arXiv subjects

Yuxuan Ren

Publications and source records attributed to Yuxuan Ren.

18 recordsLinked to original sources

arXiv2026

Chemical Chain-of-Thought Functions as a Hallucination-Prone Molecular Scratchpad

Chemical reasoning language models are expected to derive molecular answers through faithful chain-of-thought (CoT). However, across four reasoning model families and twelve chemistry tasks, hallucination is widespread and largely decoupled from answer correctness: correct answers often coexist with fabricated structural claims absent from the relevant molecules. Yet this does not make the reasoning trace computationally irrelevant. Attribution analyses suggest a shared scratchpad function expressed in model-specific forms: Chem-R and ether-0 rely on fragmented SMILES drafts, whereas ChemDFM-R emphasizes scaffold, positional, and naming cues. Notably, perturbing Chem-R's SMILES sketches degrades generation, showing that structural drafts can be causally load-bearing even when verbal structural claims are largely inert. Together, these results show that chemical CoT is neither a faithful explanation nor merely a post-hoc rationalization, but a hallucination-prone molecular scratchpad. This finding cautions against treating CoT as direct evidence of faithful reasoning and motivates process-level supervision beyond answer-only evaluation.

cs.CE↗

arXiv2026

ZGCM-1: A Fully Open and Extremely Efficient Foundation Model for Math and Agentic Search

In this work, we present ZGCM-1, a fully open 7B dense foundation model trained from scratch with extreme data, system, and algorithmic efficiency. ZGCM-1 is founded on a core premise: compact models cannot passively memorize the open web, but can overcome parametric capacity limits by coupling deliberate internal thinking with active external tool use. To support this paradigm across a 256K context, we develop an end-to-end, high-efficiency open training recipe: Architecture & System Co-design: interleaved gated sliding-window and full attention, and a stable FP8 Muon optimizer; Progressive Curriculum & MDP Mid-Training: context scaling across 16K, 64K, and 256K, and the reformulation of interaction traces into Markov Decision Processes. Furthermore, we establish an AI-native R&D workflow where agent swarms autonomously manage cluster operations, data curation, and rapid diagnostic evaluation. Extensive evaluations show that ZGCM-1-7B is competitive across 7B model family on general benchmarks. On several challenging mathematical reasoning and agentic search suites, it remains competitive with frontier models orders of magnitude larger, such as Qwen3-235B-A22B and GLM-5.1. We also show that our pre-training design offers a ~4.2x efficiency improvement in 16K pre-training time-to-loss. Across the full development lifecycle, we distill eight actionable empirical findings-spanning architectural scaling, SFT quality pruning, long-context generalization, and agentic co-training dynamics. To facilitate community research, we open-source model weights from the pre-training, mid-training, and post-training stages, intermediate checkpoints, training code, per-stage data and data recipes, and W&B logs.

cs.AI↗

arXiv2026

Molecular LLM Agents: From Architectural Design to Scientific Autonomy

Molecular science represents an important frontier for LLM-based agents. Unlike general agents that mainly operate over natural language, code, or web environments, molecular LLM agents must perceive, reason about, and act upon chemical objects across symbolic strings, molecular graphs, 3D conformations, spectra, simulations, and wet-lab measurements. Their capabilities depend on chemically faithful molecular perception, an LLM-centered agent framework, domain-specific tool grounding, and computational or experimental feedback, in addition to planning and tool use. This work develops a conceptual framework for molecular LLM agents from two complementary perspectives. First, we introduce an architectural view of molecular-agent design, covering molecular representation and perception, the agent framework, domain-specific toolboxes, and learning and optimization. Second, we propose a scientific autonomy ladder inspired by staged autonomy in engineering systems, categorizing agents into four levels: L1 assistive or fixed workflows, L2 adaptive computational agents, L3 feedback-aware physical experiment agents, and L4 scientific-agenda agents. Together, these two perspectives establish a comprehensive framework for comparing existing molecular LLM agents, identifying missing capabilities and deployment risks, and guiding the design, evaluation, and deployment of future agents in molecular discovery workflows.

cs.CL↗

arXiv2026

SinAE: A Single-Architecture Flow-Matching Autoencoder for Cross-Domain Atomic Systems

Small molecules, crystals, and proteins all reduce to atoms in 3D space, yet their generative pipelines remain fragmented across domains, each with its Small molecules, crystals, and proteins all reduce to atoms in 3D space, yet their generative pipelines remain fragmented across domains, each with its own graph, equivariant, or frame-based architecture. Cross-domain training would mitigate per-domain data scarcity, but direct generation in 3D coordinate space cannot easily handle the heterogeneous structural priors of all three domains, and no prior latent autoencoder is simultaneously lossless and architecturally general across all three. We introduce SinAE, a single-architecture flow-matching autoencoder for molecules, crystals, and proteins, with vanilla Transformer encoder and decoder and no equivariant, graph, or domain-specific operators. Rather than requiring the encoder to capture fine-grained geometry, SinAE shifts the reconstruction burden into an iterative flow-matching decoder, achieving near-lossless reconstruction across domains and reducing reconstruction errors by orders of magnitude relative to prior latent baselines. The same per-token latent supports a standard Diffusion Transformer prior that reaches strong performance on molecular, crystal, and protein generation benchmarks. Joint molecule--crystal training strictly improves both domains, providing direct evidence of cross-domain transfer through a shared atomic latent. Code is available at https://github.com/BlueWhaleLab/SinAE .

cs.LG↗

arXiv2026

MolViBench: Evaluating LLMs on Molecular Vibe Coding

Molecular Vibe Coding, a paradigm where chemists interact with LLMs to generate executable programs for molecular tasks, has emerged as a flexible alternative to chemical agents with predefined tools, enabling chemists to express arbitrarily complex, customized workflows. Unlike general coding tasks, molecular coding imposes a distinctive challenge that LLMs should jointly equip programming, molecular understanding, and domain-specific reasoning capabilities. However, existing benchmarks remain disconnected. General code generation benchmarks such as HumanEval and SWE-bench require no chemistry knowledge, while chemistry-focused benchmarks such as S^2-Bench and ChemCoTBench evaluate knowledge recall or property prediction rather than executable code generation. To bridge this gap, we introduce MolViBench, the first benchmark tailored for Molecular Vibe Coding. MolViBench comprises 358 curated tasks across five cognitive levels, ranging from single-API recall to end-to-end virtual screening pipeline design, spanning 12 real-world drug discovery workflows. To rigorously assess generated code, we also propose a multi-layered evaluation framework that combines type-aware output comparison and AST-based API-semantic fallback analysis, which jointly measures executability and chemical correctness. We systematically evaluate 9 frontier coding LLMs and compare three real-world Molecular Vibe Coding paradigms, providing a practical and fine-grained testbed for diagnosing LLMs' coding capabilities in AI-accelerated molecular discovery.

cs.CL↗

arXiv2026

Kempe Swap K-Means: A Scalable Near-Optimal Solution for Semi-Supervised Clustering

This paper presents a novel centroid-based heuristic algorithm, termed Kempe Swap K-Means, for constrained clustering under rigid must-link (ML) and cannot-link (CL) constraints. The algorithm employs a dual-phase iterative process: an assignment step that utilizes Kempe chain swaps to refine current clustering in the constrained solution space and a centroid update step that computes optimal cluster centroids. To enhance global search capabilities and avoid local optima, the framework incorporates controlled perturbations during the update phase. Empirical evaluations demonstrate that the proposed method achieves near-optimal partitions while maintaining high computational efficiency and scalability. The results indicate that Kempe Swap K-Means consistently outperforms state-of-the-art benchmarks in both clustering accuracy and algorithmic efficiency for large-scale datasets.

cs.LG↗

arXiv2026

Unified model for breathing solitons in fibre lasers: Mechanisms across below- and above-threshold regimes

The emergence of breathing solitons in mode-locked lasers presents a fundamental challenge for the theoretical modelling of mode locking, with the mechanisms underlying below- and above-threshold breathing solitons, and the origins of their distinct nonlinear dynamics, remaining poorly understood. Here, we develop a model that incorporates both spatial and temporal gain dynamics, enabling us to elucidate the origins of these two classes of pulsating states. We show that below-threshold breathing solitons arise from the interplay between Q-switching and soliton shaping, whereas Kerr nonlinearity and dispersion dominate the formation of above-threshold breathers. The model further captures the markedly different dynamical properties of these regimes. Experimental observations corroborate the simulations, validating the predictive power of the framework. Beyond providing a refined theoretical basis for ultrafast laser design, this work advances the broader understanding of non-equilibrium dynamics in mode-locked lasers and offers new perspectives on breathing soliton phenomena across diverse physical systems.

physics.optics↗

arXiv2026

Riemannian Dueling Optimization

Dueling optimization considers optimizing an objective with access to only a comparison oracle of the objective function. It finds important applications in emerging fields such as recommendation systems and robotics. Existing works on dueling optimization mainly focused on unconstrained problems in the Euclidean space. In this work, we study dueling optimization over Riemannian manifolds, which covers important applications that cannot be solved by existing dueling optimization algorithms. In particular, we propose a Riemannian Dueling Normalized Gradient Descent (RDNGD) method and establish its iteration complexity when the objective function is geodesically L-smooth or geodesically (strongly) convex. We also propose a projection-free algorithm, named Riemannian Dueling Frank-Wolfe (RDFW) method, to deal with the situation where projection is prohibited. We establish the iteration and oracle complexities for RDFW. We illustrate the effectiveness of the proposed algorithms through numerical experiments on both synthetic and real applications.

math.OC↗

arXiv2025

Constraint Decoupled Latent Diffusion for Protein Backmapping

Coarse-grained (CG) molecular dynamics simulations enable efficient exploration of protein conformational ensembles. However, reconstructing atomic details from CG structures (backmapping) remains a challenging problem. Current approaches face an inherent trade-off between maintaining atomistic accuracy and exploring diverse conformations, often necessitating complex constraint handling or extensive refinement steps. To address these challenges, we introduce a novel two-stage framework, named CODLAD (COnstraint Decoupled LAtent Diffusion). This framework first compresses atomic structures into discrete latent representations, explicitly embedding structural constraints, thereby decoupling constraint handling from generation. Subsequently, it performs efficient denoising diffusion in this latent space to produce structurally valid and diverse all-atom conformations. Comprehensive evaluations on diverse protein datasets demonstrate that CODLAD achieves state-of-the-art performance in atomistic accuracy, conformational diversity, and computational efficiency while exhibiting strong generalization across different protein systems. Code is available at https://github.com/xiaoxiaokuye/CODLAD.

cs.LG↗

arXiv2025

EPO: Diverse and Realistic Protein Ensemble Generation via Energy Preference Optimization

Accurate exploration of protein conformational ensembles is essential for uncovering function but remains hard because molecular-dynamics (MD) simulations suffer from high computational costs and energy-barrier trapping. This paper presents Energy Preference Optimization (EPO), an online refinement algorithm that turns a pretrained protein ensemble generator into an energy-aware sampler without extra MD trajectories. Specifically, EPO leverages stochastic differential equation sampling to explore the conformational landscape and incorporates a novel energy-ranking mechanism based on list-wise preference optimization. Crucially, EPO introduces a practical upper bound to efficiently approximate the intractable probability of long sampling trajectories in continuous-time generative models, making it easily adaptable to existing pretrained generators. On Tetrapeptides, ATLAS, and Fast-Folding benchmarks, EPO successfully generates diverse and physically realistic ensembles, establishing a new state-of-the-art in nine evaluation metrics. These results demonstrate that energy-only preference signals can efficiently steer generative models toward thermodynamically consistent conformational ensembles, providing an alternative to long MD simulations and widening the applicability of learned potentials in structural biology and drug discovery.

cs.LG↗

arXiv2024

Physical Consistency Bridges Heterogeneous Data in Molecular Multi-Task Learning

In recent years, machine learning has demonstrated impressive capability in handling molecular science tasks. To support various molecular properties at scale, machine learning models are trained in the multi-task learning paradigm. Nevertheless, data of different molecular properties are often not aligned: some quantities, e.g. equilibrium structure, demand more cost to compute than others, e.g. energy, so their data are often generated by cheaper computational methods at the cost of lower accuracy, which cannot be directly overcome through multi-task learning. Moreover, it is not straightforward to leverage abundant data of other tasks to benefit a particular task. To handle such data heterogeneity challenges, we exploit the specialty of molecular tasks that there are physical laws connecting them, and design consistency training approaches that allow different tasks to exchange information directly so as to improve one another. Particularly, we demonstrate that the more accurate energy data can improve the accuracy of structure prediction. We also find that consistency training can directly leverage force and off-equilibrium structure data to improve structure prediction, demonstrating a broad capability for integrating heterogeneous data.

cs.LG↗

arXiv2024

Neural P$^3$M: A Long-Range Interaction Modeling Enhancer for Geometric GNNs

Geometric graph neural networks (GNNs) have emerged as powerful tools for modeling molecular geometry. However, they encounter limitations in effectively capturing long-range interactions in large molecular systems. To address this challenge, we introduce Neural P$^3$M, a versatile enhancer of geometric GNNs to expand the scope of their capabilities by incorporating mesh points alongside atoms and reimaging traditional mathematical operations in a trainable manner. Neural P$^3$M exhibits flexibility across a wide range of molecular systems and demonstrates remarkable accuracy in predicting energies and forces, outperforming on benchmarks such as the MD22 dataset. It also achieves an average improvement of 22% on the OE62 dataset while integrating with various architectures.

cs.LG↗

arXiv2024

QCQP-Net: Reliably Learning Feasible Alternating Current Optimal Power Flow Solutions Under Constraints

At the heart of power system operations, alternating current optimal power flow (ACOPF) studies the generation of electric power in the most economical way under network-wide load requirement, and can be formulated as a highly structured non-convex quadratically constrained quadratic program (QCQP). Optimization-based solutions to ACOPF (such as ADMM or interior-point method), as the classic approach, require large amount of computation and cannot meet the need to repeatedly solve the problem as load requirement frequently changes. On the other hand, learning-based methods that directly predict the ACOPF solution given the load input incur little computational cost but often generates infeasible solutions (i.e. violate the constraints of ACOPF). In this work, we combine the best of both worlds -- we propose an innovated framework for learning ACOPF, where the input load is mapped to the ACOPF solution through a neural network in a computationally efficient and reliable manner. Key to our innovation is a specific-purpose "activation function" defined implicitly by a QCQP and a novel loss, which enforce constraint satisfaction. We show through numerical simulations that our proposed method achieves superior feasibility rate and generation cost in situations where the existing learning-based approaches fail.

math.OC↗

arXiv2022

Bayesian Risk Markov Decision Processes

We consider finite-horizon Markov Decision Processes where parameters, such as transition probabilities, are unknown and estimated from data. The popular distributionally robust approach to addressing the parameter uncertainty can sometimes be overly conservative. In this paper, we propose a new formulation, Bayesian risk Markov Decision Process (BR-MDP), to address parameter uncertainty in MDPs, where a risk functional is applied in nested form to the expected total cost with respect to the Bayesian posterior distribution of the unknown parameters. The proposed formulation provides more flexible risk attitutes towards parameter uncertainty and takes into account the availability of data in future times stages. To solve the proposed formulation with the conditional value-at-risk (CVaR) risk functional, we propose an efficient approximation algorithm by deriving an analytical approximation of the value function and utilizing the convexity of CVaR. We demonstrate the empirical performance of the BR-MDP formulation and proposed algorithms on a gambler's betting problem and an inventory control problem.

eess.SY↗

arXiv2020

Group Testing Enables Asymptomatic Screening for COVID-19 Mitigation: Feasibility and Optimal Pool Size Selection with Dilution Effects

Repeated asymptomatic screening for SARS-CoV-2 promises to control spread of the virus but would require too many resources to implement at scale. Group testing is promising for screening more people with fewer test resources: multiple samples tested together in one pool can be excluded with one negative test result. Existing approaches to group testing design for SARS-CoV-2 asymptomatic screening, however, do not consider dilution effects: that false negatives become more common with larger pools. As a consequence, they may recommend pool sizes that are too large or misestimate the benefits of screening. Modeling dilution effects, we derive closed-form expressions for the expected number of tests and false negative/positives per person screened under two popular group testing methods: the linear and square array methods. We find that test error correlation induced by a common viral load across an individual's samples results in many fewer false negatives than would be expected from less realistic but more widely assumed independent errors. This insight also suggests that false positives can be controlled through repeated tests without significantly increasing false negatives. Using these closed-form expressions to trace a Pareto frontier over error rates and tests, we design testing protocols for repeated asymptomatic screening of a large population. We minimize disease prevalence by optimizing a time-varying pool sizes and screening frequency constrained by daily test capacity and a false positive limit. This provides a testing protocol practitioners can use for mitigating COVID-19. In a case study, we demonstrate the effectiveness of this methodology in controlling spread.

q-bio.PE↗

arXiv2020

Generalized Perfect Optical Vortex along Arbitrary Trajectories

Perfect optical vortex (POV) is a type of vortex beam with an infinite thin ring and a fixed radius independent of its topological charge. Here we propose the concept of generalized perfect optical vortex along arbitrary curves beyond the regular shapes of circle and ellipse. Generalized perfect optical vortices also share the similar properties as POVs, such as defined only along infinite thin curves and owning topological charges independent of scales. Notably, they naturally degenerate to the POVs and elliptic POVs along circles and ellipses, respectively. We also experimentally generated the generalized perfect optical vortices through a digital micromirror device (DMD) and measured the phase distributions by interferometry, exhibiting good agreements with the simulations. Moreover, we derive a proper modified formula to yield the generalized perfect optical vortices with uniform intensity distribution along predesigned curves. The generalized perfect optical vortices might find the potential applications in optical tweezers and communication.

physics.optics↗

arXiv2018

High-Performance Hybrid Silicon and Lithium Niobate Mach-Zehnder Modulators for 100 Gbit/s and Beyond

Optical modulators are at the heart of optical communication links. Ideally, they should feature low insertion loss, low drive voltage, large modulation bandwidth, high linearity, compact footprint and low manufacturing cost. Unfortunately, these criteria have only been achieved on separate occasions.Based on a Silicon and Lithium Niobate hybrid integration platform, we demonstrate Mach-Zehnder modulators that simultaneously fulfill these criteria. The presented device exhibits an insertion loss of 2.5 dB, voltage-length product of 2.2 Vcm, high linearity, electro-optic bandwidth of at least 70 GHz and modulation rates up to 112 Gbit/s. The high-performance modulator is realized by seamless integration of high-contrast waveguide based on Lithium Niobate - the most mature modulator material - with compact, low-loss silicon circuits. The hybrid platform demonstrated here allows for the combination of 'best-in-breed' active and passive components, opening up new avenues for enabling future high-speed, energy efficient and cost-effective optical communication networks.

physics.app-ph↗

arXiv2016

Controllable light capsules employing modified Bessel-Gauss beams

We report, in theory and experiment, on a novel class of controlled light capsules with nearly perfect darkness, directly employing intrinsic properties of modified Bessel-Gauss beams. These beams are able to naturally create three-dimensional bottle-shaped region during propagation as long as the parameters are properly chosen. Remarkably, the optical bottle can be controlled to demonstrate various geometries through tuning the beam parameters, thereby leading to an adjustable light capsule. We provide a detailed insight into the theoretical origin and characteristics of the light capsule derived from modified Bessel-Gauss beams. Moreover, a binary digital micromirror device (DMD) based scheme is first employed to shape the bottle beams by precise amplitude and phase manipulation. Further, we demonstrate their ability for optical trapping of core-shell magnetic microparticles, which play a particular role in biomedical research, with holographic optical tweezers. Therefore, our observations provide a new route for generating and controlling bottle beams and will widen the potentials for micromanipulation of absorbing particles, aerosols or even individual atoms.

physics.optics↗