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Zehong Wang

Publications and source records attributed to Zehong Wang.

At least 19 recordsLinked to original sources
arXiv2026

The Collaboration Tax: How Much LLM Multi-Agent Systems Pay to Coordinate

Multi-agent systems built from large language models are deployed widely, yet how much performance is lost when two LLMs must coordinate rather than act alone remains unclear. We formulate the collaboration tax as the team-decentralisation loss of a two-player cooperative game with private information, with two propositions characterising its sign and its equivalence to a max-superadditivity violation. We operationalise this definition on 32 solo-tractable tasks grouped by source of grounding friction and measure it on 11 models from 7 providers. The tax is structured along two no-exception axes: a category ordering across every model and a monotonic decrease with capability. The proximate mechanism is not a reasoning deficit but a four-stage conversational cascade in which agents make ungrounded claims, fail to query the partner, skip integrating both views, and accept the answer without re-derivation. The tax is mechanically predictable from conversation features and partly tractable: a prompt intervention targeting all four stages closes a substantial fraction of the gap, with the dominant bottleneck differing across categories. In heterogeneous pairs the tax is pulled toward the stronger partner rather than the additive midpoint, empirically realising the max-superadditivity violation predicted by our framework. Together these results recast collaboration in LLM systems as a measurable, predictable, and partly tractable cost.

cs.CL↗
arXiv2026

Proteo-R1: Reasoning Foundation Models for De Novo Protein Design

Deep learning in de novo protein design has achieved atomic-level fidelity. However, existing models remain largely non-deliberative: they directly synthesize molecular geometries without explicitly reasoning about which residues or interactions are functionally essential. As a result, design decisions are entangled with continuous sampling dynamics, limiting interpretability, controllability, and systematic reuse of biochemical knowledge. We introduce Proteo-R1, a reasoning-guided protein design framework that explicitly decouples molecular understanding from geometric generation. Proteo-R1 adopts a dual-expert architecture in which a multimodal large language model (MLLM) serves as an understanding expert, analyzing protein sequences, structures, and textual context to identify key functional residues that govern binding and specificity. These residue-level decisions are then passed as hard constraints to a separate diffusion-based generation expert, which performs conditional co-design while respecting the fixed interaction anchors. This factorization mirrors how human experts approach molecular engineering: first, reasoning about critical interactions, then optimizing geometry subject to those constraints. By operationalizing reasoning as explicit residue-level commitments rather than latent textual guidance, Proteo-R1 achieves stable, interpretable, and modular integration of LLM reasoning with state-of-the-art geometric generative models. Code, data, and demos are available at https://smiles724.github.io/r1/.

cs.LG↗
arXiv2026

LatentChem: From Textual CoT to Latent Thinking in Chemical Reasoning

Current chemical large language models (LLMs) predominantly rely on explicit Chain-of-Thought (CoT) to solve complex reasoning problems. However, forcing nonverbal tacit chemical logic into discrete natural language imposes a fundamental ``modality mismatch,'' creating an artificial bottleneck for reasoning. We introduce LatentChem, a reasoning interface that decouples chemical logic from linguistic generation, enabling the model to process information via continuous thought vectors and dynamic perception. Our investigation reveals a pivotal emergent behavior: spontaneous internalization, defined here as self-selected under outcome-only optimization. When optimized for task success, the model abandons verbose textual derivations in favor of implicit latent computation, suggesting that it identifies the continuous manifold as a more native substrate for chemical logic. This paradigm shift also proves to be a superior computational strategy: LatentChem achieves a 59.88\% non-tie win rate against the strong CoT baseline on the rigorous ChemCoTBench, while delivering a broad 10.84$\times$ average reduction in reasoning step overhead (5.96$\times$ wall-clock speedup) across all evaluated benchmarks. Our results provide empirical evidence that chemical reasoning is more naturally and effectively realized as continuous latent dynamics rather than discretized linguistic trajectories.

physics.chem-ph↗
arXiv2026

Object-Centric Environment Modeling for Agentic Tasks

Large language model (LLM) agents can improve through accumulated experience, but free-form textual memories become difficult to maintain, validate, and reuse as interactions grow. Recent symbolic approaches learn executable skills or programmatic world models, yet often store local procedures or assume simplified dynamics. We propose Object-Centric Environment Modeling (OCM), which organizes experience into an executable object-centric environment model. OCM maintains two connected code bases: object knowledge, which defines environment entities and mechanisms as Python classes, and procedure knowledge, which records reusable interaction patterns that must import and use the object model. OCM works in an online setting: after each episode, OCM reflects on the trajectory, updates both knowledge bases, and verifies that all procedures execute against the updated object model. During future interaction, the agent uses progressive knowledge disclosure to inspect compact code signatures first and read source code only when needed. Experiments show that OCM achieves the best average rank across benchmarks and reduces invalid actions, demonstrating that agents can benefit from building object-centric environment models.

cs.AI↗
arXiv2026

Accretion Disk Perturbations and Their Effects on Kerr Black Hole Superradiance and Gravitational Atom Evolution

Kerr black hole (BH) superradiance can form gravitational atoms and produce characteristic gravitational-wave signals, providing a probe of ultralight bosons and dark matter. In realistic systems, accretion-disk gravity can shift energy levels and mix states, modifying the effective superradiant growth. We model the disk as a weak external perturbation via a multipole expansion and derive an effective three-level Hamiltonian for the $n=2$ subspace $\{\ket{211},\ket{210},\ket{21-1}\}$ in the weak-coupling regime. The leading disk effect is the quadrupolar ($\ell_d=2$) tidal field, whose symmetries fix the selection rules: axisymmetry gives only diagonal shifts, equatorial nonaxisymmetry activates $Δm=\pm2$ mixing ($\ket{211}\leftrightarrow\ket{21-1}$), and breaking equatorial reflection opens $Δm=\pm1$ couplings involving $\ket{210}$. As illustrations, a transient equatorial $m=2$ spiral wave drives the resulting two-level system and can suppress superradiance by populating a decaying mode, while a quasi-static warp produces full three-level mixing and can generate narrow ``growth gaps'' near accidental near-degeneracies, with the same static reshuffling also allowing enhancement when weight shifts toward the growing mode. These findings demonstrate that accretion disk perturbations are a crucial environmental factor in determining the dynamics of BH superradiance and the evolution of boson clouds, thereby providing a more reliable theoretical basis for assessing the detectability of ultralight bosons in realistic astrophysical settings.

gr-qc↗
arXiv2026

Temporal Graph Pattern Machine

Temporal graph learning is pivotal for deciphering dynamic systems, where the core challenge lies in explicitly modeling the underlying evolving patterns that govern network transformation. However, prevailing methods are predominantly task-centric and rely on restrictive assumptions -- such as short-term dependency modeling, static neighborhood semantics, and retrospective time usage. These constraints hinder the discovery of transferable temporal evolution mechanisms. To address this, we propose the Temporal Graph Pattern Machine (TGPM), a foundation framework that shifts the focus toward directly learning generalized evolving patterns. TGPM conceptualizes each interaction as an interaction patch synthesized via temporally-biased random walks, thereby capturing multi-scale structural semantics and long-range dependencies that extend beyond immediate neighborhoods. These patches are processed by a Transformer-based backbone designed to capture global temporal regularities while adapting to context-specific interaction dynamics. To further empower the model, we introduce a suite of self-supervised pre-training tasks -- specifically masked token modeling and next-time prediction -- to explicitly encode the fundamental laws of network evolution. Extensive experiments on temporal link prediction and temporal node classification show that TGPM consistently ranks among the top-performing methods, demonstrating exceptional cross-domain transferability. Our code has been released in https://github.com/antman9914/TGPM.

cs.LG↗
arXiv2026

Policy4OOD: A Knowledge-Guided World Model for Policy Intervention Simulation against the Opioid Overdose Crisis

The opioid epidemic remains one of the most severe public health crises in the United States, yet evaluating policy interventions before implementation is difficult: multiple policies interact within a dynamic system where targeting one risk pathway may inadvertently amplify another. We argue that effective opioid policy evaluation requires three capabilities -- forecasting future outcomes under current policies, counterfactual reasoning about alternative past decisions, and optimization over candidate interventions -- and propose to unify them through world modeling. We introduce Policy4OOD, a knowledge-guided spatio-temporal world model that addresses three core challenges: what policies prescribe, where effects manifest, and when effects unfold.Policy4OOD jointly encodes policy knowledge graphs, state-level spatial dependencies, and socioeconomic time series into a policy-conditioned Transformer that forecasts future opioid outcomes.Once trained, the world model serves as a simulator: forecasting requires only a forward pass, counterfactual analysis substitutes alternative policy encodings in the historical sequence, and policy optimization employs Monte Carlo Tree Search over the learned simulator. To support this framework, we construct a state-level monthly dataset (2019--2024) integrating opioid mortality, socioeconomic indicators, and structured policy encodings. Experiments demonstrate that spatial dependencies and structured policy knowledge significantly improve forecasting accuracy, validating each architectural component and the potential of world modeling for data-driven public health decision support. Our code and data have been released in https://github.com/antman9914/Policy4OOD.

cs.LG↗
arXiv2026

Generalizing GNNs with Tokenized Mixture of Experts

Deployed graph neural networks (GNNs) are frozen at deployment yet must fit clean data, generalize under distribution shifts, and remain stable to perturbations. We show that static inference induces a fundamental tradeoff: improving stability requires reducing reliance on shift-sensitive features, leaving an irreducible worst-case generalization floor. Instance-conditional routing can break this ceiling, but is fragile because shifts can mislead routing and perturbations can make routing fluctuate. We capture these effects via two decompositions separating coverage vs selection, and base sensitivity vs fluctuation amplification. Based on these insights, we propose STEM-GNN, a pretrain-then-finetune framework with a mixture-of-experts encoder for diverse computation paths, a vector-quantized token interface to stabilize encoder-to-head signals, and a Lipschitz-regularized head to bound output amplification. Across nine node, link, and graph benchmarks, STEM-GNN achieves a stronger three-way balance, improving robustness to degree/homophily shifts and to feature/edge corruptions while remaining competitive on clean graphs.

cs.LG↗
arXiv2026

ProPlay: Procedural World Models for Self-Evolving LLM Agents

Self-evolving agents are expected to improve through interaction without external supervision, but this remains difficult in partially observable environments where agents must explore actively, learn from limited feedback, and decide when to trust prior experience. Existing LLM-agent methods often rely on memory or planning modules, yet they rarely close the loop between them to continually refine an internal understanding of environment dynamics. We introduce ProPlay, a procedural world model that supports procedure-level preplay, where agents can rehearse future procedural paths using the learned world knowledge. Rather than representing experience as isolated rules or low-level action constraints, ProPlay abstracts successful trajectories into procedures and organizes them in a procedure graph that captures causal transitions among task stages. Each transition is associated with a reliability record embedding to estimate its task-specific contribution from past outcomes. Before each episode, ProPlay simulates future procedural trajectories over known graph structures as structured soft guidance; after execution, it refines the graph using environment feedback. Experiments on public benchmarks show that ProPlay consistently improves environment understanding and self-evolution capability over strong baselines. Our code has been released in https://github.com/antman9914/proplay.

cs.LG↗
arXiv2026

MDForge: Agentic Molecular Dynamics Pipeline Design under Sparse Simulator Feedback

Molecular dynamics (MD) is the canonical in-silico method for atomistic molecular science, simulating molecular behavior from first-principle physics. Designing an MD pipeline for a new system requires substantial expert knowledge: running it on even one molecule is expensive, ruling out trial-and-error. We automate this expert pipeline-design process with an LLM agent. Unlike existing MD agents that orchestrate a predefined tool set, we treat pipeline design as open-ended code generation in which the agent's behavior is reshaped online by verbal reward. Specifically, we build MDForge, an LLM agent whose in-context update rule densifies the sparse reward via a multi-agent debate among physics experts. On three SAMPL host-guest binding free-energy benchmarks, MDForge automatically designs MD pipelines competitive with human experts. Deployed on a library of unseen candidate guests, its CB[7] pipeline discovers a novel binder that wet-lab competition NMR confirms is a high-affinity, picomolar CB[7] binder. Our data and code are available at https://github.com/Zehong-Wang/MDForge.

cs.AI↗
arXiv2026

SupraBench: A Benchmark for Supramolecular Chemistry

Supramolecular chemistry, which includes the study of non-covalent host-guest assemblies, has advanced various applications. However, designing host-guest systems remains time-consuming, requiring days of dry-lab verification per candidate pair. Although LLMs have emerged as a fast alternative with strong performance on molecular binding tasks, no benchmark currently systematically evaluates LLMs for host-guest reasoning across fundamental supramolecular chemistry tasks, e.g., binding affinity prediction. To this end, we collaborate with domain experts to release the first Supramolecular Benchmark, called SupraBench, to evaluate LLMs in chemistry reasoning. Specifically, we design four fundamental tasks, i.e., binding affinity prediction, top-binder selection, solvent identification, and host-guest description, plus an auxiliary vision-based task for molecular identification. We also release SupraPMC, a curated 16M-token corpus of Supramolecular chemistry articles distilled from Europe PMC, to support the adaptation to the supramolecular domain. We benchmark a broad range of open and proprietary LLMs and find that LLMs leave substantial headroom across all tasks. Domain adaptation pretraining over SupraPMC transfers cleanly to in-distribution regression but trades off against strict letter-format output. Moreover, the difficulty profile differs sharply across task families, revealing distinct failure modes that indicate specific gaps in current supramolecular chemistry reasoning. Our source codes and benchmark datasets are available at https://github.com/Tianyi-Billy-Ma/SupraBench.

cs.LG↗
arXiv2026

Graph is a Substrate Across Data Modalities

Graphs provide a natural representation of relational structure that arises across diverse domains. Despite this ubiquity, graph structure is typically learned in a modality- and task-isolated manner, where graph representations are constructed within individual task contexts and discarded thereafter. As a result, structural regularities across modalities and tasks are repeatedly reconstructed rather than accumulated at the level of intermediate graph representations. This motivates a representation-learning question: how should graph structure be organized so that it can persist and accumulate across heterogeneous modalities and tasks? We adopt a representation-centric perspective in which graph structure is treated as a structural substrate that persists across learning contexts. To instantiate this perspective, we propose G-Substrate, a graph substrate framework that organizes learning around shared graph structures. G-Substrate comprises two complementary mechanisms: a unified structural schema that ensures compatibility among graph representations across heterogeneous modalities and tasks, and an interleaved role-based training strategy that exposes the same graph structure to multiple functional roles during learning. Experiments across multiple domains, modalities, and tasks show that G-Substrate outperforms task-isolated and naive multi-task learning methods. The codebase, model, and datasets are available at https://github.com/zmli6/G-Substrate.

cs.LG↗
arXiv2026

Why Semantic Entropy Fails: Geometry-Aware and Calibrated Uncertainty for Policy Optimization

Post-training has become central to improving reasoning and alignment in large language models, where critic-free models enable scalable learning from model-generated outputs but lack principled mechanisms to distinguish informative from noisy signals. Recent approaches leverage response-level measures as uncertainty signals to regulate group-based optimization methods such as GRPO. Yet their empirical success remains unstable and unclear in how they influence optimization dynamics. In this paper, we provide, to our knowledge, the first principled formulation that interprets uncertainty signals as mechanisms for characterizing and regulating gradient variance and learning signal quality. Based on both empirical and theoretical analysis, we identify two critical gaps of current entropy-based estimators: The anisotropic gap and The calibration gap. Motivated by this analysis, we propose Geometric-aware Calibrated Policy Optimization (GCPO), a novel framework integrating geometry-aware measures to capture semantic disagreement with reward-based calibration to align uncertainty with learning signal strength. Experiments on multiple benchmarks show that our approach more faithfully tracks gradient variability and consistently improves post-training performance. Our results highlight the importance of designing uncertainty signals that are aligned with optimization dynamics, offering a principled perspective for robust post-training.

cs.LG↗
arXiv2026

Hypergraph Pattern Machine: Compositional Tokenization for Higher-Order Interactions

Hypergraphs model higher-order relations that drive real-world decisions, from drug prescriptions to recommendations. A central structural signal in such data, beyond what pairwise relations can express, is interaction compositionality: whether a higher-order relation is compositional, emergent, or inhibitory with respect to its observed or unobserved sets. In polypharmacy, the regime decides whether a drug should be dropped, kept, or excluded: a compositional drug triple can be safely simplified, an emergent triple requires all drugs jointly, and an inhibitory triple flags a drug that disrupts an existing interaction. However, existing hypergraph learning methods, which merely propagate messages over observed hyperedges, leave this compositional signal unmodeled, allowing dangerous drug combinations to slip through and be misclassified. To this end, we propose the Hypergraph Pattern Machine (HGPM), shifting the paradigm from message passing to learning the compositional pattern of subsets. It tokenizes compositional subsets, organizes them in an inclusion DAG, and trains an inclusion-aware Transformer under masked reconstruction. On ten hypergraph benchmarks, HGPM matches or exceeds state-of-the-art methods. Notably, in a real adverse-event prediction case, HGPM correctly identifies the drug addition that inhibits the side effect among feature-identical candidates, a discrimination existing methods cannot make. The code and data are in https://github.com/KryieZhao/HGPM.git.

cs.LG↗
arXiv2026

PreScam: A Benchmark for Predicting Scam Progression from Early Conversations

Conversational scams, such as romance and investment scams, are emerging as a major form of online fraud. Unlike one-shot scam lures such as fake lottery or unpaid toll messages, they unfold through multi-turn conversations in which scammers gradually manipulate victims using evolving psychological techniques. However, existing research mainly focuses on static scam detection or synthetic scams, leaving open whether language models can understand how real-world scams progress over time. We introduce PreScam, a benchmark for modeling scam progression from early conversations. Built from user-submitted scam reports, PreScam filters and structures 177,989 raw reports into 11,573 conversational scam instances spanning 20 scam categories. Each instance is hierarchically structured according to the scam lifecycle defined by the proposed scam kill chain, and further annotated at the turn level with scammer psychological actions and victim responses. We benchmark models on two tasks: real-time termination prediction, which estimates whether a conversation is approaching the termination stage, and scammer action prediction, which forecasts the scammer's subsequent actions. Results show a clear gap between surface-level fluency and progression modeling: supervised encoders substantially outperform zero-shot LLMs on real-time termination prediction, while next-action prediction remains only moderately successful even for strong LLMs. Taken together, these results show that current models can capture some scam-related cues, yet still struggle to track how risk escalates and how manipulation unfolds across turns.

cs.CL↗
arXiv2026

On the Safety of Graph Representation Learning

Graph representation learning (GRL) has evolved from topology-only graph embeddings to task-specific supervised GNNs, and more recently to reusable representations and graph foundation models (GFMs). However, existing evaluations mainly measure clean transfer, adaptation, and task coverage. It remains unclear whether GRL methods stay reliable when deployment stresses affect graph signals, graph contexts, label support, structural groups, or predictive evidence. We introduce GRL-Safety, a multi-axis safety evaluation benchmark for GRL. GRL-Safety evaluates twelve representative methods, spanning topology-only embedding methods, supervised GNNs, self-supervised graph models, and GFMs, on twenty-five graph datasets under standardized evaluation conditions while preserving method-native adaptation. The evaluation covers five safety axes: corruption robustness, OOD generalization, class imbalance, fairness, and interpretation, with per-axis and sub-condition reporting rather than a single aggregate score. Our analysis yields three cross-axis insights that can inspire future research. First, safety behavior is shaped by the interaction between representation design and the stressed graph factor, rather than by method family alone. Second, foundation-era methods show axis-specific strengths rather than broad safety dominance. Third, several deployment regimes remain difficult even for the best evaluated method, revealing capability gaps that require new robustness, adaptation, or training objectives beyond model selection. The benchmark, evaluation protocols, and code are available at: https://github.com/GXG-CS/GRL-Safety.

cs.LG↗
arXiv2026

NoiseRater: Meta-Learned Noise Valuation for Diffusion Model Training

Diffusion models have achieved remarkable success across a wide range of generative tasks, yet their training paradigm largely treats injected noise as uniformly informative. In this work, we challenge this assumption and introduce NoiseRater, a meta-learning framework for instance-level noise valuation in diffusion model training. We propose a parametric noise rater that assigns importance scores to individual noise realizations conditioned on data and timestep, enabling adaptive reweighting of the training objective. The rater is trained via bilevel optimization to improve downstream validation performance after inner-loop diffusion updates. To enable efficient deployment, we further design a decoupled two-stage pipeline that transitions from soft weighting during meta-training to hard noise selection during standard training. Extensive experiments on FFHQ and ImageNet demonstrate that not all noise samples contribute equally, and that prioritizing informative noise improves both training efficiency and generation quality. Our results establish noise valuation as a complementary and previously underexplored axis for improving diffusion model training. Our code is available at: https://anonymous.4open.science/r/NoiseRater-DEB116.

cs.LG↗
arXiv2026

Semantic Refinement with LLMs for Graph Representations

Graph-structured data exhibit substantial heterogeneity in where their predictive signals originate: in some domains, node-level semantics dominate, while in others, structural patterns play a central role. This structure-semantics heterogeneity implies that no graph learning model with a fixed inductive bias can generalize optimally across diverse graph domains. However, most existing methods address this challenge from the model side by incrementally injecting new inductive biases, which remains fundamentally limited given the open-ended diversity of real-world graphs. In this work, we take a data-centric perspective and treat node semantics as a task-adaptive variable. We propose a Graph-Exemplar-guided Semantic Refinement (GES) framework for graph representation learning which -- unlike existing LLM-enhanced methods that generate node descriptions without graph context -- leverages structurally and semantically similar nodes from the graph itself to guide semantic refinement. Specifically, a GNN is first trained to produce predictive states, which along with structural and semantic similarity are used to retrieve in-graph exemplars that inform an LLM in refining node descriptions. We evaluate our approach on both text-rich and text-free graphs. Results show consistent improvements on semantics-rich and structure-dominated graphs, demonstrating the effectiveness of data-centric semantic refinement under structure-semantics heterogeneity.

cs.CL↗