arXiv subjects

Yuanqing Wang

Publications and source records attributed to Yuanqing Wang.

At least 19 recordsLinked to original sources

arXiv2026

Heat Field Signatures: From Point Clouds to Smooth Geometry

Bringing multiscale geometric analysis directly to irregular point clouds remains difficult: quantities such as local dimension, anisotropy, density variation, and geometric transitions are typically estimated through explicit neighborhood, manifold, or graph constructions, or left for neural networks to infer from coordinates. We introduce Heat Field Signatures (HFS), which lift a point cloud to a multiscale family of smooth ambient heat fields, providing a direct interface from discrete samples to geometric analysis. From this field, HFS computes closed-form global and local signatures directly from pairwise distances, capturing heat concentration, intrinsic dimension, anisotropy, and scale transitions. We further introduce the Heat Dimension Spectrum (HDS), a compact summary of multiscale geometric composition. HFS can be used as a closed-form descriptor, a lightweight learned representation, or a geometric feature channel for neural point-cloud models. Across synthetic and real-world benchmarks spanning subcellular, neuronal, tree, and protein data, HFS outperforms strong point-cloud and multiparameter-persistence baselines while substantially reducing end-to-end cost. On SCOP protein-fold classification, HFS improves over the strongest deep baseline by nearly $24$ percentage points using coordinates alone, while standalone HFS representations are exactly rotation-invariant by construction. More broadly, HFS turns a classical heat field into a practical interface for multiscale geometric analysis in modern point-cloud learning.

cs.LG↗

arXiv2026

RLinf-VLA: A Unified and Efficient Framework for Reinforcement Learning of Vision-Language-Action Models

Recent studies have demonstrated the potential of reinforcement learning (RL) to improve the task performance of vision-language-action (VLA) models through interaction. However, current efforts remain fragmented, lacking a unified platform for fair comparison across architectures and algorithms, as well as an efficient system design for scalable training. Therefore, we present RLinf-VLA, a unified and efficient framework for scalable RL training of VLA models. RLinf-VLA standardizes the integration of diverse VLA architectures, RL algorithms, and heterogeneous simulators through a unified interface, enabling extensibility and reproducibility. To improve efficiency, the framework adopts a flexible resource allocation architecture for rendering, inference, and training in RL pipelines. In particular, RLinf-VLA introduces a hybrid fine-grained pipeline allocation strategy that achieves a 1.61$\times$-1.88$\times$ training speedup on ManiSkill. Using this framework, RL-trained models achieve strong performance across embodied benchmarks, including 98.11% success on 130 LIBERO tasks, 97.66% success on 25 ManiSkill tasks, and 84.63% average success across 6 RoboTwin tasks. In addition, RLinf-VLA distills a set of effective practices for RL-based VLA training. We envision RLinf-VLA as a foundational framework for efficient, unified, and reproducible research in embodied intelligence.

cs.RO↗

arXiv2026

DynaTrain: Fast Online Parallelism Switching for Elastic LLM Training

Modern large language model (LLM) training is inherently dynamic: resource fluctuations, RLHF phase shifts, and cluster elasticity continually reshape the optimal parallelism layout, posing a significant challenge to existing training frameworks built around a static execution model. We present DynaTrain, a distributed training system for sub-second, online reconfiguration across arbitrary multi-dimensional parallelism. At its core, we propose a Virtual Parameter Space (VPS) abstraction that unifies all distributed training states under one logical coordinate space, turning any parallelism configuration into a deterministic mapping and collapsing complex transition into manageable geometric intersections. On top of VPS, a state routing-and-transition layer executes rank-local transfers under a memory-aware, deadlock-free schedule, and an Elastic Device Manager overlaps new-world construction with ongoing training to mask topology-change cost. On dense and MoE models up to 235B parameters, DynaTrain reconfigures a 70B dense model in under 2s and a 235B MoE model in 4.36s, outperforming state-of-the-art checkpoint-based and elastic systems by up to three orders of magnitude while preserving correctness.

cs.LG↗

arXiv2026

FEAT: Free energy Estimators with Adaptive Transport

We present Free energy Estimators with Adaptive Transport (FEAT), a novel framework for free energy estimation -- a critical challenge across scientific domains. FEAT leverages learned transports implemented via stochastic interpolants and provides consistent, minimum-variance estimators based on escorted Jarzynski equality and controlled Crooks theorem, alongside variational upper and lower bounds on free energy differences. Unifying equilibrium and non-equilibrium methods under a single theoretical framework, FEAT establishes a principled foundation for neural free energy calculations. Experimental validation on toy examples, molecular simulations, and quantum field theory demonstrates improvements over existing learning-based methods. Our PyTorch implementation is available at https://github.com/jiajunhe98/FEAT.

stat.ML↗

arXiv2025

RLinf: Flexible and Efficient Large-scale Reinforcement Learning via Macro-to-Micro Flow Transformation

Reinforcement learning (RL) has demonstrated immense potential in advancing artificial general intelligence, agentic intelligence, and embodied intelligence. However, the inherent heterogeneity and dynamicity of RL workflows often lead to low hardware utilization and slow training on existing systems. In this paper, we present RLinf, a high-performance RL training system based on our key observation that the major roadblock to efficient RL training lies in system flexibility. To maximize flexibility and efficiency, RLinf is built atop a novel RL system design paradigm called macro-to-micro flow transformation (M2Flow), which automatically breaks down high-level, easy-to-compose RL workflows at both the temporal and spatial dimensions, and recomposes them into optimized execution flows. Supported by RLinf worker's adaptive communication capability, we devise context switching and elastic pipelining to realize M2Flow transformation, and a profiling-guided scheduling policy to generate optimal execution plans. Extensive evaluations on both reasoning RL and embodied RL tasks demonstrate that RLinf consistently outperforms state-of-the-art systems, achieving $1.07\times-2.43\times$ speedup in end-to-end training throughput.

cs.LG↗

arXiv2024

Harnessing Earnings Reports for Stock Predictions: A QLoRA-Enhanced LLM Approach

Accurate stock market predictions following earnings reports are crucial for investors. Traditional methods, particularly classical machine learning models, struggle with these predictions because they cannot effectively process and interpret extensive textual data contained in earnings reports and often overlook nuances that influence market movements. This paper introduces an advanced approach by employing Large Language Models (LLMs) instruction fine-tuned with a novel combination of instruction-based techniques and quantized low-rank adaptation (QLoRA) compression. Our methodology integrates 'base factors', such as financial metric growth and earnings transcripts, with 'external factors', including recent market indices performances and analyst grades, to create a rich, supervised dataset. This comprehensive dataset enables our models to achieve superior predictive performance in terms of accuracy, weighted F1, and Matthews correlation coefficient (MCC), especially evident in the comparison with benchmarks such as GPT-4. We specifically highlight the efficacy of the llama-3-8b-Instruct-4bit model, which showcases significant improvements over baseline models. The paper also discusses the potential of expanding the output capabilities to include a 'Hold' option and extending the prediction horizon, aiming to accommodate various investment styles and time frames. This study not only demonstrates the power of integrating cutting-edge AI with fine-tuned financial data but also paves the way for future research in enhancing AI-driven financial analysis tools.

q-fin.CP↗

arXiv2024

Molecular Dynamics and Machine Learning Unlock Possibilities in Beauty Design -- A Perspective

Computational molecular design -- the endeavor to design molecules, with various missions, aided by machine learning and molecular dynamics approaches, has been widely applied to create valuable new molecular entities, from small molecule therapeutics to protein biologics. In the small data regime, physics-based approaches model the interaction between the molecule being designed and proteins of key physiological functions, providing structural insights into the mechanism. When abundant data has been collected, a quantitative structure-activity relationship (QSAR) can be more directly constructed from experimental data, from which machine learning can distill key insights to guide the design of the next round of experiment design. Machine learning methodologies can also facilitate physical modeling, from improving the accuracy of force fields and extending them to unseen chemical spaces, to more directly enhancing the sampling on the conformational spaces. We argue that these techniques are mature enough to be applied to not just extend the longevity of life, but the beauty it manifests. In this perspective, we review the current frontiers in the research \& development of skin care products, as well as the statistical and physical toolbox applicable to addressing the challenges in this industry. Feasible interdisciplinary research projects are proposed to harness the power of machine learning tools to design innovative, effective, and inexpensive skin care products.

physics.chem-ph↗

arXiv2024

Non-convolutional Graph Neural Networks

Rethink convolution-based graph neural networks (GNN) -- they characteristically suffer from limited expressiveness, over-smoothing, and over-squashing, and require specialized sparse kernels for efficient computation. Here, we design a simple graph learning module entirely free of convolution operators, coined random walk with unifying memory (RUM) neural network, where an RNN merges the topological and semantic graph features along the random walks terminating at each node. Relating the rich literature on RNN behavior and graph topology, we theoretically show and experimentally verify that RUM attenuates the aforementioned symptoms and is more expressive than the Weisfeiler-Lehman (WL) isomorphism test. On a variety of node- and graph-level classification and regression tasks, RUM not only achieves competitive performance, but is also robust, memory-efficient, scalable, and faster than the simplest convolutional GNNs.

cs.LG↗

arXiv2024

On the design space between molecular mechanics and machine learning force fields

A force field as accurate as quantum mechanics (QM) and as fast as molecular mechanics (MM), with which one can simulate a biomolecular system efficiently enough and meaningfully enough to get quantitative insights, is among the most ardent dreams of biophysicists -- a dream, nevertheless, not to be fulfilled any time soon. Machine learning force fields (MLFFs) represent a meaningful endeavor towards this direction, where differentiable neural functions are parametrized to fit ab initio energies, and furthermore forces through automatic differentiation. We argue that, as of now, the utility of the MLFF models is no longer bottlenecked by accuracy but primarily by their speed (as well as stability and generalizability), as many recent variants, on limited chemical spaces, have long surpassed the chemical accuracy of $1$ kcal/mol -- the empirical threshold beyond which realistic chemical predictions are possible -- though still magnitudes slower than MM. Hoping to kindle explorations and designs of faster, albeit perhaps slightly less accurate MLFFs, in this review, we focus our attention on the design space (the speed-accuracy tradeoff) between MM and ML force fields. After a brief review of the building blocks of force fields of either kind, we discuss the desired properties and challenges now faced by the force field development community, survey the efforts to make MM force fields more accurate and ML force fields faster, envision what the next generation of MLFF might look like.

physics.chem-ph↗

arXiv2024

Structural design of the acrylic vessel for the Jinping Neutrino Experiment

The Jinping neutrino experiment is designed to have multiple purposes in the China Jinping Underground Laboratory. Following the acrylic vessel design requirements proposal, a structural scheme has been developed and optimized. Subsequently, the stability of the acrylic shell structure was calculated using finite element analysis, as well as the load-bearing capacities under various working conditions. Further, the effects of temperature changes, rope failures, and Young's modulus of the ropes on the static behavior of the structure were analyzed. The results indicated that the stress level and structural displacement of the structure scheme satisfies the design requirements, as well as the stability of the vessel under compression. Moreover, the stress and displacement of the acrylic shell satisfies the given working conditions and temperatures. The structural scheme ensures basic safety if the rope fails.

physics.ins-det↗

arXiv2023

Machine-learned molecular mechanics force field for the simulation of protein-ligand systems and beyond

The development of reliable and extensible molecular mechanics (MM) force fields -- fast, empirical models characterizing the potential energy surface of molecular systems -- is indispensable for biomolecular simulation and computer-aided drug design. Here, we introduce a generalized and extensible machine-learned MM force field, \texttt{espaloma-0.3}, and an end-to-end differentiable framework using graph neural networks to overcome the limitations of traditional rule-based methods. Trained in a single GPU-day to fit a large and diverse quantum chemical dataset of over 1.1M energy and force calculations, \texttt{espaloma-0.3} reproduces quantum chemical energetic properties of chemical domains highly relevant to drug discovery, including small molecules, peptides, and nucleic acids. Moreover, this force field maintains the quantum chemical energy-minimized geometries of small molecules and preserves the condensed phase properties of peptides, self-consistently parametrizing proteins and ligands to produce stable simulations leading to highly accurate predictions of binding free energies. This methodology demonstrates significant promise as a path forward for systematically building more accurate force fields that are easily extensible to new chemical domains of interest.

physics.chem-ph↗

arXiv2023

OpenMM 8: Molecular Dynamics Simulation with Machine Learning Potentials

Machine learning plays an important and growing role in molecular simulation. The newest version of the OpenMM molecular dynamics toolkit introduces new features to support the use of machine learning potentials. Arbitrary PyTorch models can be added to a simulation and used to compute forces and energy. A higher-level interface allows users to easily model their molecules of interest with general purpose, pretrained potential functions. A collection of optimized CUDA kernels and custom PyTorch operations greatly improves the speed of simulations. We demonstrate these features on simulations of cyclin-dependent kinase 8 (CDK8) and the green fluorescent protein (GFP) chromophore in water. Taken together, these features make it practical to use machine learning to improve the accuracy of simulations at only a modest increase in cost.

physics.chem-ph↗

arXiv2023

EspalomaCharge: Machine learning-enabled ultra-fast partial charge assignment

Atomic partial charges are crucial parameters in molecular dynamics (MD) simulation, dictating the electrostatic contributions to intermolecular energies, and thereby the potential energy landscape. Traditionally, the assignment of partial charges has relied on surrogates of \textit{ab initio} semiempirical quantum chemical methods such as AM1-BCC, and is expensive for large systems or large numbers of molecules. We propose a hybrid physical / graph neural network-based approximation to the widely popular AM1-BCC charge model that is orders of magnitude faster while maintaining accuracy comparable to differences in AM1-BCC implementations. Our hybrid approach couples a graph neural network to a streamlined charge equilibration approach in order to predict molecule-specific atomic electronegativity and hardness parameters, followed by analytical determination of optimal charge-equilibrated parameters that preserves total molecular charge. This hybrid approach scales linearly with the number of atoms, enabling, for the first time, the use of fully consistent charge models for small molecules and biopolymers for the construction of next-generation self-consistent biomolecular force fields. Implemented in the free and open source package \texttt{espaloma\_charge}, this approach provides drop-in replacements for both AmberTools \texttt{antechamber} and the Open Force Field Toolkit charging workflows, in addition to stand-alone charge generation interfaces. Source code is available at \url{https://github.com/choderalab/espaloma_charge}.

cs.LG↗

arXiv2023

Spatial Attention Kinetic Networks with E(n)-Equivariance

Neural networks that are equivariant to rotations, translations, reflections, and permutations on n-dimensional geometric space have shown promise in physical modeling for tasks such as accurately but inexpensively modeling complex potential energy surfaces to guiding the sampling of complex dynamical systems or forecasting their time evolution. Current state-of-the-art methods employ spherical harmonics to encode higher-order interactions among particles, which are computationally expensive. In this paper, we propose a simple alternative functional form that uses neurally parametrized linear combinations of edge vectors to achieve equivariance while still universally approximating node environments. Incorporating this insight, we design spatial attention kinetic networks with E(n)-equivariance, or SAKE, which are competitive in many-body system modeling tasks while being significantly faster.

cs.LG↗

arXiv2023

Distilling Accurate Descriptors from Multi-Source Experimental Data for Discovering Highly Active Perovskite OER Catalysts

Perovskite oxides are promising catalysts for oxygen evolution reaction (OER), yet the huge chemical space remains largely unexplored due to the lack of effective approaches. Here, we report the distilling of accurate descriptors from multi-source experimental data for accelerated catalysts discovery by using the new method SCMT-SISSO that overcomes the challenge of data inconsistency between different sources. While many previous descriptors for the catalytic activity were proposed based on respective small datasets, we obtained the new 2D descriptor (d_B, n_B) based on 13 experimental datasets collected from different publications and the SCMT-SISSO. Great universality and predictive accuracy, and the bulk-surface correspondence, of this descriptor have been demonstrated. With this descriptor, hundreds of unreported candidate perovskites with activity greater than the benchmark catalyst Ba0.5Sr0.5Co0.8Fe0.2O3 were identified from a large chemical space. Our experimental validations on five candidates confirmed the three highly active new perovskite catalysts SrCo0.6Ni0.4O3, Rb0.1Sr0.9Co0.7Fe0.3O3, and Cs0.1Sr0.9Co0.4Fe0.6O3.

cond-mat.mtrl-sci↗

arXiv2022

SPICE, A Dataset of Drug-like Molecules and Peptides for Training Machine Learning Potentials

Machine learning potentials are an important tool for molecular simulation, but their development is held back by a shortage of high quality datasets to train them on. We describe the SPICE dataset, a new quantum chemistry dataset for training potentials relevant to simulating drug-like small molecules interacting with proteins. It contains over 1.1 million conformations for a diverse set of small molecules, dimers, dipeptides, and solvated amino acids. It includes 15 elements, charged and uncharged molecules, and a wide range of covalent and non-covalent interactions. It provides both forces and energies calculated at the ωB97M-D3(BJ)/def2-TZVPPD level of theory, along with other useful quantities such as multipole moments and bond orders. We train a set of machine learning potentials on it and demonstrate that they can achieve chemical accuracy across a broad region of chemical space. It can serve as a valuable resource for the creation of transferable, ready to use potential functions for use in molecular simulations.

physics.chem-ph↗

arXiv2022

End-to-End Differentiable Molecular Mechanics Force Field Construction

Molecular mechanics (MM) potentials have long been a workhorse of computational chemistry. Leveraging accuracy and speed, these functional forms find use in a wide variety of applications in biomolecular modeling and drug discovery, from rapid virtual screening to detailed free energy calculations. Traditionally, MM potentials have relied on human-curated, inflexible, and poorly extensible discrete chemical perception rules or applying parameters to small molecules or biopolymers, making it difficult to optimize both types and parameters to fit quantum chemical or physical property data. Here, we propose an alternative approach that uses graph neural networks to perceive chemical environments, producing continuous atom embeddings from which valence and nonbonded parameters can be predicted using invariance-preserving layers. Since all stages are built from smooth neural functions, the entire process is modular and end-to-end differentiable with respect to model parameters, allowing new force fields to be easily constructed, extended, and applied to arbitrary molecules. We show that this approach is not only sufficiently expressive to reproduce legacy atom types, but that it can learn to accurately reproduce and extend existing molecular mechanics force fields. Trained with arbitrary loss functions, it can construct entirely new force fields self-consistently applicable to both biopolymers and small molecules directly from quantum chemical calculations, with superior fidelity than traditional atom or parameter typing schemes. When trained on the same quantum chemical small molecule dataset used to parameterize the openff-1.2.0 small molecule force field augmented with a peptide dataset, the resulting espaloma model shows superior accuracy vis-à-vis experiments in computing relative alchemical free energy calculations for a popular benchmark set.

physics.comp-ph↗

arXiv2021

Stochastic Aggregation in Graph Neural Networks

Graph neural networks (GNNs) manifest pathologies including over-smoothing and limited discriminating power as a result of suboptimally expressive aggregating mechanisms. We herein present a unifying framework for stochastic aggregation (STAG) in GNNs, where noise is (adaptively) injected into the aggregation process from the neighborhood to form node embeddings. We provide theoretical arguments that STAG models, with little overhead, remedy both of the aforementioned problems. In addition to fixed-noise models, we also propose probabilistic versions of STAG models and a variational inference framework to learn the noise posterior. We conduct illustrative experiments clearly targeting oversmoothing and multiset aggregation limitations. Furthermore, STAG enhances general performance of GNNs demonstrated by competitive performance in common citation and molecule graph benchmark datasets.

stat.ML↗