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Hao Chen

Publications and source records attributed to Hao Chen.

At least 91 records · Page 5Linked to original sources
arXiv2026

Correlation-Guided Flow Matching with Annealed Masking for Spatial Transcriptomics Generation

Spatial transcriptomics (ST) provides spatially resolved gene expression profiling but remains expensive, motivating the prediction of ST from histology images. Generative models have emerged as a mainstream paradigm for ST prediction due to their ability to model the conditional distribution of gene expression and capture its inherent stochasticity. However, these methods typically treat genes as independent prediction targets and overlook the intrinsic gene-gene interactions in biological systems, which limits their ability to preserve biologically meaningful co-expression patterns. We argue that gene-gene interactions, which reflect shared pathways and regulatory mechanisms, are essential for generating numerically accurate and biologically coherent ST profiles. In this paper, we propose CorrFlow, a correlation-guided flow matching framework for histology-to-ST prediction that explicitly models gene-gene dependencies through two complementary mechanisms. First, we introduce an annealed masked flow matching strategy, where subsets of genes are progressively masked following a timestep-dependent annealing schedule, encouraging the model to infer masked genes conditioned on the remaining genes and promoting joint conditional modeling beyond per-gene marginal estimation. Second, we devise a gene graph-regularized optimization scheme that integrates prior knowledge from the STRING database and data-driven co-expression estimated by WGCNA to construct a gene affinity graph, which enforces both local consistency and global smoothness in the predicted expression. Extensive experiments across 12 datasets show that CorrFlow achieves the best average PCC and HPCC among evaluated methods, leading to more biologically coherent ST predictions.

cs.LG↗
arXiv2026

Improving Richardson--Lucy Deconvolution with Diffusion Priors for Fluorescence Microscopy

Richardson--Lucy (RL) deconvolution improves fluorescence microscopy images by recovering details lost to diffraction. It estimates the fluorescence signal most likely to have produced the measured photon counts under a Poisson imaging model. However, deconvolution remains ill-posed, especially at low photon counts, when weak biological structures become difficult to distinguish from shot noise and the prior strongly influences the reconstruction. RL recovers structure in early iterations but can amplify noise and become unstable, while regularizers such as total variation (TV) reduce these artifacts at the cost of oversmoothing. Instead, we learn a prior from real fluorescence microscopy images and use its gradient within an inverse-problem framework. The prior is estimated using an unconditional score-based diffusion model trained on a large microscopy dataset. At each step, the learned prior guides RL toward plausible specimen structures, while RL enforces Poisson consistency with the measured counts. Across diverse biological samples and cellular morphologies, the framework reduces RL noise amplification while better preserving weak structures at low photon counts.

eess.IV↗
arXiv2026

Graph Engineering in the Era of LLM Agents: From Individual Intelligence to System Intelligence

LLMs have evolved from language generators to autonomous agents capable of complex, long-horizon tasks. This evolution has produced paradigms including Prompt Engineering to elicit model capabilities, Context Engineering to manage information access, Harness Engineering to organize external tools and resources, and Loop Engineering to support continual reflection and self-improvement. Yet as tasks grow more complex, individual intelligence faces a fundamental limit: many tasks require heterogeneous expertise, interdependent subtasks, parallel execution, independent verification, and persistent state, exceeding any single agent's organizational capacity. Augmenting one agent's capabilities or context cannot resolve this architectural mismatch; intelligence must instead be distributed across specialized agents and organized at the system level. We call this System Intelligence: an agent system's ability to organize and coordinate multiple intelligent components into a coherent, adaptive whole pursuing a shared objective. Achieving it requires more than adding agents; it demands explicit structures to organize work, coordinate heterogeneous agents, and maintain evolving execution states. We introduce Graph Engineering, an emerging paradigm for next-generation agent systems. Unlike prior paradigms that mainly optimize individual interactions or agent-level behavior, Graph Engineering constructs explicit, dynamic, evolving graph structures representing tasks, agents, and system states. These abstractions provide a unified foundation for organizing complex objectives, orchestrating heterogeneous agents, modeling system dynamics, and enabling scalable agent evolution. We systematically review the principles, methodologies, and applications of Graph Engineering for LLM agents. Related papers, open-source data, and projects are collected at https://github.com/DEEP-JLU/Awesome-Graph-Engineering.

cs.IR↗
arXiv2026

OmniPhys: A Unified Multimodal Benchmark for Physics Understanding and Generation from Chinese Educational Corpora

Multimodal Large Language Models (MLLMs) have demonstrated strong abilities in solving diverse visual and textual reasoning tasks. However, their development in the physics domain is significantly hindered by the lack of a comprehensive benchmark. To fill this gap, we introduce OmniPhys, a large-scale benchmark for multimodal physics understanding and reasoning, covering middle school through university-level problems from Chinese Educational Corpora. OmniPhys consists of 15,246 questions and 19,850 images, accompanied by detailed annotations that support fine-grained analysis of reasoning processes and knowledge usage. Beyond conventional evaluation, OmniPhys is a benchmark that systematically evaluates multimodal outputs in the physics domain, including models' ability to generate structured physics diagrams, which constitute a fundamental component of authentic physics problem solving. Extensive evaluations reveal critical gaps in the capabilities of current MLLMs, especially in complex reasoning and visual generation. To address this, we release OmniPhys to serve as a foundational resource for advancing multimodal intelligence in physics and scientific domains. Codes and data are available at https://github.com/ECNU-RAIL/OmniPhys-EMNLP2026.

cs.CL↗
arXiv2026

Continuous Adversarial Flow Models

We propose continuous adversarial flow models, a type of continuous-time flow model trained with an adversarial objective. Unlike flow matching, which uses a fixed mean-squared-error criterion, our approach introduces a learned discriminator to guide training. This change in objective induces a different generalized distribution, which empirically produces samples that are better aligned with the target data distribution. Our method is primarily proposed for post-training existing flow-matching models, although it can also train models from scratch. On the ImageNet 256px generation task, our post-training substantially improves the guidance-free FID of latent-space SiT from 8.26 to 3.63 and of pixel-space JiT from 7.17 to 3.57. It also improves guided generation, reducing FID from 2.06 to 1.53 for SiT and from 1.86 to 1.80 for JiT. We further evaluate our approach on text-to-image generation, where it achieves improved results on both the GenEval and DPG benchmarks.

cs.LG↗
arXiv2026

What FID Hides: Detecting, Ranking, and Diagnosing Deviations in Generative Evaluation

Generative models are commonly ranked by Fréchet Inception Distance (FID) and Kernel Inception Distance (KID), yet FID's first-two-moment summary can miss distributional differences, and a reported scalar gap alone is not a calibrated test against sampling variation. FID's moment restriction has concrete consequences: on ImageNet, visually unrecognizable images optimized only to match the reference Inception mean and covariance obtain FID $24.7$ versus $58.6$ for held-out real images (lower is better). Moreover, FID and KID are scalar discrepancies that are unchanged when the two samples are exchanged and therefore do not encode the direction of a dispersion change: under-dispersion, as can occur in mode collapse, versus over-dispersion. We introduce \textbf{ZID} (\emph{Z-resolved Integrated Diagnostic}), which combines six standardized location- and dispersion-sensitive arms from a rank graph (RISE) and Gaussian kernels (GPK at two bandwidths). Rather than asking one scalar to serve incompatible roles, ZID reports three linked outputs: an index for ranking departure magnitude, a permutation $p$-value for testing distributional equality, and a signed dispersion readout for diagnosis. In controlled experiments, ZID detects a broad range of departures, and its score tracks increasing severity along the corresponding sweeps, including cases in which FID is flat or reversed. On DiT-XL/2 and SiT-XL/2 guidance sweeps, ZID detects departure from real data, and its signed readout labels the high-guidance diversity collapse as under-dispersion.

stat.ML↗
arXiv2026

Do Robotic World Models Really Follow Actions? Diagnosing and Aligning Action-Conditioned Generation for Policy Learning

Action-conditioned world models are increasingly used as learned simulators for policy evaluation and improvement, yet their effectiveness rests on an unverified assumption: generated futures faithfully reflect arbitrary valid actions. Existing benchmarks are typically confined to expert demonstrations, leaving off-expert action following inadequately evaluated. To address this gap, we introduce WorldEcho, which probes action following over a broader action distribution using visual integrity and SE(3) trajectory alignment. Our diagnosis shows that current world models reasonably execute expert actions but struggle with diverse off-expert trajectories, either ignoring the commanded actions or producing visually invalid rollouts. We further propose WorldSync, which strengthens action following along three complementary axes: distributional coverage, representational grounding, and intervention-effect alignment. It broadens the training distribution over action consequences, grounds intermediate video representations in action-induced robot dynamics through an Action-Forcing Expert, and aligns predicted changes under action interventions with the corresponding changes in ground-truth futures. Experiments on RoboTwin benchmarks and real-robot tasks show that WorldSync improves WorldEcho metrics and serves as a more reliable simulator for iterative policy improvement, enabling policies to achieve higher success rates.

cs.RO↗
arXiv2026

Negative Refraction of Terahertz Phonons via Interfacial Momentum Compensation

Negative refraction provides a route to steer and focus wave energy flow, but it remains difficult to realize for coherent terahertz (THz) phonons. The difficulty stems from conventional dispersion-based mechanisms, which require strongly anisotropic or negative-curvature dispersions, while the long-wavelength acoustic phonons most favorable for coherent transport are nearly isotropic. Here we overcome this limitation by introducing a momentum compensation mechanism mediated by discrete translational symmetry. Discrete translational symmetry parallel to the interface supplies a compensating tangential momentum, reopening transmitted channels beyond the conventional critical condition and enabling negative refraction when this compensation reverses the tangential component. Mode-resolved calculations for hBN/graphene heterostructures establish this mechanism in laterally stitched in-plane interfaces and show how twisted van der Waals moire superlattices shift the negative-refraction window to lower frequencies. These results identify periodic crystalline interfaces as symmetry-engineered elements for THz phonon momentum conversion and wavefront control.

cond-mat.mes-hall↗
arXiv2026

The Greatness of Science Cannot Be Planned: Agentic Auto-Research is Fuzz Testing

Agentic auto-research is emerging, but most systems treat scientific discovery as goal-oriented optimization against a final benchmark. This paradigm rewards a sparse final verdict and ignores the exploration that precedes it. When agents optimize only the final score, they overfit to the test conditions and sample blindly rather than search. Within a declared research problem, a research agent and a greybox fuzzer for software analysis face the same sparse feedback. A fuzzer rarely finds a bug directly, but coverage makes partial progress observable on every execution. Fuzzers use that dense signal to mutate inputs and allocate effort, rather than merely rank completed runs. Auto-research needs the same two capabilities. First, each experiment must expose a cheap, dense signal of epistemic progress before final scientific validation is available. Second, that signal must determine the next intervention so the agent searches rather than repeatedly samples. Because the progress signal provides guidance rather than a final verdict, final validation must still evaluate claims using evidence protected from adaptive reuse. We propose controlled tests to determine whether candidate signals predict validated progress, whether feedback-directed search yields more validated discoveries per unit cost than repeated sampling, and whether protected validation reduces false discoveries. In a simulated physics environment, an AI research agent that tracks its intermediate epistemic progress discovers a hidden physical law. Optimization-driven baselines fail because they repeatedly sample and overfit to their existing data instead of probing unfamiliar regimes. Feedback architecture, not generation capacity, is the central bottleneck in auto-research.

cs.AI↗
arXiv2026

CoAL-RAG: A Complexity-Aware Legal Retrieval-Augmented Generation Method

Legal consultation questions exhibit multi-level complexity. A single retrieval strategy often leads to over-reasoning for simple questions and poor interpretability for complex ones, making it difficult to meet the requirements for both answer quality and efficiency in high-risk scenarios. To address this issue, this paper proposes CoAL-RAG, a complexity-aware legal retrieval-augmented generation method, which constructs a multi-dimensional evaluation mechanism based on ``question essence'' and ``retrieval consistency'' to enable adaptive routing of retrieval strategies. First, the reasoning demand is quantified according to the logical structure of the question. Then, the discrepancy between semantic retrieval and keyword retrieval is utilized to indirectly reflect problem complexity, thereby selecting the most appropriate retrieval strategy and dynamically filtering contextual information. Experimental results demonstrate that the proposed method significantly outperforms baseline models not only on Chinese legal benchmarks (SocialLawQA, LawBench) but also demonstrates strong cross-jurisdictional generalization on English datasets (LexGLUE, CaseHold). Specifically, on Chinese datasets, the BLEU score improves by 42.5\% and ROUGE-L reaches 3.6 times that of knowledge graph-based methods. On English benchmarks, CoAL-RAG maintains highly competitive accuracy, achieving an optimal balance between generation quality, deep logical reasoning, and system efficiency across different legal systems.

cs.CL↗
arXiv2026

ForeDreamer: A Self-Evolving Dual-Agent Memory Architecture for Future Event Prediction

Open-web future event prediction requires agents to distill reliable signals from noisy, redundant, and incomplete evidence. Existing retrieval/memory mechanisms directly feed retrieved information to agents or rely on simple memory functions such as storing and reusing prior information for prediction, leaving them insufficient for open-web forecasting. We propose to transform raw web evidence into structured memory before prediction, enabling agents to reason over distilled, question-specific evidence rather than noisy retrieval results. This paper presents ForeDreamer, a self-evolving dual-agent framework for managing memory over open-web evidence. ForeDreamer separates factual memory, a question-specific evidence state for the current forecast, from experiential memory, persistent agent experience accumulated across forecasting episodes. It uses a main agent for search and prediction, and a memory-processing subagent to convert search results into factual memory with dedicated tools. ForeDreamer further evolves experiential memory through two tracks, improving both forecasting decisions and factual-memory construction. Experiments on Prophet Arena and FutureX demonstrate the effectiveness of ForeDreamer. Project page: https://zhongzero.github.io/ForeDreamer

cs.CL↗
arXiv2026

Efficient Self-Evaluation for Diffusion Language Models via Sequence Regeneration

Diffusion large language models (dLLMs) have recently attracted significant attention for their ability to enhance diversity, controllability, and parallelism. However, their non-sequential, bidirectionally masked generation makes quality assessment difficult, underscoring the need for effective self-evaluation. In this work, we propose DiSE, a simple yet effective self-evaluation confidence quantification method for dLLMs. DiSE quantifies confidence by computing the probability of regenerating the tokens in the entire generated sequence, given the full context. This method enables more efficient and reliable quality assessment by leveraging token regeneration probabilities, facilitating both likelihood estimation and robust uncertainty quantification. Building upon DiSE, we further introduce a flexible-length generation framework, which adaptively controls the sequence length based on the model's self-assessment of its own output. We analyze and validate the feasibility of DiSE from the perspective of dLLM generalization, and empirically demonstrate that DiSE is positively correlated with both semantic coherence and answer accuracy. Extensive experiments on likelihood evaluation, uncertainty quantification, and flexible-length generation further confirm the effectiveness of the proposed DiSE. Project page: https://zhongzero.github.io/DiSE/

cs.CL↗
arXiv2026

A continually expandable foundation model for brain MRI

Brain magnetic resonance imaging (MRI) is central to neuroscience and clinical assessment, but models are commonly developed for individual diseases, populations or imaging protocols. Foundation models promise more general representations, yet they are usually pretrained once and can lose earlier capabilities when updated with new data. Here we show that Alcmaeon, a three-dimensional brain MRI foundation model pretrained without manual labels on more than 425,000 volumes and derived imaging maps, can be expanded sequentially across clinical domains. Alcmaeon combines volumetric encoding and latent diffusion generation with Graph-Blueprint Pruning (GBP), which protects network modules important to earlier domains while leaving the remaining capacity trainable. Across expansion from healthy ageing and neurodegeneration to developmental, psychiatric and tumour imaging, GBP showed less forgetting than sequential adaptation and elastic weight consolidation across voxel-level reconstruction measures, with its largest advantage after adaptation to tumour imaging. The blueprints provided an inspectable record of how model capacity was protected and reused. Representations from different model levels supported image synthesis, disease classification, survival modelling and postoperative prediction, although no single representation was optimal for every task. These findings provide a route towards brain MRI foundation models that can grow with emerging data while retaining earlier capabilities.

cs.CV↗
arXiv2026

HarvestPoint-ACT: Explicit Target Selection and Harvest-Point Conditioning for Robotic Fruit Harvesting under Occlusion

End-to-end imitation learning avoids hand-made robot motion for approaching and grasping, but the policy must still decide which fruit to pick and where to close the gripper. Occlusion can make the policy lose the selected fruit during harvesting, and the correct closing point is difficult to infer from pixels alone. This paper presents HarvestPoint-ACT, which makes both decisions explicit in perception and provides them to the policy. An instance segmentation front end with a keypoint branch predicts a mask and a harvest point for each visible fruit, where the harvest point specifies the location to close the gripper. A scheduler ranks detected candidates by occlusion and travel distance and selects one target. After each attempt, it redetects and reranks the candidates because the canopy may have changed. The selected fruit is encoded for an action chunking transformer as an eight-dimensional state, containing the absolute harvest point, the vector from the gripper to that point, a validity flag, and a confidence score. When the selected fruit is temporarily undetected, the system retains the last harvest point estimate in the robot base frame and marks it as stale, and aborts the attempt if the loss persists. On a canopy mock-up, HarvestPoint-ACT achieves a success rate of 88%, and of 75% under heavy occlusion.

cs.RO↗
arXiv2026

Backward Layout Search for Sequence-Constrained Robotic Assembly

Robotic assembly layout planning must determine the assembly site and the initial pose of each part while ensuring collision-free execution of a prescribed assembly sequence. This problem is challenging because the obstacle environment changes after each assembly step, and unassembled parts re maining in the workspace may block robot motions. We observe that the feasibility of each assembly step depends only on the initial poses of the current and later-assembled parts. Based on this dependency, we propose Backward Layout Search (BLS), which assigns initial part poses in reverse assembly order. Each expansion performs geometric, kinematic, grasp, and prescribed-motion checks, while collision masks and candidate set filtering remove infeasible initial part pose candidates. Promising partial layouts are retained through beam selection, and complete layouts are validated by full motion planning in forward assembly order. Experiments on five assembly models show that BLS produces collision-free executable layouts and reduces step evaluations and search time compared with a matched forward search.

cs.RO↗
arXiv2026

Constructing Good Abelian Codes via Shift Bounds and Genetic Algorithms

This paper investigates the construction of linear codes via abelian codes over finite fields. By exploiting the algebraic structure of multivariate polynomial quotient rings, we derive lower bounds on the minimum distance using a generalized shift bound, which extends the classical van Lint-Wilson bound for cyclic codes. Several infinite families of abelian codes are explicitly constructed, including binary and ternary cases that extend previously known cyclic constructions. To find more abelian codes with good parameters, we apply a genetic algorithm that searches over defining sets represented as binary chromosomes of cyclotomic cosets; the fitness function compares the computed minimum distance against the best known linear code (BKLC) bounds. The search yields multiple record-breaking codes over F_3 and F_4, with improvements over Grassl's tables. Furthermore, the nested structure of these codes enables the application of Construction X, yielding additional linear codes with improved parameters. The results demonstrate that abelian codes, combined with heuristic search, form a viable way for discovering linear codes with unknown parameters.

cs.IT↗
arXiv2026

A Multimodal Agentic Pathology Co-pilot via Evidence Grounded Reasoning

Pathology is the cornerstone of modern medicine, where accurate decision-making relies heavily on evidence-based practices. While artificial intelligence (AI) has the potential to transform clinical workflows, the intersection of AI and evidence-based medicine remains under-explored, with primitive attempts restricted to text-only general medicine. In this work, we present PathPocket, a multimodal AI agentic co-pilot designed specifically for evidence grounded pathology. We construct the most comprehensive pathology evidence corpus to date, encompassing approximately 110,472 public and authorized documents structured across a rigorous hierarchy of evidence from clinical guideline to expert opinion. From this meticulously graded foundation, we build a large-scale multimodal pathology hypergraph containing over 4.55 million entities and 7.10 million relations. Serving as a robust knowledge engine, this hypergraph provides traceable evidence for a collaborative multi-agent reasoning framework integrating input understanding, evidence retrieval, filtering, and diagnosis generation. This enables PathPocket to seamlessly resolve a wide spectrum of clinical tasks, ranging from text-only queries to complex multimodal diagnostics involving region-of-interest (ROI) and gigapixel whole-slide images (WSIs). We rigorously evaluate the system on a multidimensional benchmark of over 200,000 real-world cases, where it significantly outperforms existing state-of-the-arts. Crucially, extensive user studies demonstrate that PathPocket substantially improves the diagnostic accuracy and confidence of pathologists. By directly grounding pathology interpretations in verifiable literature, PathPocket offers a practical and scalable solution for the future of evidence grounded computational pathology.

cs.AI↗
arXiv2026

EgoCITE: Context-Augmented Indexing and Time-Aware Retrieval for Long-Horizon Egocentric Memory

Long-horizon egocentric memory transforms continuous first-person video and audio into a searchable record of past experiences. We demonstrate two bottlenecks in existing systems: indices built from context-poor captions are unreliable for agentic search, while retrieval ignores a question's temporal intent. To address both bottlenecks, we introduce EgoCITE (Egocentric Context-augmented Indexing and Time-aware Evidence retrieval), a long-horizon agentic memory framework for egocentric QA. EgoCITE comprises three components. EgoScheme uses local multimodal context to turn fragmentary video captions and speech transcripts into self-contained atomic memory indices. EgoIndex organizes complementary action, activity, utterance, and conversation representations into searchable multi-view memory indices at multiple granularities. EgoRetrv combines semantic search with question-conditioned temporal relevance scoring and curation of retrieved evidence. We evaluate EgoCITE on EgoLifeQA, EgoMem, and EgoR1-Bench in terms of answer accuracy and target-event retrieval alignment. EgoCITE improves accuracy over agentic memory baselines by at least 4.4--14.2% while achieving 36$\times$ lower cost than long-context LLM agents.

cs.CV↗