Learning for Quantum Chemistry Using Symmetry-Adapted Atomic-Orbital Features

We introduce a machine learning method in which energy solutions from the Schrodinger equation are predicted using symmetry adapted atomic orbitals features and a graph neural-network architecture. \textsc{OrbNet} is shown to outperform existing methods in terms of learning efficiency and transferability for the prediction of density functional theory results while employing low-cost features that are obtained from semi-empirical electronic structure calculations. For applications to datasets of drug-like molecules, including QM7b-T, QM9, GDB-13-T, DrugBank, and the conformer benchmark dataset of Folmsbee and Hutchison, \textsc{OrbNet} predicts energies within chemical accuracy of DFT at a computational cost that is thousand-fold or more reduced.

physics.chem-ph↗

arXiv2021

OrbNet Denali: A machine learning potential for biological and organic chemistry with semi-empirical cost and DFT accuracy

We present OrbNet Denali, a machine learning model for electronic structure that is designed as a drop-in replacement for ground-state density functional theory (DFT) energy calculations. The model is a message-passing neural network that uses symmetry-adapted atomic orbital features from a low-cost quantum calculation to predict the energy of a molecule. OrbNet Denali is trained on a vast dataset of 2.3 million DFT calculations on molecules and geometries. This dataset covers the most common elements in bio- and organic chemistry (H, Li, B, C, N, O, F, Na, Mg, Si, P, S, Cl, K, Ca, Br, I) as well as charged molecules. OrbNet Denali is demonstrated on several well-established benchmark datasets, and we find that it provides accuracy that is on par with modern DFT methods while offering a speedup of up to three orders of magnitude. For the GMTKN55 benchmark set, OrbNet Denali achieves WTMAD-1 and WTMAD-2 scores of 7.19 and 9.84, on par with modern DFT functionals. For several GMTKN55 subsets, which contain chemical problems that are not present in the training set, OrbNet Denali produces a mean absolute error comparable to those of DFT methods. For the Hutchison conformers benchmark set, OrbNet Denali has a median correlation coefficient of R^2=0.90 compared to the reference DLPNO-CCSD(T) calculation, and R^2=0.97 compared to the method used to generate the training data (wB97X-D3/def2-TZVP), exceeding the performance of any other method with a similar cost. Similarly, the model reaches chemical accuracy for non-covalent interactions in the S66x10 dataset. For torsional profiles, OrbNet Denali reproduces the torsion profiles of wB97X-D3/def2-TZVP with an average MAE of 0.12 kcal/mol for the potential energy surfaces of the diverse fragments in the TorsionNet500 dataset.

physics.chem-ph↗

arXiv2020

Multi-task learning for electronic structure to predict and explore molecular potential energy surfaces

We refine the OrbNet model to accurately predict energy, forces, and other response properties for molecules using a graph neural-network architecture based on features from low-cost approximated quantum operators in the symmetry-adapted atomic orbital basis. The model is end-to-end differentiable due to the derivation of analytic gradients for all electronic structure terms, and is shown to be transferable across chemical space due to the use of domain-specific features. The learning efficiency is improved by incorporating physically motivated constraints on the electronic structure through multi-task learning. The model outperforms existing methods on energy prediction tasks for the QM9 dataset and for molecular geometry optimizations on conformer datasets, at a computational cost that is thousand-fold or more reduced compared to conventional quantum-chemistry calculations (such as density functional theory) that offer similar accuracy.

physics.chem-ph↗