arXiv subjects

Hongyu Guo

Publications and source records attributed to Hongyu Guo.

At least 19 recordsLinked to original sources

arXiv2026

Evidence Blindness in Direct Corpus Interaction: Persistent Navigation with AtlasNav

Large language model agents are moving beyond conventional retrieval-augmented generation toward direct interaction with external corpora. Direct Corpus Interaction (DCI) keeps the full corpus accessible, yet reachable evidence can remain unusable under finite interaction budgets. Required evidence may fail to surface, a surfaced supporting document may remain unopened, or an opened document may fail to expose its decisive fragment. We call this progressive silent loss Evidence Blindness and quantify it through stage-wise evidence realization. Within the DCI paradigm, raw interaction adds little reusable corpus organization, while dynamic-workspace methods reconstruct a query-conditioned interaction space from each query and trajectory. In both cases, useful structure is recovered largely online. We instead formulate large-scale agentic search as finite-budget navigation over reusable corpus structure. We introduce AtlasNav, a persistent multi-view corpus-navigation framework that retains direct corpus interaction but organizes the corpus once into a Corpus Atlas, allowing each query to navigate adaptively rather than reconstruct shared structure. On BrowseComp-Plus, AtlasNav achieves 92.05% strict accuracy while reducing recorded online inference cost by 30.21% relative to the prior dynamic-workspace state of the art. Under matched budgets, it realizes the complete required evidence earlier and approaches the same model's evidence-supplied empirical reference more rapidly. The same representation principle remains effective under PhantomWiki's distinct corpus organization and controlled 10K-1M scaling, and transfers competitively to heterogeneous enterprise knowledge. These results show that agentic search depends not only on accessible evidence, but also on how the corpus is represented so that limited interaction becomes effective navigation.

cs.AI↗

arXiv2026

Decoupling Parcellation from Classification: Systematic Benchmark of Fast Brain Segmentation Methods for Alzheimer's Disease Detection

Brain parcellation and classification are typically evaluated in isolation, yet downstream AD detection performance depends on their interaction. We decouple these components and systematically benchmark fast deep learning parcellation methods (SynthSeg+, OpenMAP-T1) against the FreeSurfer (FS-HV) clinical baseline through down- stream AD classification on OASIS-1. Our factorial design evaluates three parcellation methods, two volumetry strategies (hard vs. soft), and four classifier paradigms (clinical thresholds, supervised feedforward networks, ensemble methods, and foundation models with zero/few-shot prompting), with all results quantified using BCa Bootstrap 95% confidence intervals.

eess.IV↗

arXiv2026

On the Diversity of Analogy Making in Large Language Models

Large Language Models (LLMs) have demonstrated remarkable potential for analogy making, a core cognitive capability that drives novelty and creativity. While prior research has extensively investigated the applications and underlying mechanisms of LLM-based analogy making, its output diversity remains largely unexplored, despite being essential for broadening cross-domain connections and fostering scientific innovation. In this work, we present a comprehensive evaluation of analogy diversity across ten state-of-the-art open- and closed-source LLMs. Our findings highlight a concerning issue of domain homogeneity, a prevalent tendency for LLMs to generate analogies from a narrow set of target domains, limiting both inter-query and intra-model diversity. Furthermore, our analysis reveals a fundamental trade-off in existing LLM diversity-enhancement methods: increasing output diversity often comes at the expense of output quality. Finally, our causal analysis of LLM information flow reveals substantial differences in the model-sensitive regions governing analogy diversity across LLMs, suggesting a potential mechanism for the observed diversity-quality trade-off. To our knowledge, this is among the first studies to systematically investigate output diversity in LLM-based analogy making.

cs.CL↗

arXiv2026

From Answers to States: Verifiable Process-Level Evaluation of Chemical Reasoning in Large Language Models

Large language models are increasingly used as chemistry assistants, yet most chemistry benchmarks still score only final answers. This masks a critical failure mode: a model may output the correct molecule, product, or option while its reasoning violates chemical logic. Existing process-level evaluators are hard to scale because LLM judges and human step-level process annotation are costly, inconsistent, and vulnerable to hallucination. We introduce ChemCoTBench-V2, a rule-verifiable diagnostic benchmark for low-cost, auditable evaluation of structured, verifier-addressable chemical reasoning traces. It spans molecular understanding, molecule editing, molecular optimization, and reaction prediction, with 5,620 evaluation samples across 18 reporting tasks. Models must expose key intermediate steps in expert-designed templates, and those steps are checked with deterministic chemistry rules and, for closed-answer tasks, reference traces rather than another LLM judge. Open-ended molecular optimization is evaluated with oracle-verifiable state constraints rather than strict trace matching. The benchmark reports three separate signals: final-answer correctness, template adherence, and step-wise verifier correctness over expert-refined intermediate commitments. Experiments on frontier models reveal a persistent gap between final-answer success and structured-reasoning-state consistency: models often follow the requested format while failing chemical-step checks, or answer correctly with weak supporting reasoning. ChemCoTBench-V2 enables fine-grained model comparison and identifies the concrete step at which the trace first violates the verifier.

cs.AI↗

arXiv2026

Plausibility Is Not Prediction: Contrastive Evidence for LLM-Based Cellular Perturbation Reasoning

Perturbation experiments are central to understanding cellular mechanisms, but remain costly and sparse, motivating prediction of gene expression responses for unobserved conditions. A promising recent direction leverages large language models (LLMs) as "virtual cell" simulators-using stepwise, knowledge-grounded mechanistic reasoning to infer differential expression-pointing toward an interpretable, knowledge-driven paradigm that transcends purely data-driven approaches. However, we find that plausibility is not prediction: despite producing biologically plausible explanations, these methods fail to capture perturbation-specific effects: systematically overestimating differential expression, often underperforming a simple gene-frequency baseline in aggregate evaluations, and collapsing to chance-level performance at the per-gene level. This reveals a reliance on intrinsic gene response tendencies rather than true perturbation reasoning. We trace this failure to how evidence is presented: existing methods evaluate perturbation-gene pairs in isolation, without exposing how related perturbations differ in their effects on the same gene. To address this limitation, we introduce CORE (Contrastive Organization of Relational Evidence), which reframes prediction as a comparison task by organizing evidence into positive and negative outcomes from related perturbations. Using a biomedical knowledge graph for evidence retrieval, CORE improves calibration and substantially boosts perturbation-specific prediction in both LLM-based and non-LLM settings: for example, on drug-perturbation data, CORE-Reasoning improves Qwen3.5-9B aggregate metrics by up to 28.6%, while on generic perturbation data, CORE-Voting raises macro-per-gene AUROC from chance to 0.703 in average across four cell lines. This highlights contrastive evidence organization as essential to reliable LLM-based perturbation reasoning

cs.LG↗

arXiv2026

A Comparative Study of Molecular Dynamics Approaches for Simulating Ionic Conductivity in Solid Lithium Electrolytes

Accurate prediction of ionic conductivity is critical for the design of high-performance solid-state electrolytes in next-generation batteries. We benchmark molecular dynamics (MD) approaches for computing ionic conductivity in 21 lithium solid electrolytes for which experimental ionic conductivity has been previously reported in the literature. In particular, we compare simulations driven by density functional theory (DFT) and by universal machine-learning interatomic potentials (uMLIPs), namely a MACE foundation model. We find comparable performance between DFT and MACE, despite MACE on one GPU more than 350 times faster than DFT on a 64-CPU node. The framework developed here is designed to enable systematic comparisons with additional uMLIPs and fine-tuned models in future work.

cond-mat.mtrl-sci↗

arXiv2026

Rigidity-Aware Geometric Pretraining for Protein Design and Conformational Ensembles

Generative models have recently advanced $\textit{de novo}$ protein design by learning the statistical regularities of natural structures. However, current approaches face three key limitations: (1) Existing methods cannot jointly learn protein geometry and design tasks, where pretraining can be a solution; (2) Current pretraining methods mostly rely on local, non-rigid atomic representations for property prediction downstream tasks, limiting global geometric understanding for protein generation tasks; and (3) Existing approaches have yet to effectively model the rich dynamic and conformational information of protein structures. To overcome these issues, we introduce $\textbf{RigidSSL}$ ($\textit{Rigidity-Aware Self-Supervised Learning}$), a geometric pretraining framework that front-loads geometry learning prior to generative finetuning. Phase I (RigidSSL-Perturb) learns geometric priors from 432K structures from the AlphaFold Protein Structure Database with simulated perturbations. Phase II (RigidSSL-MD) refines these representations on 1.3K molecular dynamics trajectories to capture physically realistic transitions. Underpinning both phases is a bi-directional, rigidity-aware flow matching objective that jointly optimizes translational and rotational dynamics to maximize mutual information between conformations. Empirically, RigidSSL variants improve designability by up to 43% while enhancing novelty and diversity in unconditional generation. Furthermore, RigidSSL-Perturb improves the success rate by 5.8% in zero-shot motif scaffolding and RigidSSL-MD captures more biophysically realistic conformational ensembles in G protein-coupled receptor modeling.

cs.LG↗

arXiv2026

PerturbDiff: Functional Diffusion for Single-Cell Perturbation Modeling

Building Virtual Cells that can accurately simulate cellular responses to perturbations is a long-standing goal in systems biology. A fundamental challenge is that high-throughput single-cell sequencing is destructive: the same cell cannot be observed both before and after a perturbation. Thus, perturbation prediction requires mapping unpaired control and perturbed populations. Existing models address this by learning maps between distributions, but typically assume a single fixed response distribution when conditioned on observed cellular context (e.g., cell type) and the perturbation type. In reality, responses vary systematically due to unobservable latent factors such as microenvironmental fluctuations and complex batch effects, forming a manifold of possible distributions for the same observed conditions. To account for this variability, we introduce PerturbDiff, which shifts modeling from individual cells to entire distributions. By embedding distributions as points in a Hilbert space, we define a diffusion-based generative process operating directly over probability distributions. This allows PerturbDiff to capture population-level response shifts across hidden factors. Benchmarks on established datasets show that PerturbDiff achieves state-of-the-art performance in single-cell response prediction and generalizes substantially better to unseen perturbations. See our project page (https://katarinayuan.github.io/PerturbDiff-ProjectPage/), where code and data will be made publicly available (https://github.com/DeepGraphLearning/PerturbDiff).

cs.LG↗

arXiv2026

GeneZip: Region-Aware Compression for Long Context DNA Modeling

Long-context DNA models are limited by token-mixing cost and by how compression allocates representational budget across the genome. Existing approaches operate close to base-pair resolution, apply fixed downsampling, or learn content-dependent chunks without an explicit genomic budget, making long-context pretraining expensive and difficult to control. We introduce GeneZip, a region-aware DNA compression framework that combines H-Net-style dynamic routing with a Region-Aware Ratio (RAR) objective and bounded routing. GeneZip uses static gene-structure annotations during compression training to specify region-wise base-pairs-per-token (BPT) targets; at inference time, it compresses raw unseen DNA without annotations. GeneZip provides three main benefits. First, it is effective: GeneZip variants achieve the best validation PPL among encoder-based compressors, with GeneZip-70M operating at 137.6 BPT, and across four reproducible DNALongBench tasks--contact map prediction, eQTL prediction, enhancer-target gene prediction, and transcription-initiation signal prediction--GeneZip obtains the best average rank among compared sequence models. Second, it is redundancy-aware: a post-hoc RepeatMasker/TRF analysis shows that, without repeat supervision, GeneZip assigns higher local BPT to TE-derived interspersed repeats and tandem repeats, two major classes of repetitive DNA sequence redundancy. Third, it is efficient: by reducing the effective token-mixing length, GeneZip enables longer-context and larger-capacity pretraining, including 128K-context and 636M-parameter variants on a single A100 80GB GPU, and fine-tunes the eQTL task 50.4x faster than JanusDNA (50 vs. 2520 minutes). These results establish GeneZip as an effective, redundancy-aware, and efficient compression interface for long-context DNA modeling.

q-bio.GN↗

arXiv2025

First-Order Axiom Systems $\mathscr{E}_{d}$ and $\mathscr{E}_{da}$ Extending Tarski's $\mathscr{E}_{2}$ with Distance and Angle Function Symbols for Quantitative Euclidean Geometry

Tarski's first-order axiom system $\mathscr{E}_{2}$ for Euclidean geometry is notable for its completeness and decidability. However, the Pythagorean theorem -- either in its modern algebraic form $a^{2}+b^{2}=c^{2}$ or in Euclid's Elements -- cannot be directly expressed in $\mathscr{E}_{2}$, since neither distance nor area is a primitive notion in the language of $\mathscr{E}_{2}$. In this paper, we introduce an alternative axiom system $\mathscr{E}_{d}$ in a two-sorted language, which takes a two-place distance function $d$ as the only geometric primitive. We also present a conservative extension $\mathscr{E}_{da}$ of it, which also incorporates a three-place angle function $a$. The system $\mathscr{E}_{d}$ has two distinctive features: it is simple (with a single geometric primitive) and it is quantitative. Numerical distance can be directly expressed in this language. The Axiom of Similarity plays a central role in $\mathscr{E}_{d}$, effectively killing two birds with one stone: it provides a rigorous foundation for the theory of proportion and similarity, and it implies Euclid's Parallel Postulate (EPP). The Axiom of Similarity can be viewed as a quantitative formulation of EPP. The Pythagorean theorem and other quantitative results from similarity theory can be directly expressed in the languages of $\mathscr{E}_{d}$ and $\mathscr{E}_{da}$, motivating the name Quantitative Euclidean Geometry. The traditional analytic geometry can be united under synthetic geometry in $\mathscr{E}_{d}$. Namely, analytic geometry is not treated as a model of $\mathscr{E}_{d}$, but rather, its statements can be expressed as first-order formal sentences in the language of $\mathscr{E}_{d}$. The system $\mathscr{E}_{d}$ is shown to be consistent, complete, and decidable. Finally, we extend the theories to hyperbolic geometry and Euclidean geometry in higher dimensions.

math.LO↗

arXiv2025

InertialAR: Autoregressive 3D Molecule Generation with Inertial Frames

Transformer-based autoregressive models have emerged as a unifying paradigm across modalities such as text and images, but their extension to 3D molecule generation remains underexplored. The gap stems from two fundamental challenges: (1) how to tokenize molecules into a canonical 1D sequence of tokens that is invariant to both SE(3) transformations and atom index permutations, and (2) how to design an architecture capable of modeling hybrid atom-based tokens that couple discrete atom types with continuous 3D coordinates. To address these challenges, we introduce InertialAR. It first performs generation-oriented canonical tokenization by aligning each molecule to a canonical inertial frame and reordering atoms, thereby converting arbitrary 3D structures into a unique, SE(3)- and permutation-invariant sequence of tokens for autoregressive generation. Built upon this canonical tokenization, we propose geometric positional encoding (GeoPE), which endows Transformer attention with 3D geometric awareness. Finally, InertialAR utilizes a hierarchical autoregressive paradigm to decode the next atom, consecutively predicting the atom type and 3D coordinates via Diffusion Loss. Experimentally, InertialAR achieves state-of-the-art performance on 8 of the 10 evaluation metrics for unconditional generation across QM9, GEOM-Drugs, and B3LYP. Moreover, it significantly outperforms baselines in controllable generation for targeted chemical functionality, attaining state-of-the-art results across all 5 metrics. Code is available at github.com/HaoruiLi46/InertialAR.

cs.LG↗

arXiv2025

LacMaterial: Large Language Models as Analogical Chemists for Materials Discovery

Analogical reasoning, the transfer of relational structures across contexts (e.g., planet is to sun as electron is to nucleus), is fundamental to scientific discovery. Yet human insight is often constrained by domain expertise and surface-level biases, limiting access to deeper, structure-driven analogies both within and across disciplines. Large language models (LLMs), trained on vast cross-domain data, present a promising yet underexplored tool for analogical reasoning in science. Here, we demonstrate that LLMs can generate novel battery materials by (1) retrieving cross-domain analogs and analogy-guided exemplars to steer exploration beyond conventional dopant substitutions, and (2) constructing in-domain analogical templates from few labeled examples to guide targeted exploitation. These explicit analogical reasoning strategies yield candidates outside established compositional spaces and outperform standard prompting baselines. Our findings position LLMs as interpretable, expert-like hypothesis generators that leverage analogy-driven generalization for scientific innovation.

cs.LG↗

arXiv2025

UniFGVC: Universal Training-Free Few-Shot Fine-Grained Vision Classification via Attribute-Aware Multimodal Retrieval

Few-shot fine-grained visual classification (FGVC) aims to leverage limited data to enable models to discriminate subtly distinct categories. Recent works mostly finetuned the pre-trained visual language models to achieve performance gain, yet suffering from overfitting and weak generalization. To deal with this, we introduce UniFGVC, a universal training-free framework that reformulates few-shot FGVC as multimodal retrieval. First, we propose the Category-Discriminative Visual Captioner (CDV-Captioner) to exploit the open-world knowledge of multimodal large language models (MLLMs) to generate a structured text description that captures the fine-grained attribute features distinguishing closely related classes. CDV-Captioner uses chain-of-thought prompting and visually similar reference images to reduce hallucination and enhance discrimination of generated captions. Using it we can convert each image into an image-description pair, enabling more comprehensive feature representation, and construct the multimodal category templates using few-shot samples for the subsequent retrieval pipeline. Then, off-the-shelf vision and text encoders embed query and template pairs, and FGVC is accomplished by retrieving the nearest template in the joint space. UniFGVC ensures broad compatibility with diverse MLLMs and encoders, offering reliable generalization and adaptability across few-shot FGVC scenarios. Extensive experiments on 12 FGVC benchmarks demonstrate its consistent superiority over prior few-shot CLIP-based methods and even several fully-supervised MLLMs-based approaches.

cs.CV↗

arXiv2025

IDRBench: Understanding the Capability of Large Language Models on Interdisciplinary Research

Innovation is a key driving force of human civilization. As the body of knowledge has grown considerably, bridging knowledge across different disciplines, where significant innovation often emerges, has become increasingly challenging. The recent advancements in machine learning models, particularly Large Language Models (LLMs), have provided effective access to extensive knowledge sources and shown impressive abilities in reasoning, rendering significant opportunities for interdisciplinary discovery. Our research aims to understand the capabilities of state-of-the-art LLMs in integrating knowledge from different fields for interdisciplinary research (IDR). To address this fundamental problem, we introduce IDRBench, a pioneering framework that includes both datasets and evaluation tasks: (1) IDR Paper Identification, (2) IDR Idea Integration, and (3) IDR Idea Recommendation. Our study on ten mainstream LLMs provides a comprehensive analysis of their behavior and establishes benchmarks and baselines for future research. To the best of our knowledge, IDRBench is the first to provide a comprehensive investigation of LLMs' IDR capability.

cs.CL↗

arXiv2025

NeuralOS: Towards Simulating Operating Systems via Neural Generative Models

We introduce NeuralOS, a neural framework that simulates graphical user interfaces (GUIs) of operating systems by directly predicting screen frames in response to user inputs such as mouse movements, clicks, and keyboard events. NeuralOS combines a recurrent neural network (RNN), which tracks computer state, with a diffusion-based neural renderer that generates screen images. The model is trained on a dataset of Ubuntu XFCE recordings, which include both randomly generated interactions and realistic interactions produced by AI agents. Experiments show that NeuralOS successfully renders realistic GUI sequences, accurately captures mouse interactions, and reliably predicts state transitions like application launches. Beyond reproducing existing systems, NeuralOS shows that synthesized training data can teach the model to simulate applications that were never installed, as illustrated by a Doom application, and suggests a path toward learning user interfaces purely from synthetic demonstrations.

cs.CV↗

arXiv2025

Referring Expression Instance Retrieval and A Strong End-to-End Baseline

Using natural language to query visual information is a fundamental need in real-world applications. Text-Image Retrieval (TIR) retrieves a target image from a gallery based on an image-level description, while Referring Expression Comprehension (REC) localizes a target object within a given image using an instance-level description. However, real-world applications often present more complex demands. Users typically query an instance-level description across a large gallery and expect to receive both relevant image and the corresponding instance location. In such scenarios, TIR struggles with fine-grained descriptions and object-level localization, while REC is limited in its ability to efficiently search large galleries and lacks an effective ranking mechanism. In this paper, we introduce a new task called \textbf{Referring Expression Instance Retrieval (REIR)}, which supports both instance-level retrieval and localization based on fine-grained referring expressions. First, we propose a large-scale benchmark for REIR, named REIRCOCO, constructed by prompting advanced vision-language models to generate high-quality referring expressions for instances in the MSCOCO and RefCOCO datasets. Second, we present a baseline method, Contrastive Language-Instance Alignment with Relation Experts (CLARE), which employs a dual-stream architecture to address REIR in an end-to-end manner. Given a referring expression, the textual branch encodes it into a query embedding. The visual branch detects candidate objects and extracts their instance-level visual features. The most similar candidate to the query is selected for bounding box prediction. CLARE is first trained on object detection and REC datasets to establish initial grounding capabilities, then optimized via Contrastive Language-Instance Alignment (CLIA) for improved retrieval across images. We will release our code and benchmark publicly.

cs.CV↗

arXiv2025

DisProtEdit: Exploring Disentangled Representations for Multi-Attribute Protein Editing

We introduce DisProtEdit, a controllable protein editing framework that leverages dual-channel natural language supervision to learn disentangled representations of structural and functional properties. Unlike prior approaches that rely on joint holistic embeddings, DisProtEdit explicitly separates semantic factors, enabling modular and interpretable control. To support this, we construct SwissProtDis, a large-scale multimodal dataset where each protein sequence is paired with two textual descriptions, one for structure and one for function, automatically decomposed using a large language model. DisProtEdit aligns protein and text embeddings using alignment and uniformity objectives, while a disentanglement loss promotes independence between structural and functional semantics. At inference time, protein editing is performed by modifying one or both text inputs and decoding from the updated latent representation. Experiments on protein editing and representation learning benchmarks demonstrate that DisProtEdit performs competitively with existing methods while providing improved interpretability and controllability. On a newly constructed multi-attribute editing benchmark, the model achieves a both-hit success rate of up to 61.7%, highlighting its effectiveness in coordinating simultaneous structural and functional edits.

q-bio.QM↗

arXiv2025

OBELiX: A Curated Dataset of Crystal Structures and Experimentally Measured Ionic Conductivities for Lithium Solid-State Electrolytes

Solid-state electrolyte batteries are expected to replace liquid electrolyte lithium-ion batteries in the near future thanks to their higher theoretical energy density and improved safety. However, their adoption is currently hindered by their lower effective ionic conductivity, a quantity that governs charge and discharge rates. Identifying highly ion-conductive materials using conventional theoretical calculations and experimental validation is both time-consuming and resource-intensive. While machine learning holds the promise to expedite this process, relevant ionic conductivity and structural data is scarce. Here, we present OBELiX, a database of $\sim$600 synthesized solid electrolyte materials and their experimentally measured room temperature ionic conductivities gathered from literature and curated by domain experts. Each material is described by their measured composition, space group and lattice parameters. A full-crystal description in the form of a crystallographic information file (CIF) is provided for $\sim$320 structures for which atomic positions were available. We discuss various statistics and features of the dataset and provide training and testing splits carefully designed to avoid data leakage. Finally, we benchmark seven existing ML models on the task of predicting ionic conductivity and discuss their performance. The goal of this work is to facilitate the use of machine learning for solid-state electrolyte materials discovery.

cond-mat.mtrl-sci↗