Minghao Guo

Minghao Guo, Veronika Thost, Beichen Li et al.

The problem of molecular generation has received significant attention recently. Existing methods are typically based on deep neural networks and require training on large datasets with tens of thousands of samples. In practice, however, the size of class-specific chemical datasets is usually limited (e.g., dozens of samples) due to labor-intensive experimentation and data collection. This presents a considerable challenge for the deep learning generative models to comprehensively describe the molecular design space. Another major challenge is to generate only physically synthesizable molecules. This is a non-trivial task for neural network-based generative models since the relevant chemical knowledge can only be extracted and generalized from the limited training data. In this work, we propose a data-efficient generative model that can be learned from datasets with orders of magnitude smaller sizes than common benchmarks. At the heart of this method is a learnable graph grammar that generates molecules from a sequence of production rules. Without any human assistance, these production rules are automatically constructed from training data. Furthermore, additional chemical knowledge can be incorporated in the model by further grammar optimization. Our learned graph grammar yields state-of-the-art results on generating high-quality molecules for three monomer datasets that contain only ${\sim}20$ samples each. Our approach also achieves remarkable performance in a challenging polymer generation task with only $117$ training samples and is competitive against existing methods using $81$k data points. Code is available at https://github.com/gmh14/data_efficient_grammar.

Michael Sun, Alston Lo, Minghao Guo et al.

Designing synthetically accessible molecules and recommending analogs to unsynthesizable molecules are important problems for accelerating molecular discovery. We reconceptualize both problems using ideas from program synthesis. Drawing inspiration from syntax-guided synthesis approaches, we decouple the syntactic skeleton from the semantics of a synthetic tree to create a bilevel framework for reasoning about the combinatorial space of synthesis pathways. Given a molecule we aim to generate analogs for, we iteratively refine its skeletal characteristics via Markov Chain Monte Carlo simulations over the space of syntactic skeletons. Given a black-box oracle to optimize, we formulate a joint design space over syntactic templates and molecular descriptors and introduce evolutionary algorithms that optimize both syntactic and semantic dimensions synergistically. Our key insight is that once the syntactic skeleton is set, we can amortize over the search complexity of deriving the program's semantics by training policies to fully utilize the fixed horizon Markov Decision Process imposed by the syntactic template. We demonstrate performance advantages of our bilevel framework for synthesizable analog generation and synthesizable molecule design. Notably, our approach offers the user explicit control over the resources required to perform synthesis and biases the design space towards simpler solutions, making it particularly promising for autonomous synthesis platforms. Code is at https://github.com/shiningsunnyday/SynthesisNet.

Minghao Guo, Veronika Thost, Samuel W Song et al.

The prediction of molecular properties is a crucial task in the field of material and drug discovery. The potential benefits of using deep learning techniques are reflected in the wealth of recent literature. Still, these techniques are faced with a common challenge in practice: Labeled data are limited by the cost of manual extraction from literature and laborious experimentation. In this work, we propose a data-efficient property predictor by utilizing a learnable hierarchical molecular grammar that can generate molecules from grammar production rules. Such a grammar induces an explicit geometry of the space of molecular graphs, which provides an informative prior on molecular structural similarity. The property prediction is performed using graph neural diffusion over the grammar-induced geometry. On both small and large datasets, our evaluation shows that this approach outperforms a wide spectrum of baselines, including supervised and pre-trained graph neural networks. We include a detailed ablation study and further analysis of our solution, showing its effectiveness in cases with extremely limited data. Code is available at https://github.com/gmh14/Geo-DEG.

Minghao Guo, Victor Zordan, Sheldon Andrews et al.

We introduce Kinematic Kitbashing, an optimization framework that synthesizes articulated 3D objects by assembling reusable parts conditioned on an abstract kinematic graph. Given the graph and a library of articulated parts, our method optimizes per-part similarity transformations that place, orient, and scale each component into a coherent articulated object; optional graph edits further enable novel assemblies beyond the prescribed connectivity. Central to our method is an exemplar-based analogy for part placement: each reused component is paired with a single source asset that exemplifies how it attaches to its parent. We capture this attachment context using vector distance fields and measure consistency by integrating the matching error over the joint's full motion range. This yields a kinematics-aware attachment energy that favors placements that preserve the exemplar's local attachment neighborhood throughout articulation. To incorporate task-level functionality, we use this attachment energy as a prior in an annealed Langevin sampling framework, enabling gradient-free optimization of black-box functionality objectives. We demonstrate the versatility of kinematic kitbashing across diverse applications, including instantiating kinematic graphs from user-selected or automatically retrieved parts, synthesizing assemblies with user-defined functionality, and re-targeting articulations via graph edits.

Haixu Wu, Minghao Guo, Zongyi Li et al.

Neural simulators promise efficient surrogates for physics simulation, but scaling them is bottlenecked by the prohibitive cost of generating high-fidelity training data. Pre-training on abundant off-the-shelf geometries offers a natural alternative, yet faces a fundamental gap: supervision on static geometry alone ignores dynamics and can lead to negative transfer on physics tasks. We present GeoPT, a unified pre-trained model for general physics simulation based on lifted geometric pre-training. The core idea is to augment geometry with synthetic dynamics, enabling dynamics-aware self-supervision without physics labels. Pre-trained on over one million samples, GeoPT consistently improves industrial-fidelity benchmarks spanning fluid mechanics for cars, aircraft, and ships, and solid mechanics in crash simulation, reducing labeled data requirements by 20-60% and accelerating convergence by 2$\times$. These results show that lifting with synthetic dynamics bridges the geometry-physics gap, unlocking a scalable path for neural simulation and potentially beyond. Code is available at https://github.com/Physics-Scaling/GeoPT.

Fei Hua, Yuwei Jin, Ang Li et al.

Near-term quantum systems tend to be noisy. Crosstalk noise has been recognized as one of several major types of noises in superconducting Noisy Intermediate-Scale Quantum (NISQ) devices. Crosstalk arises from the concurrent execution of two-qubit gates on nearby qubits, such as \texttt{CX}. It might significantly raise the error rate of gates in comparison to running them individually. Crosstalk can be mitigated through scheduling or hardware machine tuning. Prior scientific studies, however, manage crosstalk at a really late phase in the compilation process, usually after hardware mapping is done. It may miss great opportunities of optimizing algorithm logic, routing, and crosstalk at the same time. In this paper, we push the envelope by considering all these factors simultaneously at the very early compilation stage. We propose a crosstalk-aware quantum program compilation framework called CQC that can enhance crosstalk mitigation while achieving satisfactory circuit depth. Moreover, we identify opportunities for translation from intermediate representation to the circuit for application-specific crosstalk mitigation, for instance, the \texttt{CX} ladder construction in variational quantum eigensolvers (VQE). Evaluations through simulation and on real IBM-Q devices show that our framework can significantly reduce the error rate by up to 6$\times$, with only $\sim$60\% circuit depth compared to state-of-the-art gate scheduling approaches. In particular, for VQE, we demonstrate 49\% circuit depth reduction with 9.6\% fidelity improvement over prior art on the H4 molecule using IBMQ Guadalupe. Our CQC framework will be released on GitHub.

Xi Zhu, Ziqi Wang, Kai Mei et al.

Retrieval-augmented generation (RAG) improves large language models (LLMs) by incorporating external evidence, but it also introduces knowledge conflicts when retrieved contextual knowledge (CK) and parametric knowledge (PK) disagree or are both unreliable. Existing approaches mainly coordinate which source to use, without explicitly asking whether each answer path is correct. We argue that faithful RAG requires LLM self-awareness, namely the ability to recognize the limits of its own knowledge and reasoning. To ground this problem, we construct a model-specific, ground-truth-aligned knowledge-conflict benchmark by evaluating LLM backbones on PK-only and CK-conditioned answer paths over approximately 69K query-context instances per backbone, drawn from five conflict-QA datasets. We then introduce SABER, a Self-Aware Belief Estimator for RAG that requires no LLM fine-tuning. SABER combines a self-prior with PK-side and CK-side conditional reasoning representations from multi-trace inference, then estimates reliability beliefs with two lightweight predictors to drive a 4-cell decision over trust PK, trust CK, trust either, or abstain. Across four LLM backbones, SABER improves end-to-end accuracy and conflict-specific faithfulness over ten inference-time and fine-tuning baselines, with the largest gains on conflict-heavy datasets. Under abstention, SABER's risk-coverage curve Pareto-dominates every prompt-based abstainer, providing a tunable balance between coverage and answer risk. Our code is available at https://github.com/xizhu1022/SABER.

Alexandra Irger, Ella Hugie, Minghao Guo et al.

Visualization is central to scientific discovery, yet authoring tools remain split between information and scientific visualization, and expertise in one rarely transfers to the other. Large Language Model (LLM) based systems promise to bridge this gap through natural language, but current approaches generate code non-deterministically, with no guarantee of correctness and no protection against silent data fabrication. We present Raiven, a conversational system that mediates visualization authoring through a formally defined domain-specific language. RaivenDSL unifies scientific and information visualization in a single representation spanning 2D, 3D, and tabular data. The LLM produces a compact RaivenDSL specification under schema-guided constraints, and a deterministic compiler translates it to executable D3 or VTK.js code. Because the LLM operates only on dataset metadata, outputs are deterministic, specifications are verifiable before execution, and data fabrication is impossible by construction. In a 100-task benchmark, Raiven achieves 100% compilation, is up to six times faster and six times cheaper than state-of-the-art LLMs, while improving interaction quality, correctness, and data faithfulness. An expert user study shows that Raiven significantly reduces debugging effort and makes it easier to produce correct visualizations.

Yian Wang, Han Yang, Minghao Guo et al.

Automatically generating interactive 3D environments is crucial for scaling up robotic data collection in simulation. While prior work has primarily focused on 3D asset placement, it often overlooks the physical relationships between objects (e.g., contact, support, balance, and containment), which are essential for creating complex and realistic manipulation scenarios such as tabletop arrangements, shelf organization, or box packing. Compared to classical 3D layout generation, producing complex physical scenes introduces additional challenges: (a) higher object density and complexity (e.g., a small shelf may hold dozens of books), (b) richer supporting relationships and compact spatial layouts, and (c) the need to accurately model both spatial placement and physical properties. To address these challenges, we propose PhyScensis, an LLM agent-based framework powered by a physics engine, to produce physically plausible scene configurations with high complexity. Specifically, our framework consists of three main components: an LLM agent iteratively proposes assets with spatial and physical predicates; a solver, equipped with a physics engine, realizes these predicates into a 3D scene; and feedback from the solver informs the agent to refine and enrich the configuration. Moreover, our framework preserves strong controllability over fine-grained textual descriptions and numerical parameters (e.g., relative positions, scene stability), enabled through probabilistic programming for stability and a complementary heuristic that jointly regulates stability and spatial relations. Experimental results show that our method outperforms prior approaches in scene complexity, visual quality, and physical accuracy, offering a unified pipeline for generating complex physical scene layouts for robotic manipulation.

Wujiang Xu, Jiaojiao Han, Minghao Guo et al.

LLM agents increasingly operate in open-ended environments spanning hundreds of sequential episodes, yet they remain largely stateless: each task is solved from scratch without converting past experience into better future behavior. The central obstacle is not \emph{what} to remember but \emph{how to use} what has been remembered, including which retrieval policy to apply, how to interpret prior outcomes, and when the current strategy itself must change. We introduce \emph{Agent Evolving Learning} (\ael{}), a two-timescale framework that addresses this obstacle. At the fast timescale, a Thompson Sampling bandit learns which memory retrieval policy to apply at each episode; at the slow timescale, LLM-driven reflection diagnoses failure patterns and injects causal insights into the agent's decision prompt, giving it an interpretive frame for the evidence it retrieves. On a sequential portfolio benchmark (10 sector-diverse tickers, 208 episodes, 5 random seeds), \ael{} achieves a Sharpe ratio of 2.13$\pm$0.47, outperforming five published self-improving methods and all non-LLM baselines while maintaining the lowest variance among all LLM-based approaches. A nine-variant ablation reveals a ``less is more'' pattern: memory and reflection together produce a 58\% cumulative improvement over the stateless baseline, yet every additional mechanism we test (planner evolution, per-tool selection, cold-start initialization, skill extraction, and three credit assignment methods) \emph{degrades} performance. This demonstrates that the bottleneck in agent self-improvement is \emph{self-diagnosing how to use} experience rather than adding architectural complexity. Code and data: https://github.com/WujiangXu/AEL.

Xi Zhu, Haochen Xue, Ziwei Zhao et al.

Text-Attributed Graphs (TAGs), where each node is associated with text descriptions, are ubiquitous in real-world scenarios. They typically exhibit distinctive structure and domain-specific knowledge, motivating the development of a Graph Foundation Model (GFM) that generalizes across diverse graphs and tasks. Despite large efforts to integrate Large Language Models (LLMs) and Graph Neural Networks (GNNs) for TAGs, existing approaches suffer from decoupled architectures with two-stage alignment, limiting their synergistic potential. Even worse, existing methods assign out-of-vocabulary (OOV) tokens to graph nodes, leading to graph-specific semantics, token explosion, and incompatibility with task-oriented prompt templates, which hinders cross-graph and cross-task transferability. To address these challenges, we propose PromptGFM, a versatile GFM for TAGs grounded in graph vocabulary learning. PromptGFM comprises two key components: (1) Graph Understanding Module, which explicitly prompts LLMs to replicate the finest GNN workflow within the text space, facilitating seamless GNN-LLM integration and elegant graph-text alignment; (2) Graph Inference Module, which establishes a language-based graph vocabulary ensuring expressiveness, transferability, and scalability, enabling readable instructions for LLM fine-tuning. Extensive experiments demonstrate our superiority and transferability across diverse graphs and tasks. The code is available at this: https://github.com/agiresearch/PromptGFM.

Ziqi Wang, Xi Zhu, Shuhang Lin et al.

Retrieval-augmented generation (RAG) has evolved into a family of paradigms with distinct performance profiles and resource demands, turning paradigm selection into a multi-criteria, context-dependent decision problem. Nevertheless, existing studies largely focus on isolated method improvements or query-only benchmarking, without systematically examining how RAG paradigms behave across diverse query-corpus contexts and effectiveness-efficiency trade-offs. In this work, we introduce RAGRouter-Bench, the first dataset and benchmark for adaptive RAG routing. Grounded in query-corpus compatibility, the benchmark integrates three canonical query types, fine-grained corpus indicators capturing structural and semantic properties, and a unified protocol for evaluating both generation quality and resource consumption. Then, we implement standardized RAG paradigms with multiple backbone LLMs across all query-corpus combinations, constructing a comprehensive benchmark with quantitative metrics and LLM-as-a-Judge evaluations to inform context-aware and cost-effective RAG routing decisions. We further formulate routing as context-dependent paradigm selection and benchmark a range of query-corpus routers on the constructed dataset. Extensive experiments demonstrate that no one-size-fits-all paradigm exists across query-corpus pairs, and that adaptive routing yields more favorable effectiveness-efficiency trade-offs than fixed paradigm selection. These findings establish query-corpus compatibility as a central principle for adaptive RAG routing and position RAGRouter-Bench as a systematic testbed for next-generation RAG systems.

Minghao Guo, Qingyue Jiao, Zeru Shi et al.

Long-term agent memory is increasingly multimodal, yet existing evaluations rarely test whether agents preserve the visual evidence needed for later reasoning. In prior work, many visually grounded questions can be answered using only captions or textual traces, allowing answers to be inferred without preserving the fine-grained visual evidence. Meanwhile, harder cases that require reasoning over changing visual states are largely absent. Therefore, we introduce MemEye, a framework that evaluates memory capabilities from two dimensions: one measures the granularity of decisive visual evidence (from scene-level to pixel-level evidence), and the other measures how retrieved evidence must be used (from single evidence to evolutionary synthesis). Under this framework, we construct a new benchmark across 8 life-scenario tasks, with ablation-driven validation gates for assessing answerability, shortcut resistance, visual necessity, and reasoning structure. By evaluating 13 memory methods across 4 VLM backbones, we show that current architectures still struggle to preserve fine-grained visual details and reason about state changes over time. Our findings show that long-term multimodal memory depends on evidence routing, temporal tracking, and detail extraction.

Minghao Guo, Ziyi Ye, Wujiang Xu et al.

Large Language Models (LLMs) have demonstrated remarkable human-like capabilities, yet their ability to replicate a specific individual remains under-explored. This paper presents a case study to investigate LLM-based individual simulation with a volunteer-contributed archive of private messaging history spanning over ten years. Based on the messaging data, we propose the "Individual Turing Test" to evaluate whether acquaintances of the volunteer can correctly identify which response in a multi-candidate pool most plausibly comes from the volunteer. We investigate prevalent LLM-based individual simulation approaches including: fine-tuning, retrieval-augmented generation (RAG), memory-based approach, and hybrid methods that integrate fine-tuning and RAG or memory. Empirical results show that current LLM-based simulation methods do not pass the Individual Turing Test, but they perform substantially better when the same test is conducted on strangers to the target individual. Additionally, while fine-tuning improves the simulation in daily chats representing the language style of the individual, retrieval-augmented and memory-based approaches demonstrate stronger performance on questions involving personal opinions and preferences. These findings reveal a fundamental trade-off between parametric and non-parametric approaches to individual simulation with LLMs when given a longitudinal context.

Kaidong Zhang, Jian Zhang, Rongtao Xu et al.

Vision--Language--Action (VLA) models have emerged as a powerful paradigm for open-world robot manipulation, but their practical deployment is often constrained by \emph{cost}: billion-scale VLM backbones and iterative diffusion/flow-based action heads incur high latency and compute, making real-time control expensive on commodity hardware. We present A1, a fully open-source and transparent VLA framework designed for low-cost, high-throughput inference without sacrificing manipulation success; Our approach leverages pretrained VLMs that provide implicit affordance priors for action generation. We release the full training stack (training code, data/data-processing pipeline, intermediate checkpoints, and evaluation scripts) to enable end-to-end reproducibility. Beyond optimizing the VLM alone, A1 targets the full inference pipeline by introducing a budget-aware adaptive inference scheme that jointly accelerates the backbone and the \emph{action head}. Specifically, we monitor action consistency across intermediate VLM layers to trigger early termination, and propose Inter-Layer Truncated Flow Matching that warm-starts denoising across layers, enabling accurate actions with substantially fewer effective denoising iterations. Across simulation benchmarks (LIBERO, VLABench) and real robots (Franka, AgiBot), A1 achieves state-of-the-art success rates while significantly reducing inference cost (e.g., up to 72% lower per-episode latency for flow-matching inference and up to 76.6% backbone computation reduction with minor performance degradation). On RoboChallenge, A1 achieves an average success rate of 29.00%, outperforming baselines including pi0(28.33%), X-VLA (21.33%), and RDT-1B (15.00%).

Minghao Guo, Qingcheng Zeng, Xujiang Zhao et al.

Large Language Models (LLMs) excel at many reasoning tasks but struggle with knowledge-intensive queries due to their inability to dynamically access up-to-date or domain-specific information. Retrieval-Augmented Generation (RAG) has emerged as a promising solution, enabling LLMs to ground their responses in external sources. However, existing RAG methods lack fine-grained control over both the query and source sides, often resulting in noisy retrieval and shallow reasoning. In this work, we introduce DeepSieve, an agentic RAG framework that incorporates information sieving via LLM-as-a-knowledge-router. DeepSieve decomposes complex queries into structured sub-questions and recursively routes each to the most suitable knowledge source, filtering irrelevant information through a multi-stage distillation process. Our design emphasizes modularity, transparency, and adaptability, leveraging recent advances in agentic system design. Experiments on multi-hop QA tasks across heterogeneous sources demonstrate improved reasoning depth, retrieval precision, and interpretability over conventional RAG approaches. Our codes are available at https://github.com/MinghoKwok/DeepSieve.

Caoliwen Wang, Minghao Guo, Siyuan Chen et al.

A unified simulator that can model diverse physical phenomena without solver-specific redesign is a long-standing goal across simulation science. We present a learning-based particle simulator built on a single transformer architecture to model cloth, elastic solds, Newtonian and non-Newtonian fluids, granular materials, and molecular dynamics. Our model follows a prediction-correction design on a shared Lagrangian particle representation. An explicit predictor first advances particles under the known external forces, producing an intermediate state that captures externally driven motion but not inter-particle interactions. A learned corrector then predicts the residual position and velocity updates through three stages: a particle tokenizer that encodes local particle-particle, particle-boundary, and topology-guided interactions; a super-token encoder that hierarchically merges particle tokens into a compact set of super tokens via alternating self-attention and token merging; and a super-token decoder that lifts these super tokens back to particle resolution through cross-attention to predict per-particle position and velocity corrections. Progressive token merging reduces the attention cost at successive encoder layers by halving the token count at each level, and the decoder communicates through the compact super-token set rather than full particle-to-particle attention. Across the six dynamics categories, the same architecture generalizes to unseen materials, boundary configurations, initial conditions, and external forces. We further demonstrate downstream interactive control, inverse design, and learning from real-world manipulation data, reducing the need for per-phenomenon solver engineering.

Jingyuan Huang, Xi Zhu, Minghao Guo et al.

Web 2.0 social platforms are inherently centralized, with user data and algorithmic decisions controlled by the platform. However, users can only passively receive social predictions without being able to choose the underlying algorithm, which limits personalization. Fortunately, with the emergence of blockchain, users are allowed to choose algorithms that are tailored to their local situation, improving prediction results in a personalized way. In a blockchain environment, each user possesses its own model to perform the social prediction, capturing different perspectives on social interactions. In our work, we propose DeSocial, a decentralized social network learning framework deployed on an Ethereum (ETH) local development chain that integrates distributed data storage, node-level consensus, and user-driven model selection through Ganache. In the first stage, each user leverages DeSocial to evaluate multiple backbone models on their local subgraph. DeSocial coordinates the execution and returns model-wise prediction results, enabling the user to select the most suitable backbone for personalized social prediction. Then, DeSocial uniformly selects several validation nodes that possess the algorithm specified by each user, and aggregates the prediction results by majority voting, to prevent errors caused by any single model's misjudgment. Extensive experiments show that DeSocial has an evident improvement compared to the five classical centralized social network learning models, promoting user empowerment in blockchain-based decentralized social networks, showing the importance of multi-node validation and personalized algorithm selection based on blockchain. Our implementation is available at: https://github.com/agiresearch/DeSocial.

Carl Osborne, Minghao Guo, Crystal Owens et al.

Neural preconditioners for real-time physics simulation offer promising data-driven priors, but they often fail to capture long-range couplings efficiently because they inherit local message passing or sparse-operator access patterns. We introduce the Hierarchical Transformer Preconditioner, a neural preconditioner anchored to a weak-admissibility H-matrix partition. The partition provides a multiscale structural prior (dense diagonal leaves plus coarsening off-diagonal tiles) that enables full-graph approximate-inverse computation with O(N) scaling at fixed block sizes. The network models the inverse through low-rank far-field factors and uses highway connections (axial buffers plus a global summary token) to propagate context across transformer depth. At each PCG iteration, preconditioner application reduces to batched dense GEMMs with regular memory access. The key training contribution is a cosine-Hutchinson probe objective that learns the action of MA on convergence-critical spectral subspaces, optimizing angular alignment of MAz with z rather than forcing eigenvalue clusters to a prescribed location. This removes unnecessary spectral-placement constraints from SAI-style objectives and improves conditioning on irregular spectra. Because both inference and apply are dense, dependency-free tensor programs, the full solve loop is captured as a single CUDA Graph. On stiff multiphase Poisson systems (up to 100:1 density contrast, N = 1,024-16,384), the solver runs from ~143 to ~21 fps. At N = 8,192, it reaches 17.9 ms/frame, with 2.2x speedup over GPU Jacobi, ~28x over GPU IC/DILU (AMGX multicolor_dilu), and 2.7x over neural SPAI retrained per scale on the same benchmark.

Daniel Xu, Yuxin Xie, Minghao Guo et al.

Classical deep learning typically operates on individual cases. Despite its success, real-world usage often requires repeated inference to estimate statistical quantities for complex decision-making tasks involving uncertainty or extreme-value analysis, resulting in substantial latency. We introduce neural statistical functions, a new family of models learned from pre-trained single-sample predictors and scattered data samples, which can directly infer statistics over continuous operating condition ranges without explicit sampling. By introducing the notion of prefix statistics, we transform and unify diverse statistical functions (e.g., integrals, quantiles, and maxima) into an interval-conditional framework, in which a principled identity between the prefix statistics and the individual-case regression serves as the learning objective. Neural statistical functions achieve strong performance in estimating essential statistics of complex physical processes, including accumulated energy in dynamical systems, quantiles of aerodynamic responses, and maximum stress in crash processes, while achieving up to a 100$\times$ reduction in model evaluations.

Haixu Wu, Minghao Guo, Yuezhou Ma et al.

Attention with bias, which extends standard attention by introducing prior knowledge as an additive bias matrix to the query-key scores, has been widely deployed in vision, language, protein-folding and other advanced scientific models, underscoring its status as a key evolution of this foundational module. However, introducing bias terms creates a severe efficiency bottleneck in attention computation. It disrupts the tightly fused memory-compute pipeline that underlies the speed of accelerators like FlashAttention, thereby stripping away most of their performance gains and leaving biased attention computationally expensive. Surprisingly, despite its common usage, targeted efficiency optimization for attention with bias remains absent, which seriously hinders its application in complex tasks. Diving into the computation of FlashAttention, we prove that its optimal efficiency is determined by the rank of the attention weight matrix. Inspired by this theoretical result, this paper presents FlashBias based on the low-rank compressed sensing theory, which can provide fast-exact computation for many widely used attention biases and a fast-accurate approximation for biases in general formalizations. FlashBias can fully take advantage of the extremely optimized matrix multiplication operation in modern GPUs, achieving 1.5$\times$ speedup for Pairformer in AlphaFold 3, and over 2$\times$ speedup for attention with bias in vision and language models without loss of accuracy. Code is available at this repository: https://github.com/thuml/FlashBias.

Zhaoyang Lyu, Minghao Guo, Tong Wu et al.

Recent works have shown that interval bound propagation (IBP) can be used to train verifiably robust neural networks. Reseachers observe an intriguing phenomenon on these IBP trained networks: CROWN, a bounding method based on tight linear relaxation, often gives very loose bounds on these networks. We also observe that most neurons become dead during the IBP training process, which could hurt the representation capability of the network. In this paper, we study the relationship between IBP and CROWN, and prove that CROWN is always tighter than IBP when choosing appropriate bounding lines. We further propose a relaxed version of CROWN, linear bound propagation (LBP), that can be used to verify large networks to obtain lower verified errors than IBP. We also design a new activation function, parameterized ramp function (ParamRamp), which has more diversity of neuron status than ReLU. We conduct extensive experiments on MNIST, CIFAR-10 and Tiny-ImageNet with ParamRamp activation and achieve state-of-the-art verified robustness. Code and the appendix are available at https://github.com/ZhaoyangLyu/VerifiablyRobustNN.

Minghao Guo, Yuzhe Yang, Rui Xu et al.

Recent advances in adversarial attacks uncover the intrinsic vulnerability of modern deep neural networks. Since then, extensive efforts have been devoted to enhancing the robustness of deep networks via specialized learning algorithms and loss functions. In this work, we take an architectural perspective and investigate the patterns of network architectures that are resilient to adversarial attacks. To obtain the large number of networks needed for this study, we adopt one-shot neural architecture search, training a large network for once and then finetuning the sub-networks sampled therefrom. The sampled architectures together with the accuracies they achieve provide a rich basis for our study. Our "robust architecture Odyssey" reveals several valuable observations: 1) densely connected patterns result in improved robustness; 2) under computational budget, adding convolution operations to direct connection edge is effective; 3) flow of solution procedure (FSP) matrix is a good indicator of network robustness. Based on these observations, we discover a family of robust architectures (RobNets). On various datasets, including CIFAR, SVHN, Tiny-ImageNet, and ImageNet, RobNets exhibit superior robustness performance to other widely used architectures. Notably, RobNets substantially improve the robust accuracy (~5% absolute gains) under both white-box and black-box attacks, even with fewer parameter numbers. Code is available at https://github.com/gmh14/RobNets.

Zhiyang Dou, Minghao Guo, Haixu Wu et al.

Learning-based simulation of multi-object rigid-body dynamics remains difficult because contact is discontinuous and errors compound over long horizons. Most existing methods remain tied to mesh connectivity and vertex-level message passing, which limits their applicability to mesh-free inputs such as point clouds and leads to high computational cost. Efficiently modeling high-fidelity rigid-body dynamics from mesh-free representations, therefore, remains challenging. We introduce RigidFormer, an object-centric Transformer-based model that learns mesh-free rigid-body dynamics with controllable integration step sizes. RigidFormer reasons at the object level and advances each object through compact anchors; Anchor-Vertex Pooling enriches these anchors with local vertex features, retaining contact-relevant geometry without dense vertex-level interaction. We propose Anchor-based RoPE to inject anchor geometry into attention while respecting the unordered nature of objects and anchors: object-token processing is permutation-equivariant, and the mean-pooled anchor descriptor is invariant to anchor reindexing while preserving shape extent. RigidFormer further enforces rigidity by projecting updates onto the rigid-body manifold using differentiable Kabsch alignment. On standard benchmarks, RigidFormer outperforms or matches mesh-based baselines using point inputs, runs faster, generalizes to unseen point resolutions and across datasets, and scales to 200+ objects; we also show a preliminary extension to command-conditioned articulated bodies by treating body parts as interacting object-level components.

Pingchuan Ma, Tsun-Hsuan Wang, Minghao Guo et al.

Large Language Models have recently gained significant attention in scientific discovery for their extensive knowledge and advanced reasoning capabilities. However, they encounter challenges in effectively simulating observational feedback and grounding it with language to propel advancements in physical scientific discovery. Conversely, human scientists undertake scientific discovery by formulating hypotheses, conducting experiments, and revising theories through observational analysis. Inspired by this, we propose to enhance the knowledge-driven, abstract reasoning abilities of LLMs with the computational strength of simulations. We introduce Scientific Generative Agent (SGA), a bilevel optimization framework: LLMs act as knowledgeable and versatile thinkers, proposing scientific hypotheses and reason about discrete components, such as physics equations or molecule structures; meanwhile, simulations function as experimental platforms, providing observational feedback and optimizing via differentiability for continuous parts, such as physical parameters. We conduct extensive experiments to demonstrate our framework's efficacy in constitutive law discovery and molecular design, unveiling novel solutions that differ from conventional human expectations yet remain coherent upon analysis.

Minghao Guo, Yan Gao, Zheng Pan

Converting a parametric curve into the implicit form, which is called implicitization, has always been a popular but challenging problem in geometric modeling and related applications. However, the existing methods mostly suffer from the problems of maintaining geometric features and choosing a reasonable implicit degree. The present paper has two contributions. We first introduce a new regularization constraint(called the weak gradient constraint) for both polynomial and non-polynomial curves, which efficiently possesses shape preserving. We then propose two adaptive algorithms of approximate implicitization for polynomial and non-polynomial curves respectively, which find the ``optimal'' implicit degree based on the behavior of the weak gradient constraint. More precisely, the idea is gradually increasing the implicit degree, until there is no obvious improvement in the weak gradient loss of the outputs. Experimental results have shown the effectiveness and high quality of our proposed methods.

Michael Sun, Minghao Guo, Weize Yuan et al.

Recent research in molecular discovery has primarily been devoted to small, drug-like molecules, leaving many similarly important applications in material design without adequate technology. These applications often rely on more complex molecular structures with fewer examples that are carefully designed using known substructures. We propose a data-efficient and interpretable model for representing and reasoning over such molecules in terms of graph grammars that explicitly describe the hierarchical design space featuring motifs to be the design basis. We present a novel representation in the form of random walks over the design space, which facilitates both molecule generation and property prediction. We demonstrate clear advantages over existing methods in terms of performance, efficiency, and synthesizability of predicted molecules, and we provide detailed insights into the method's chemical interpretability.

Minghao Guo, Xi Zhu, Haochen Xue et al.

Graph Neural Networks (GNNs) have achieved remarkable success in graph-based learning by propagating information among neighbor nodes via predefined aggregation mechanisms. However, such fixed schemes often suffer from two key limitations. First, they cannot handle the imbalance in node informativeness -- some nodes are rich in information, while others remain sparse. Second, predefined message passing primarily leverages local structural similarity while ignoring global semantic relationships across the graph, limiting the model's ability to capture distant but relevant information. We propose Retrieval-augmented Graph Agentic Network (ReaGAN), an agent-based framework that empowers each node with autonomous, node-level decision-making. Each node acts as an agent that independently plans its next action based on its internal memory, enabling node-level planning and adaptive message propagation. Additionally, retrieval-augmented generation (RAG) allows nodes to access semantically relevant content and build global relationships in the graph. ReaGAN achieves competitive performance under few-shot in-context settings using a frozen LLM backbone without fine-tuning, showcasing the potential of agentic planning and local-global retrieval in graph learning.

Zhiyong He, Dewen Guo, Minghao Guo et al.

Simulating large-scale articulated assemblies poses a significant challenge due to the numerical stiffness and geometric complexity of jointed structures. Conventional rigid body solvers struggle with the high nonlinearity induced by rotation parameterization. This difficulty becomes more pronounced for multiple two-way-coupled bodies. This paper introduces a novel framework that leverages the linear kinematic mapping of Affine Body Dynamics (ABD). As ABD targets near-rigid objects, the constitutive variations of different materials become negligible, which justifies a co-rotational approach to isolate geometric nonlinearities of the system. This insight enables the use of constant system matrices that can be pre-factorized throughout the simulation, even with fully implicit integration schemes. To manage the high DOF counts of large-scale systems, we map primal body coordinates onto a compact dual space defined by minimal joint degrees of freedom. By solving the resulting KKT systems, our method ensures exact constraint enforcement and physically accurate motion propagation. We provide a suite of specialized solvers tailored for diverse joint topologies, including chains, trees, closed loops, and irregular networks. Experimental results show that our approach achieves interactive rates for systems with hundreds of thousands of bodies on a single CPU core, while maintaining excellent stability at large time steps.

Xiang Gao, Yuanpeng Liu, Xinmu Wang et al.

Neural representations for 3D meshes are emerging as an effective solution for compact storage and efficient processing. Existing methods often rely on neural overfitting, where a coarse mesh is stored and progressively refined through multiple decoder networks. While this can restore high-quality surfaces, it is computationally expensive due to successive decoding passes and the irregular structure of mesh data. In contrast, images have a regular structure that enables powerful super-resolution and restoration frameworks, but applying these advantages to meshes is difficult because their irregular connectivity demands complex encoder-decoder architectures. Our key insight is that a geometry image-based representation transforms irregular meshes into a regular image grid, making efficient image-based neural processing directly applicable. Building on this idea, we introduce our neural geometry image-based representation, which is decoder-free, storage-efficient, and naturally suited for neural processing. It stores a low-resolution geometry-image mipmap of the surface, from which high-quality meshes are restored in a single forward pass. To construct geometry images, we leverage Optimal Transport (OT), which resolves oversampling in flat regions and undersampling in feature-rich regions, and enables continuous levels of detail (LoD) through geometry-image mipmapping. Experimental results demonstrate state-of-the-art storage efficiency and restoration accuracy, measured by compression ratio (CR), Chamfer distance (CD), and Hausdorff distance (HD).

Bangde Du, Minghao Guo, Songming He et al.

Large Language Models (LLMs) are exhibiting emergent human-like abilities and are increasingly envisioned as the foundation for simulating an individual's communication style, behavioral tendencies, and personality traits. However, current evaluations of LLM-based persona simulation remain limited: most rely on synthetic dialogues, lack systematic frameworks, and lack analysis of the capability requirement. To address these limitations, we introduce TwinVoice, a comprehensive benchmark for assessing persona simulation across diverse real-world contexts. TwinVoice encompasses three dimensions: Social Persona (public social interactions), Interpersonal Persona (private dialogues), and Narrative Persona (role-based expression). It further decomposes the evaluation of LLM performance into six fundamental capabilities, including opinion consistency, memory recall, logical reasoning, lexical fidelity, persona tone, and syntactic style. Experimental results reveal that while advanced models achieve moderate accuracy in persona simulation, they still fall short of capabilities such as syntactic style and memory recall. Consequently, the average performance achieved by LLMs remains considerably below the human baseline.

Siyuan Chen, Minghao Guo, Caoliwen Wang et al.

Biomolecular interaction modeling has been substantially advanced by foundation models, yet they often produce all-atom structures that violate basic steric feasibility. We address this limitation by enforcing physical validity as a strict constraint during both training and inference with a uniffed module. At its core is a differentiable projection that maps the provisional atom coordinates from the diffusion model to the nearest physically valid conffguration. This projection is achieved using a Gauss-Seidel scheme, which exploits the locality and sparsity of the constraints to ensure stable and fast convergence at scale. By implicit differentiation to obtain gradients, our module integrates seamlessly into existing frameworks for end-to-end ffnetuning. With our Gauss-Seidel projection module in place, two denoising steps are sufffcient to produce biomolecular complexes that are both physically valid and structurally accurate. Across six benchmarks, our 2-step model achieves the same structural accuracy as state-of-the-art 200-step diffusion baselines, delivering approximately 10 times faster wall-clock speed while guaranteeing physical validity.

Haobo Yang, Minghao Guo, Dequan Yang et al.

Contemporary deep learning models have achieved impressive performance in image classification by primarily leveraging statistical regularities within large datasets, but they rarely incorporate structured insights drawn directly from perceptual psychology. To explore the potential of perceptually motivated inductive biases, we propose integrating classic geometric visual illusions well-studied phenomena from human perception into standard image-classification training pipelines. Specifically, we introduce a synthetic, parametric geometric-illusion dataset and evaluate three multi-source learning strategies that combine illusion recognition tasks with ImageNet classification objectives. Our experiments reveal two key conceptual insights: (i) incorporating geometric illusions as auxiliary supervision systematically improves generalization, especially in visually challenging cases involving intricate contours and fine textures; and (ii) perceptually driven inductive biases, even when derived from synthetic stimuli traditionally considered unrelated to natural image recognition, can enhance the structural sensitivity of both CNN and transformer-based architectures. These results demonstrate a novel integration of perceptual science and machine learning and suggest new directions for embedding perceptual priors into vision model design.

Pingchuan Ma, Benjamin Tod Jones, Tsun-Hsuan Wang et al.

This position paper argues that machine learning for scientific discovery should shift from inductive pattern recognition to axiom-based reasoning. We propose a game design framework in which scientific inquiry is recast as a rule-evolving system: agents operate within environments governed by axioms and modify them to explain outlier observations. Unlike conventional ML approaches that operate within fixed assumptions, our method enables the discovery of new theoretical structures through systematic rule adaptation. We demonstrate the feasibility of this approach through preliminary experiments in logic-based games, showing that agents can evolve axioms that solve previously unsolvable problems. This framework offers a foundation for building machine learning systems capable of creative, interpretable, and theory-driven discovery.

Kevin Tirta Wijaya, Michael Sun, Minghao Guo et al.

Accurate prediction of continuous properties is essential to many scientific and engineering tasks. Although deep-learning regressors excel with abundant labels, their accuracy deteriorates in data-scarce regimes. We introduce RankRefine, a model-agnostic, plug-and-play post hoc method that refines regression with expert knowledge coming from pairwise rankings. Given a query item and a small reference set with known properties, RankRefine combines the base regressor's output with a rank-based estimate via inverse variance weighting, requiring no retraining. In molecular property prediction task, RankRefine achieves up to 10% relative reduction in mean absolute error using only 20 pairwise comparisons obtained through a general-purpose large language model (LLM) with no finetuning. As rankings provided by human experts or general-purpose LLMs are sufficient for improving regression across diverse domains, RankRefine offers practicality and broad applicability, especially in low-data settings.

Peter Yichen Chen, Minghao Guo, Hanspeter Pfister et al.

Computer graphics, often associated with films, games, and visual effects, has long been a powerful tool for addressing scientific challenges--from its origins in 3D visualization for medical imaging to its role in modern computational modeling and simulation. This course explores the deep and evolving relationship between computer graphics and science, highlighting past achievements, ongoing contributions, and open questions that remain. We show how core methods, such as geometric reasoning and physical modeling, provide inductive biases that help address challenges in both fields, especially in data-scarce settings. To that end, we aim to reframe graphics as a modeling language for science by bridging vocabulary gaps between the two communities. Designed for both newcomers and experts, Graphics4Science invites the graphics community to engage with science, tackle high-impact problems where graphics expertise can make a difference, and contribute to the future of scientific discovery. Additional details are available on the course website: https://graphics4science.github.io

Kevin Tirta Wijaya, Minghao Guo, Michael Sun et al.

Molecular deep learning models have achieved remarkable success in property prediction, but they often require large amounts of labeled data. The challenge is that, in real-world applications, labels are extremely scarce, as obtaining them through laboratory experimentation is both expensive and time-consuming. In this work, we introduce MoleVers, a versatile pretrained molecular model designed for various types of molecular property prediction in the wild, i.e., where experimentally-validated labels are scarce. MoleVers employs a two-stage pretraining strategy. In the first stage, it learns molecular representations from unlabeled data through masked atom prediction and extreme denoising, a novel task enabled by our newly introduced branching encoder architecture and dynamic noise scale sampling. In the second stage, the model refines these representations through predictions of auxiliary properties derived from computational methods, such as the density functional theory or large language models. Evaluation on 22 small, experimentally-validated datasets demonstrates that MoleVers achieves state-of-the-art performance, highlighting the effectiveness of its two-stage framework in producing generalizable molecular representations for diverse downstream properties.

Minghao Guo, Wan Shou, Liane Makatura et al.

Polymers are widely-studied materials with diverse properties and applications determined by different molecular structures. It is essential to represent these structures clearly and explore the full space of achievable chemical designs. However, existing approaches are unable to offer comprehensive design models for polymers because of their inherent scale and structural complexity. Here, we present a parametric, context-sensitive grammar designed specifically for the representation and generation of polymers. As a demonstrative example, we implement our grammar for polyurethanes. Using our symbolic hypergraph representation and 14 simple production rules, our PolyGrammar is able to represent and generate all valid polyurethane structures. We also present an algorithm to translate any polyurethane structure from the popular SMILES string format into our PolyGrammar representation. We test the representative power of PolyGrammar by translating a dataset of over 600 polyurethane samples collected from literature. Furthermore, we show that PolyGrammar can be easily extended to the other copolymers and homopolymers such as polyacrylates. By offering a complete, explicit representation scheme and an explainable generative model with validity guarantees, our PolyGrammar takes an important step toward a more comprehensive and practical system for polymer discovery and exploration. As the first bridge between formal languages and chemistry, PolyGrammar also serves as a critical blueprint to inform the design of similar grammars for other chemistries, including organic and inorganic molecules.

Rui Xu, Minghao Guo, Jiaqi Wang et al.

Patch-based methods and deep networks have been employed to tackle image inpainting problem, with their own strengths and weaknesses. Patch-based methods are capable of restoring a missing region with high-quality texture through searching nearest neighbor patches from the unmasked regions. However, these methods bring problematic contents when recovering large missing regions. Deep networks, on the other hand, show promising results in completing large regions. Nonetheless, the results often lack faithful and sharp details that resemble the surrounding area. By bringing together the best of both paradigms, we propose a new deep inpainting framework where texture generation is guided by a texture memory of patch samples extracted from unmasked regions. The framework has a novel design that allows texture memory retrieval to be trained end-to-end with the deep inpainting network. In addition, we introduce a patch distribution loss to encourage high-quality patch synthesis. The proposed method shows superior performance both qualitatively and quantitatively on three challenging image benchmarks, i.e., Places, CelebA-HQ, and Paris Street-View datasets.

Chuming Li, Yuan Xin, Chen Lin et al.

Designing an effective loss function plays an important role in visual analysis. Most existing loss function designs rely on hand-crafted heuristics that require domain experts to explore the large design space, which is usually sub-optimal and time-consuming. In this paper, we propose AutoML for Loss Function Search (AM-LFS) which leverages REINFORCE to search loss functions during the training process. The key contribution of this work is the design of search space which can guarantee the generalization and transferability on different vision tasks by including a bunch of existing prevailing loss functions in a unified formulation. We also propose an efficient optimization framework which can dynamically optimize the parameters of loss function's distribution during training. Extensive experimental results on four benchmark datasets show that, without any tricks, our method outperforms existing hand-crafted loss functions in various computer vision tasks.

Chen Lin, Minghao Guo, Chuming Li et al.

Data augmentation is critical to the success of modern deep learning techniques. In this paper, we propose Online Hyper-parameter Learning for Auto-Augmentation (OHL-Auto-Aug), an economical solution that learns the augmentation policy distribution along with network training. Unlike previous methods on auto-augmentation that search augmentation strategies in an offline manner, our method formulates the augmentation policy as a parameterized probability distribution, thus allowing its parameters to be optimized jointly with network parameters. Our proposed OHL-Auto-Aug eliminates the need of re-training and dramatically reduces the cost of the overall search process, while establishes significantly accuracy improvements over baseline models. On both CIFAR-10 and ImageNet, our method achieves remarkable on search accuracy, 60x faster on CIFAR-10 and 24x faster on ImageNet, while maintaining competitive accuracies.

Yung-Hsiang Lu, George K. Thiruvathukal, Ahmed S. Kaseb et al.

Millions of network cameras have been deployed worldwide. Real-time data from many network cameras can offer instant views of multiple locations with applications in public safety, transportation management, urban planning, agriculture, forestry, social sciences, atmospheric information, and more. This paper describes the real-time data available from worldwide network cameras and potential applications. Second, this paper outlines the CAM2 System available to users at https://www.cam2project.net/. This information includes strategies to discover network cameras and create the camera database, user interface, and computing platforms. Third, this paper describes many opportunities provided by data from network cameras and challenges to be addressed.

Minghao Guo, Zhao Zhong, Wei Wu et al.

In this paper, we propose an inverse reinforcement learning method for architecture search (IRLAS), which trains an agent to learn to search network structures that are topologically inspired by human-designed network. Most existing architecture search approaches totally neglect the topological characteristics of architectures, which results in complicated architecture with a high inference latency. Motivated by the fact that human-designed networks are elegant in topology with a fast inference speed, we propose a mirror stimuli function inspired by biological cognition theory to extract the abstract topological knowledge of an expert human-design network (ResNeXt). To avoid raising a too strong prior over the search space, we introduce inverse reinforcement learning to train the mirror stimuli function and exploit it as a heuristic guidance for architecture search, easily generalized to different architecture search algorithms. On CIFAR-10, the best architecture searched by our proposed IRLAS achieves 2.60% error rate. For ImageNet mobile setting, our model achieves a state-of-the-art top-1 accuracy 75.28%, while being 2~4x faster than most auto-generated architectures. A fast version of this model achieves 10% faster than MobileNetV2, while maintaining a higher accuracy.