arXiv subjects

Yanyan Xu

Publications and source records attributed to Yanyan Xu.

At least 19 recordsLinked to original sources

arXiv2026

A General-Purpose Framework for Chemical Reaction Representation with Atomic Correspondence and Flexible Condition Adaptation

Motivation: Organic synthesis is fundamental to the chemical industry, particularly in domains such as pharmaceutical development. While artificial intelligence offers powerful tools for modeling chemical reactions, current approaches are primarily limited to two paradigms: those that rely on hand-crafted, domain-specific features, and those that apply generic deep learning models through simplistic concatenation or aggregation of reaction components. The former often struggles to scale effectively with increasing data volumes, while the latter relies on simple input- or feature-level concatenation to combine different reaction components. Such simplistic aggregation prevents these models from directly capturing the structural transformations between reactants and products, and also makes it difficult to adapt or extend them to datasets that include non-molecular reaction conditions without modifying their model architectures. Results: This paper introduces Align-React, a novel chemical reaction representation learning framework designed for a wide range of organic reaction tasks. Our approach integrates atomic correspondence between reactants and products to discern precise molecular transformations, thereby improving the model's comprehension of molecular transformation patterns. We incorporate an adapter structure to embed reaction conditions into the representation, enhancing adaptability across varied datasets and tasks. Furthermore, a Reaction-Center-Aware attention mechanism is proposed to enable the model to focus on critical functional groups, yielding more powerful and informative representations. Evaluated across multiple downstream tasks, our model demonstrates superior performance, significantly outperforming existing chemical reaction representation learning architectures on most benchmark datasets.

cs.LG↗

arXiv2026

MS-GPT: Rethinking MS/MS De Novo Structure Elucidation as Spectrum-Induced Posterior Querying of a Molecule-Language Model

Molecular structure elucidation from tandem mass spectra (MS/MS) is a central inverse problem in analytical chemistry. Most existing approaches to MS/MS identification remain tied to reference libraries or predefined candidate sets, whereas de novo methods aim to generate structures directly from spectra. A common de novo route predicts a molecular fingerprint from the spectrum and then decodes structures from it, enabling decoder pretraining on large molecule-only corpora. However, this paradigm creates a training-inference mismatch: the decoder is trained on oracle fingerprints computed from molecules, but at inference it is queried with a noisy spectrum-induced fingerprint posterior that is typically collapsed to a single thresholded fingerprint. We introduce MS-GPT, which recasts fingerprint-mediated de novo elucidation as spectrum-induced posterior querying of a conditional molecule-language model. MS-GPT conditions a molecule-language model on fingerprints and formulas, then converts the spectrum-induced posterior into a band of fingerprint queries near the oracle-fingerprint manifold through active-bit density calibration. Candidates sampled across this band are pooled and ranked by generation-frequency consensus. A lightweight LoRA adapter further mitigates domain-specific posterior bias while preserving the pretrained molecular prior. On NPLIB1 and MassSpecGym, MS-GPT sets a new state of the art, reaching Top-1/Top-10 exact-match accuracy of 29.8\%/41.1\% and 23.9\%/28.7\%, respectively. Candidate-pool scaling shows that efficient autoregressive molecular generation continues to improve recall with a little additional inference cost. The source code and model checkpoints are available at https://github.com/VIKI623/MS-GPT.

cs.LG↗

arXiv2026

Transferable Human Mobility Network Reconstruction with neuroGravity

Accurate modeling of human mobility is critical for tackling urban planning and public health challenges. In undeveloped regions, the absence of comprehensive travel surveys necessitates reconstructing mobility networks from publicly available data. Here we develop neuroGravity, a physics-informed deep learning model that reliably reconstructs mobility flows from limited observations and transfers to unobserved cities. Using only urban facility and population distributions, we find that neuroGravity's regional representations strongly correlate with socioeconomic and livability status, offering scalable proxies for costly surveys. Furthermore, we uncover that spatial income segregation plays a key role in model transferability: mobility networks are most reliably reconstructed when target cities share similar segregation levels with the source. We design an index to quantify this segregation and accurately predict transferability. Finally, we generate mobility flow proxies for over 1,200 cities worldwide, highlighting neuroGravity's potential to mitigate critical data shortages in resource-limited, underdeveloped areas.

cs.AI↗

arXiv2026

R3DP: Real-Time 3D-Aware Policy for Embodied Manipulation

Embodied manipulation requires accurate 3D understanding of objects and their spatial relations to plan and execute contact-rich actions. While large-scale 3D vision models provide strong priors, their computational cost incurs prohibitive latency for real-time control. We propose Real-time 3D-aware Policy (R3DP), which integrates powerful 3D priors into manipulation policies without sacrificing real-time performance. A core innovation of R3DP is the asynchronous fast-slow collaboration module, which seamlessly integrates large-scale 3D priors into the policy without compromising real-time performance. The system maintains real-time efficiency by querying the pre-trained slow system (VGGT) only on sparse key frames, while simultaneously employing a lightweight Temporal Feature Prediction Network (TFPNet) to predict features for all intermediate frames. By leveraging historical data to exploit temporal correlations, TFPNet explicitly improves task success rates through consistent feature estimation. Additionally, to enable more effective multi-view fusion, we introduce a Multi-View Feature Fuser (MVFF) that aggregates features across views by explicitly incorporating camera intrinsics and extrinsics. R3DP offers a plug-and-play solution for integrating large models into real-time inference systems. We evaluate R3DP against multiple baselines across different visual configurations. R3DP effectively harnesses large-scale 3D priors to achieve superior results, outperforming single-view and multi-view DP by 32.9% and 51.4% in average success rate, respectively. Furthermore, by decoupling heavy 3D reasoning from policy execution, R3DP achieves a 44.8% reduction in inference time compared to a naive DP+VGGT integration.

cs.RO↗

arXiv2025

Text-Augmented Multimodal LLMs for Chemical Reaction Condition Recommendation

Identifying reaction conditions that are broadly applicable across diverse substrates is a longstanding challenge in chemical and pharmaceutical research. While many methods are available to generate conditions with acceptable performance, a universal approach for reliably discovering effective conditions during reaction exploration is rare. Consequently, current reaction optimization processes are often labor-intensive, time-consuming, and costly, relying heavily on trial-and-error experimentation. Nowadays, large language models (LLMs) are capable of tackling chemistry-related problems, such as molecule design and chemical reasoning tasks. Here, we report the design, implementation and application of Chemma-RC, a text-augmented multimodal LLM to identify effective conditions through task-specific dialogue and condition generation. Chemma-RC learns a unified representation of chemical reactions by aligning multiple modalities-including text corpus, reaction SMILES, and reaction graphs-within a shared embedding module. Performance benchmarking on datasets showed high precision in identifying optimal conditions, with up to 17% improvement over the current state-of-the-art methods. A palladium-catalysed imidazole C-H arylation reaction was investigated experimentally to evaluate the functionalities of the Chemma-RC in practice. Our findings suggest that Chemma-RC holds significant potential to accelerate high-throughput condition screening in chemical synthesis.

cs.AI↗

arXiv2025

Where to Go Next Day: Multi-scale Spatial-Temporal Decoupled Model for Mid-term Human Mobility Prediction

Predicting individual mobility patterns is crucial across various applications. While current methods mainly focus on predicting the next location for personalized services like recommendations, they often fall short in supporting broader applications such as traffic management and epidemic control, which require longer period forecasts of human mobility. This study addresses mid-term mobility prediction, aiming to capture daily travel patterns and forecast trajectories for the upcoming day or week. We propose a novel Multi-scale Spatial-Temporal Decoupled Predictor (MSTDP) designed to efficiently extract spatial and temporal information by decoupling daily trajectories into distinct location-duration chains. Our approach employs a hierarchical encoder to model multi-scale temporal patterns, including daily recurrence and weekly periodicity, and utilizes a transformer-based decoder to globally attend to predicted information in the location or duration chain. Additionally, we introduce a spatial heterogeneous graph learner to capture multi-scale spatial relationships, enhancing semantic-rich representations. Extensive experiments, including statistical physics analysis, are conducted on large-scale mobile phone records in five cities (Boston, Los Angeles, SF Bay Area, Shanghai, and Tokyo), to demonstrate MSTDP's advantages. Applied to epidemic modeling in Boston, MSTDP significantly outperforms the best-performing baseline, achieving a remarkable 62.8% reduction in MAE for cumulative new cases.

cs.AI↗

arXiv2025

ChemActor: Enhancing Automated Extraction of Chemical Synthesis Actions with LLM-Generated Data

With the increasing interest in robotic synthesis in the context of organic chemistry, the automated extraction of chemical procedures from literature is critical. However, this task remains challenging due to the inherent ambiguity of chemical language and the high cost of human annotation required for developing reliable computer-aided extraction protocols. Here, we present ChemActor, a fully fine-tuned large language model (LLM), as a chemical executor to convert between unstructured experimental procedures and structured action sequences. We propose a sequential LLM-generated data framework to address the challenges of insufficient and low-quality annotated data. This framework integrates a data selection module that selects data based on distribution divergence, with a general-purpose LLM, to generate machine-executable actions from a single molecule input. Additionally, we introduce a novel multi-round LLMs circle review metric, which reflects the model's advanced understanding of chemical experimental procedures. Extensive experiments on reaction-to-description (R2D) and description-to-action (D2A) tasks demonstrate that ChemActor, augmented by LLM-generated data, achieves state-of-the-art performance, outperforming the baseline model by 10%. The code is available at: https://github.com/Zhanghahah/ChemActor.

cs.AI↗

arXiv2025

Large Language Models to Accelerate Organic Chemistry Synthesis

Chemical synthesis, as a foundational methodology in the creation of transformative molecules, exerts substantial influence across diverse sectors from life sciences to materials and energy. Current chemical synthesis practices emphasize laborious and costly trial-and-error workflows, underscoring the urgent need for advanced AI assistants. Nowadays, large language models (LLMs), typified by GPT-4, have been introduced as an efficient tool to facilitate scientific research. Here, we present Chemma, a fully fine-tuned LLM with 1.28 million pairs of Q&A about reactions, as an assistant to accelerate organic chemistry synthesis. Chemma surpasses the best-known results in multiple chemical tasks, e.g., single-step retrosynthesis and yield prediction, which highlights the potential of general AI for organic chemistry. Via predicting yields across the experimental reaction space, Chemma significantly improves the reaction exploration capability of Bayesian optimization. More importantly, integrated in an active learning framework, Chemma exhibits advanced potential for autonomous experimental exploration and optimization in open reaction spaces. For an unreported Suzuki-Miyaura cross-coupling reaction of cyclic aminoboronates and aryl halides for the synthesis of $α$-Aryl N-heterocycles, the human-AI collaboration successfully explored suitable ligand and solvent (1,4-dioxane) within only 15 runs, achieving an isolated yield of 67%. These results reveal that, without quantum-chemical calculations, Chemma can comprehend and extract chemical insights from reaction data, in a manner akin to human experts. This work opens avenues for accelerating organic chemistry synthesis with adapted large language models.

physics.chem-ph↗

arXiv2024

TrajGEOS: Trajectory Graph Enhanced Orientation-based Sequential Network for Mobility Prediction

Human mobility studies how people move to access their needed resources and plays a significant role in urban planning and location-based services. As a paramount task of human mobility modeling, next location prediction is challenging because of the diversity of users' historical trajectories that gives rise to complex mobility patterns and various contexts. Deep sequential models have been widely used to predict the next location by leveraging the inherent sequentiality of trajectory data. However, they do not fully leverage the relationship between locations and fail to capture users' multi-level preferences. This work constructs a trajectory graph from users' historical traces and proposes a \textbf{Traj}ectory \textbf{G}raph \textbf{E}nhanced \textbf{O}rientation-based \textbf{S}equential network (TrajGEOS) for next-location prediction tasks. TrajGEOS introduces hierarchical graph convolution to capture location and user embeddings. Such embeddings consider not only the contextual feature of locations but also the relation between them, and serve as additional features in downstream modules. In addition, we design an orientation-based module to learn users' mid-term preferences from sequential modeling modules and their recent trajectories. Extensive experiments on three real-world LBSN datasets corroborate the value of graph and orientation-based modules and demonstrate that TrajGEOS outperforms the state-of-the-art methods on the next location prediction task.

cs.AI↗

arXiv2024

Optimizing Multispectral Object Detection: A Bag of Tricks and Comprehensive Benchmarks

Multispectral object detection, utilizing RGB and TIR (thermal infrared) modalities, is widely recognized as a challenging task. It requires not only the effective extraction of features from both modalities and robust fusion strategies, but also the ability to address issues such as spectral discrepancies, spatial misalignment, and environmental dependencies between RGB and TIR images. These challenges significantly hinder the generalization of multispectral detection systems across diverse scenarios. Although numerous studies have attempted to overcome these limitations, it remains difficult to clearly distinguish the performance gains of multispectral detection systems from the impact of these "optimization techniques". Worse still, despite the rapid emergence of high-performing single-modality detection models, there is still a lack of specialized training techniques that can effectively adapt these models for multispectral detection tasks. The absence of a standardized benchmark with fair and consistent experimental setups also poses a significant barrier to evaluating the effectiveness of new approaches. To this end, we propose the first fair and reproducible benchmark specifically designed to evaluate the training "techniques", which systematically classifies existing multispectral object detection methods, investigates their sensitivity to hyper-parameters, and standardizes the core configurations. A comprehensive evaluation is conducted across multiple representative multispectral object detection datasets, utilizing various backbone networks and detection frameworks. Additionally, we introduce an efficient and easily deployable multispectral object detection framework that can seamlessly optimize high-performing single-modality models into dual-modality models, integrating our advanced training techniques.

cs.CV↗

arXiv2024

UAlign: Pushing the Limit of Template-free Retrosynthesis Prediction with Unsupervised SMILES Alignment

Motivation: Retrosynthesis planning poses a formidable challenge in the organic chemical industry. Single-step retrosynthesis prediction, a crucial step in the planning process, has witnessed a surge in interest in recent years due to advancements in AI for science. Various deep learning-based methods have been proposed for this task in recent years, incorporating diverse levels of additional chemical knowledge dependency. Results: This paper introduces UAlign, a template-free graph-to-sequence pipeline for retrosynthesis prediction. By combining graph neural networks and Transformers, our method can more effectively leverage the inherent graph structure of molecules. Based on the fact that the majority of molecule structures remain unchanged during a chemical reaction, we propose a simple yet effective SMILES alignment technique to facilitate the reuse of unchanged structures for reactant generation. Extensive experiments show that our method substantially outperforms state-of-the-art template-free and semi-template-based approaches. Importantly, our template-free method achieves effectiveness comparable to, or even surpasses, established powerful template-based methods. Scientific contribution: We present a novel graph-to-sequence template-free retrosynthesis prediction pipeline that overcomes the limitations of Transformer-based methods in molecular representation learning and insufficient utilization of chemical information. We propose an unsupervised learning mechanism for establishing product-atom correspondence with reactant SMILES tokens, achieving even better results than supervised SMILES alignment methods. Extensive experiments demonstrate that UAlign significantly outperforms state-of-the-art template-free methods and rivals or surpasses template-based approaches, with up to 5\% (top-5) and 5.4\% (top-10) increased accuracy over the strongest baseline.

physics.chem-ph↗

arXiv2024

SA-LSPL:Sequence-Aware Long- and Short- Term Preference Learning for next POI recommendation

The next Point of Interest (POI) recommendation aims to recommend the next POI for users at a specific time. As users' check-in records can be viewed as a long sequence, methods based on Recurrent Neural Networks (RNNs) have recently shown good applicability to this task. However, existing methods often struggle to fully explore the spatio-temporal correlations and dependencies at the sequence level, and don't take full consideration for various factors influencing users' preferences. To address these issues, we propose a novel approach called Sequence-Aware Long- and Short-Term Preference Learning (SA-LSPL) for next-POI recommendation. We combine various information features to effectively model users' long-term preferences. Specifically, our proposed model uses a multi-modal embedding module to embed diverse check-in details, taking into account both user's personalized preferences and social influences comprehensively. Additionally, we consider explicit spatio-temporal correlations at the sequence level and implicit sequence dependencies. Furthermore, SA-LSPL learns the spatio-temporal correlations of consecutive and non-consecutive visits in the current check-in sequence, as well as transition dependencies between categories, providing a comprehensive capture of user's short-term preferences. Extensive experiments on two real-world datasets demonstrate the superiority of SA-LSPL over state-of-the-art baseline methods.

cs.CY↗

arXiv2023

Swap-based Deep Reinforcement Learning for Facility Location Problems in Networks

Facility location problems on graphs are ubiquitous in real world and hold significant importance, yet their resolution is often impeded by NP-hardness. Recently, machine learning methods have been proposed to tackle such classical problems, but they are limited to the myopic constructive pattern and only consider the problems in Euclidean space. To overcome these limitations, we propose a general swap-based framework that addresses the p-median problem and the facility relocation problem on graphs and a novel reinforcement learning model demonstrating a keen awareness of complex graph structures. Striking a harmonious balance between solution quality and running time, our method surpasses handcrafted heuristics on intricate graph datasets. Additionally, we introduce a graph generation process to simulate real-world urban road networks with demand, facilitating the construction of large datasets for the classic problem. For the initialization of the locations of facilities, we introduce a physics-inspired strategy for the p-median problem, reaching more stable solutions than the random strategy. The proposed pipeline coupling the classic swap-based method with deep reinforcement learning marks a significant step forward in addressing the practical challenges associated with facility location on graphs.

cs.LG↗

arXiv2023

Understanding vehicular routing behavior with location-based service data

Properly extracting patterns of individual mobility with high resolution data sources such as the one extracted from smartphone applications offers important opportunities. Potential opportunities not offered by call detailed records (CDRs), which offer resolutions triangulated from antennas, are route choices, travel modes detection and close encounters. Nowadays, there is not a standard and large scale data set collected over long periods that allows us to characterize these. In this work we thoroughly examine the use of data from smartphone applications, also referred to as location-based services (LBS) data, to extract and understand the vehicular route choice behavior. Taking the Dallas-Fort Worth metroplex as an example, we first extract the vehicular trips with simple rules and reconstruct the origin-destination matrix by coupling the extracted vehicular trips of the active LBS users and the United States census data. We then present a method to derive the commonly used routes by individuals from the LBS traces with varying sample rate intervals. We further inspect the relation between the number of routes and the trip characteristics, including the departure time, trip length and travel time. Specifically, we consider the travel time index and buffer index for the LBS users taking different number of routes. Empirical results demonstrate that during the peak hours, travelers tend to reduce the impact of traffic congestion by taking alternative routes. Overall, the proposed data analysis framework is cost-effective to treat sparse data generated from the use of smartphones to inform routing behavior. The potential in practice is to inform demand management strategies, by targeting individual users while generating large scale estimates of congestion mitigation.

physics.soc-ph↗

arXiv2023

Modeling Complex Mathematical Reasoning via Large Language Model based MathAgent

Large language models (LLMs) face challenges in solving complex mathematical problems that require comprehensive capacities to parse the statements, associate domain knowledge, perform compound logical reasoning, and integrate the intermediate rationales. Tackling all these problems once could be arduous for LLMs, thus leading to confusion in generation. In this work, we explore the potential of enhancing LLMs with agents by meticulous decomposition and modeling of mathematical reasoning process. Specifically, we propose a formal description of the mathematical solving and extend LLMs with an agent-based zero-shot framework named $\bf{P}$lanner-$\bf{R}$easoner-$\bf{E}$xecutor-$\bf{R}$eflector (PRER). We further provide and implement two MathAgents that define the logical forms and inherent relations via a pool of actions in different grains and orientations: MathAgent-M adapts its actions to LLMs, while MathAgent-H aligns with humankind. Experiments on miniF2F and MATH have demonstrated the effectiveness of PRER and proposed MathAgents, achieving an increase of $12.3\%$($53.9\%\xrightarrow{}66.2\%$) on the MiniF2F, $9.2\%$ ($49.8\%\xrightarrow{}59.0\%$) on MATH, and $13.2\%$($23.2\%\xrightarrow{}35.4\%$) for level-5 problems of MATH against GPT-4. Further analytical results provide more insightful perspectives on exploiting the behaviors of LLMs as agents.

cs.AI↗

arXiv2023

Enhancing Unsupervised Anomaly Detection with Score-Guided Network

Anomaly detection plays a crucial role in various real-world applications, including healthcare and finance systems. Owing to the limited number of anomaly labels in these complex systems, unsupervised anomaly detection methods have attracted great attention in recent years. Two major challenges faced by the existing unsupervised methods are: (i) distinguishing between normal and abnormal data in the transition field, where normal and abnormal data are highly mixed together; (ii) defining an effective metric to maximize the gap between normal and abnormal data in a hypothesis space, which is built by a representation learner. To that end, this work proposes a novel scoring network with a score-guided regularization to learn and enlarge the anomaly score disparities between normal and abnormal data. With such score-guided strategy, the representation learner can gradually learn more informative representation during the model training stage, especially for the samples in the transition field. We next propose a score-guided autoencoder (SG-AE), incorporating the scoring network into an autoencoder framework for anomaly detection, as well as other three state-of-the-art models, to further demonstrate the effectiveness and transferability of the design. Extensive experiments on both synthetic and real-world datasets demonstrate the state-of-the-art performance of these score-guided models (SGMs).

cs.LG↗

arXiv2023

Human Mobility Prediction with Causal and Spatial-constrained Multi-task Network

Modeling human mobility helps to understand how people are accessing resources and physically contacting with each other in cities, and thus contributes to various applications such as urban planning, epidemic control, and location-based advertisement. Next location prediction is one decisive task in individual human mobility modeling and is usually viewed as sequence modeling, solved with Markov or RNN-based methods. However, the existing models paid little attention to the logic of individual travel decisions and the reproducibility of the collective behavior of population. To this end, we propose a Causal and Spatial-constrained Long and Short-term Learner (CSLSL) for next location prediction. CSLSL utilizes a causal structure based on multi-task learning to explicitly model the "\textit{when$\rightarrow$what$\rightarrow$where}", a.k.a. "\textit{time$\rightarrow$activity$\rightarrow$location}" decision logic. We next propose a spatial-constrained loss function as an auxiliary task, to ensure the consistency between the predicted and actual spatial distribution of travelers' destinations. Moreover, CSLSL adopts modules named Long and Short-term Capturer (LSC) to learn the transition regularities across different time spans. Extensive experiments on three real-world datasets show promising performance improvements of CSLSL over baselines and confirm the effectiveness of introducing the causality and consistency constraints. The implementation is available at https://github.com/urbanmobility/CSLSL.

cs.AI↗

arXiv2023

Reconstructing human activities via coupling mobile phone data with location-based social networks

In the era of big data, the ubiquity of location-aware portable devices provides an unprecedented opportunity to understand inhabitants' behavior and their interactions with the built environments. Among the widely used data resources, mobile phone data is the one passively collected and has the largest coverage in the population. However, mobile operators cannot pinpoint one user within meters, leading to the difficulties in activity inference. To that end, we propose a data analysis framework to identify user's activity via coupling the mobile phone data with location-based social networks (LBSN) data. The two datasets are integrated into a Bayesian inference module, considering people's circadian rhythms in both time and space. Specifically, the framework considers the pattern of arrival time to each type of facility and the spatial distribution of facilities. The former can be observed from the LBSN Data and the latter is provided by the points of interest (POIs) dataset. Taking Shanghai as an example, we reconstruct the activity chains of 1,000,000 active mobile phone users and analyze the temporal and spatial characteristics of each activity type. We assess the results with some official surveys and a real-world check-in dataset collected in Shanghai, indicating that the proposed method can capture and analyze human activities effectively. Next, we cluster users' inferred activity chains with a topic model to understand the behavior of different groups of users. This data analysis framework provides an example of reconstructing and understanding the activity of the population at an urban scale with big data fusion.

cs.SI↗