arXiv subjects

Yichi Zhang

Publications and source records attributed to Yichi Zhang.

At least 127 records · Page 7Linked to original sources

arXiv2025

Atomic Diffusion Models for Small Molecule Structure Elucidation from NMR Spectra

Nuclear Magnetic Resonance (NMR) spectroscopy is a cornerstone technique for determining the structures of small molecules and is especially critical in the discovery of novel natural products and clinical therapeutics. Yet, interpreting NMR spectra remains a time-consuming, manual process requiring extensive domain expertise. We introduce ChefNMR (CHemical Elucidation From NMR), an end-to-end framework that directly predicts an unknown molecule's structure solely from its 1D NMR spectra and chemical formula. We frame structure elucidation as conditional generation from an atomic diffusion model built on a non-equivariant transformer architecture. To model the complex chemical groups found in natural products, we generated a dataset of simulated 1D NMR spectra for over 111,000 natural products. ChefNMR predicts the structures of challenging natural product compounds with an unsurpassed accuracy of over 65%. This work takes a significant step toward solving the grand challenge of automating small-molecule structure elucidation and highlights the potential of deep learning in accelerating molecular discovery. Code is available at https://github.com/ml-struct-bio/chefnmr.

cs.LG↗

arXiv2025

Rethinking Intracranial Aneurysm Vessel Segmentation: A Perspective from Computational Fluid Dynamics Applications

The precise segmentation of intracranial aneurysms and their parent vessels (IA-Vessel) is a critical step for hemodynamic analyses, which mainly depends on computational fluid dynamics (CFD). However, current segmentation methods predominantly focus on image-based evaluation metrics, often neglecting their practical effectiveness in subsequent CFD applications. To address this deficiency, we present the Intracranial Aneurysm Vessel Segmentation (IAVS) dataset, the first comprehensive, multi-center collection comprising 641 3D MRA images with 587 annotations of aneurysms and IA-Vessels. In addition to image-mask pairs, IAVS dataset includes detailed hemodynamic analysis outcomes, addressing the limitations of existing datasets that neglect topological integrity and CFD applicability. To facilitate the development and evaluation of clinically relevant techniques, we construct two evaluation benchmarks including global localization of aneurysms (Stage I) and fine-grained segmentation of IA-Vessel (Stage II) and develop a simple and effective two-stage framework, which can be used as a out-of-the-box method and strong baseline. For comprehensive evaluation of applicability of segmentation results, we establish a standardized CFD applicability evaluation system that enables the automated and consistent conversion of segmentation masks into CFD models, offering an applicability-focused assessment of segmentation outcomes. The dataset, code, and model will be public available at https://github.com/AbsoluteResonance/IAVS.

cs.CV↗

arXiv2025

Arithmetic-Mean $μ$P for Modern Architectures: A Unified Learning-Rate Scale for CNNs and ResNets

Choosing an appropriate learning rate remains a key challenge in scaling depth of modern deep networks. The classical maximal update parameterization ($μ$P) enforces a fixed per-layer update magnitude, which is well suited to homogeneous multilayer perceptrons (MLPs) but becomes ill-posed in heterogeneous architectures where residual accumulation and convolutions introduce imbalance across layers. We introduce Arithmetic-Mean $μ$P (AM-$μ$P), which constrains not each individual layer but the network-wide average one-step pre-activation second moment to a constant scale. Combined with a residual-aware He fan-in initialization - scaling residual-branch weights by the number of blocks ($\mathrm{Var}[W]=c/(K\cdot \mathrm{fan\text{-}in})$) - AM-$μ$P yields width-robust depth laws that transfer consistently across depths. We prove that, for one- and two-dimensional convolutional networks, the maximal-update learning rate satisfies $η^\star(L)\propto L^{-3/2}$; with zero padding, boundary effects are constant-level as $N\gg k$. For standard residual networks with general conv+MLP blocks, we establish $η^\star(L)=Θ(L^{-3/2})$, with $L$ the minimal depth. Empirical results across a range of depths confirm the $-3/2$ scaling law and enable zero-shot learning-rate transfer, providing a unified and practical LR principle for convolutional and deep residual networks without additional tuning overhead.

cs.LG↗

arXiv2025

Mitigating Overthinking in Large Reasoning Models via Manifold Steering

Recent advances in Large Reasoning Models (LRMs) have demonstrated remarkable capabilities in solving complex tasks such as mathematics and coding. However, these models frequently exhibit a phenomenon known as overthinking during inference, characterized by excessive validation loops and redundant deliberation, leading to substantial computational overheads. In this paper, we aim to mitigate overthinking by investigating the underlying mechanisms from the perspective of mechanistic interpretability. We first showcase that the tendency of overthinking can be effectively captured by a single direction in the model's activation space and the issue can be eased by intervening the activations along this direction. However, this efficacy soon reaches a plateau and even deteriorates as the intervention strength increases. We therefore systematically explore the activation space and find that the overthinking phenomenon is actually tied to a low-dimensional manifold, which indicates that the limited effect stems from the noises introduced by the high-dimensional steering direction. Based on this insight, we propose Manifold Steering, a novel approach that elegantly projects the steering direction onto the low-dimensional activation manifold given the theoretical approximation of the interference noise. Extensive experiments on DeepSeek-R1 distilled models validate that our method reduces output tokens by up to 71% while maintaining and even improving the accuracy on several mathematical benchmarks. Our method also exhibits robust cross-domain transferability, delivering consistent token reduction performance in code generation and knowledge-based QA tasks. Code is available at: https://github.com/Aries-iai/Manifold_Steering.

cs.LG↗

arXiv2025

DeceptionBench: A Comprehensive Benchmark for AI Deception Behaviors in Real-world Scenarios

Despite the remarkable advances of Large Language Models (LLMs) across diverse cognitive tasks, the rapid enhancement of these capabilities also introduces emergent deceptive behaviors that may induce severe risks in high-stakes deployments. More critically, the characterization of deception across realistic real-world scenarios remains underexplored. To bridge this gap, we establish DeceptionBench, the first benchmark that systematically evaluates how deceptive tendencies manifest across different societal domains, what their intrinsic behavioral patterns are, and how extrinsic factors affect them. Specifically, on the static count, the benchmark encompasses 150 meticulously designed scenarios in five domains, i.e., Economy, Healthcare, Education, Social Interaction, and Entertainment, with over 1,000 samples, providing sufficient empirical foundations for deception analysis. On the intrinsic dimension, we explore whether models exhibit self-interested egoistic tendencies or sycophantic behaviors that prioritize user appeasement. On the extrinsic dimension, we investigate how contextual factors modulate deceptive outputs under neutral conditions, reward-based incentivization, and coercive pressures. Moreover, we incorporate sustained multi-turn interaction loops to construct a more realistic simulation of real-world feedback dynamics. Extensive experiments across LLMs and Large Reasoning Models (LRMs) reveal critical vulnerabilities, particularly amplified deception under reinforcement dynamics, demonstrating that current models lack robust resistance to manipulative contextual cues and the urgent need for advanced safeguards against various deception behaviors. Code and resources are publicly available at https://github.com/Aries-iai/DeceptionBench.

cs.CL↗

arXiv2025

PET2Rep: Towards Vision-Language Model-Drived Automated Radiology Report Generation for Positron Emission Tomography

Positron emission tomography (PET) is a cornerstone of modern oncologic and neurologic imaging, distinguished by its unique ability to illuminate dynamic metabolic processes that transcend the anatomical focus of traditional imaging technologies. Radiology reports are essential for clinical decision making, yet their manual creation is labor-intensive and time-consuming. Recent advancements of vision-language models (VLMs) have shown strong potential in medical applications, presenting a promising avenue for automating report generation. However, existing applications of VLMs in the medical domain have predominantly focused on structural imaging modalities, while the unique characteristics of molecular PET imaging have largely been overlooked. To bridge the gap, we introduce PET2Rep, a large-scale comprehensive benchmark for evaluation of general and medical VLMs for radiology report generation for PET images. PET2Rep stands out as the first dedicated dataset for PET report generation with metabolic information, uniquely capturing whole-body image-report pairs that cover dozens of organs to fill the critical gap in existing benchmarks and mirror real-world clinical comprehensiveness. In addition to widely recognized natural language generation metrics, we introduce a series of clinical efficacy metrics to evaluate the quality of radiotracer uptake pattern description in key organs in generated reports. We conduct a head-to-head comparison of 30 cutting-edge general-purpose and medical-specialized VLMs. The results show that the current state-of-the-art VLMs perform poorly on PET report generation task, falling considerably short of fulfilling practical needs. Moreover, we identify several key insufficiency that need to be addressed to advance the development in medical applications.

eess.IV↗

arXiv2025

Evaluating LLM-Contaminated Crowdsourcing Data Without Ground Truth

The recent success of generative AI highlights the crucial role of high-quality human feedback in building trustworthy AI systems. However, the increasing use of large language models (LLMs) by crowdsourcing workers poses a significant challenge: datasets intended to reflect human input may be compromised by LLM-generated responses. Existing LLM detection approaches often rely on high-dimensional training data such as text, making them unsuitable for annotation tasks like multiple-choice labeling. In this work, we investigate the potential of peer prediction -- a mechanism that evaluates the information within workers' responses without using ground truth -- to mitigate LLM-assisted cheating in crowdsourcing with a focus on annotation tasks. Our approach quantifies the correlations between worker answers while conditioning on (a subset of) LLM-generated labels available to the requester. Building on prior research, we propose a training-free scoring mechanism with theoretical guarantees under a crowdsourcing model that accounts for LLM collusion. We establish conditions under which our method is effective and empirically demonstrate its robustness in detecting low-effort cheating on real-world crowdsourcing datasets.

cs.AI↗

arXiv2025

PETWB-REP: A Multi-Cancer Whole-Body FDG PET/CT and Radiology Report Dataset for Medical Imaging Research

Publicly available, large-scale medical imaging datasets are crucial for developing and validating artificial intelligence models and conducting retrospective clinical research. However, datasets that combine functional and anatomical imaging with detailed clinical reports across multiple cancer types remain scarce. Here, we present PETWB-REP, a curated dataset comprising whole-body 18F-Fluorodeoxyglucose (FDG) Positron Emission Tomography/Computed Tomography (PET/CT) scans and corresponding radiology reports from 490 patients diagnosed with various malignancies. The dataset primarily includes common cancers such as lung cancer, liver cancer, breast cancer, prostate cancer, and ovarian cancer. This dataset includes paired PET and CT images, de-identified textual reports, and structured clinical metadata. It is designed to support research in medical imaging, radiomics, artificial intelligence, and multi-modal learning.

cs.CV↗

arXiv2025

Thermoelectricity of moiré heavy fermions in MoTe2/WSe2 bilayers

Tunable Kondo lattice and heavy fermion physics have been recently reported in moiré materials, but most of the studies have focused on the electrical and magnetic properties. Quantitative thermoelectric measurements, which can reveal entropic information of the heavy fermions, have yet to be achieved. Here, we report a comprehensive thermoelectric study on the moiré heavy fermion phase realized in hole-doped angle-aligned MoTe2/WSe2 bilayers. By electrically gating the material to the Kondo lattice region of the phase diagram, we observe a sign change in the Seebeck coefficient near the Kondo coherence temperature, where the heavy fermion phase with an electron-like Fermi surface evolves into an itinerant Fermi liquid with a hole-like Fermi surface. We compare the results with the semiclassical Mott relation and discuss the observed discrepancies. In addition to the thermal dissociation of Kondo singlets in the heavy Fermi liquid, a sign change accompanied by a strong peak in the Seebeck coefficient is also observed near a Zeeman breakdown of the Kondo singlets, signaling an entropy accumulation. Our results provide entropic information on both the formation and breakdown of heavy fermions in moiré semiconductors.

cond-mat.str-el↗

arXiv2025

Your Dense Retriever is Secretly an Expeditious Reasoner

Dense retrievers enhance retrieval by encoding queries and documents into continuous vectors, but they often struggle with reasoning-intensive queries. Although Large Language Models (LLMs) can reformulate queries to capture complex reasoning, applying them universally incurs significant computational cost. In this work, we propose Adaptive Query Reasoning (AdaQR), a hybrid query rewriting framework. Within this framework, a Reasoner Router dynamically directs each query to either fast dense reasoning or deep LLM reasoning. The dense reasoning is achieved by the Dense Reasoner, which performs LLM-style reasoning directly in the embedding space, enabling a controllable trade-off between efficiency and accuracy. Experiments on large-scale retrieval benchmarks BRIGHT show that AdaQR reduces reasoning cost by 28% while preserving-or even improving-retrieval performance by 7%.

cs.IR↗

arXiv2025

Variational Masked Diffusion Models

Masked diffusion models have recently emerged as a flexible framework for discrete generative modeling. However, a key limitation of standard masked diffusion is its inability to effectively capture dependencies among tokens that are predicted concurrently, leading to degraded generation quality when dependencies among tokens are important. To explicitly model dependencies among tokens, we propose Variational Masked Diffusion (VMD), a framework that introduces latent variables into the masked diffusion process. Through controlled experiments on synthetic datasets, we demonstrate that VMD successfully learns dependencies that conventional masked diffusion fails to capture. We further validate the effectiveness of our approach on Sudoku puzzles and text datasets, where learning of dependencies among tokens improves global consistency. Across these domains, VMD enhances both generation quality and dependency awareness, highlighting the value of integrating variational inference into masked diffusion. Our code is available at: https://riccizz.github.io/VMD.

cs.LG↗

arXiv2025

Adaptive Reasoning Executor: A Collaborative Agent System for Efficient Reasoning

Recent advances in Large Language Models (LLMs) demonstrate that chain-of-thought prompting and deep reasoning substantially enhance performance on complex tasks, and multi-agent systems can further improve accuracy by enabling model debates. However, applying deep reasoning to all problems is computationally expensive. To mitigate these costs, we propose a complementary agent system integrating small and large LLMs. The small LLM first generates an initial answer, which is then verified by the large LLM. If correct, the answer is adopted directly; otherwise, the large LLM performs in-depth reasoning. Experimental results show that, for simple problems, our approach reduces the computational cost of the large LLM by more than 50% with negligible accuracy loss, while consistently maintaining robust performance on complex tasks.

cs.AI↗

arXiv2025

Oyster-I: Beyond Refusal -- Constructive Safety Alignment for Responsible Language Models

Large language models (LLMs) typically deploy safety mechanisms to prevent harmful content generation. Most current approaches focus narrowly on risks posed by malicious actors, often framing risks as adversarial events and relying on defensive refusals. However, in real-world settings, risks also come from non-malicious users seeking help while under psychological distress (e.g., self-harm intentions). In such cases, the model's response can strongly influence the user's next actions. Simple refusals may lead them to repeat, escalate, or move to unsafe platforms, creating worse outcomes. We introduce Constructive Safety Alignment (CSA), a human-centric paradigm that protects against malicious misuse while actively guiding vulnerable users toward safe and helpful results. Implemented in Oyster-I (Oy1), CSA combines game-theoretic anticipation of user reactions, fine-grained risk boundary discovery, and interpretable reasoning control, turning safety into a trust-building process. Oy1 achieves state-of-the-art safety among open models while retaining high general capabilities. On our Constructive Benchmark, it shows strong constructive engagement, close to GPT-5, and unmatched robustness on the Strata-Sword jailbreak dataset, nearing GPT-o1 levels. By shifting from refusal-first to guidance-first safety, CSA redefines the model-user relationship, aiming for systems that are not just safe, but meaningfully helpful. We release Oy1, code, and the benchmark to support responsible, user-centered AI.

cs.AI↗

arXiv2025

CAPSim: A Fast CPU Performance Simulator Using Attention-based Predictor

CPU simulators are vital for computer architecture research, primarily for estimating performance under different programs. This poses challenges for fast and accurate simulation of modern CPUs, especially in multi-core systems. Modern CPU peformance simulators such as GEM5 adopt the cycle-accurate and event-driven approach, which is timeconsuming to simulate the extensive microarchitectural behavior of a real benchmark running on out-of-order CPUs. Recently, machine leaning based approach has been proposed to improve simulation speed, but they are currently limited to estimating the cycles of basic blocks rather than the complete benchmark program. This paper introduces a novel ML-based CPU simulator named CAPSim, which uses an attention-based neural network performance predictor and instruction trace sampling method annotated with context. The attention mechanism effectively captures long-range influence within the instruction trace, emphasizing critical context information. This allows the model to improve performance prediction accuracy by focusing on important code instruction. CAPSim can predict the execution time of unseen benchmarks at a significantly fast speed compared with an accurate O3 simulator built with gem5. Our evaluation on a commercial Intel Xeon CPU demonstrates that CAPSim achieves a 2.2 - 8.3x speedup compared to using gem5 built simulator, which is superior to the cutting-edge deep learning approach

cs.PF↗

arXiv2025

Exploring the Generalizability of Factual Hallucination Mitigation via Enhancing Precise Knowledge Utilization

Large Language Models (LLMs) often struggle to align their responses with objective facts, resulting in the issue of factual hallucinations, which can be difficult to detect and mislead users without relevant knowledge. Although post-training techniques have been employed to mitigate the issue, existing methods usually suffer from poor generalization and trade-offs in other different capabilities. In this paper, we propose to address these by directly augmenting LLM's fundamental ability to precisely leverage its knowledge and introduce PKUE (Precise Knowledge Utilization Enhancement), which fine-tunes the model on self-generated responses to precise and simple factual questions through preference optimization. Furthermore, we construct FactualBench, a comprehensive and precise factual QA dataset containing 181k Chinese data spanning 21 domains, to facilitate both evaluation and training. Extensive experiments demonstrate that PKUE significantly improves LLM overall performance, with consistent enhancement across factual tasks of various forms, general tasks beyond factuality, and tasks in different language.

cs.CL↗

arXiv2025

Brain Harmony: A Multimodal Foundation Model Unifying Morphology and Function into 1D Tokens

We present Brain Harmony (BrainHarmonix), the first multimodal brain foundation model that unifies structural morphology and functional dynamics into compact 1D token representations. The model was pretrained on two of the largest neuroimaging datasets to date, encompassing 64,594 T1-weighted structural MRI 3D volumes (~ 14 million images) and 70,933 functional MRI (fMRI) time series. BrainHarmonix is grounded in two foundational neuroscience principles: structure complements function - structural and functional modalities offer distinct yet synergistic insights into brain organization; function follows structure - brain functional dynamics are shaped by cortical morphology. The modular pretraining process involves single-modality training with geometric pre-alignment followed by modality fusion through shared brain hub tokens. Notably, our dynamics encoder uniquely handles fMRI time series with heterogeneous repetition times (TRs), addressing a major limitation in existing models. BrainHarmonix is also the first to deeply compress high-dimensional neuroimaging signals into unified, continuous 1D tokens, forming a compact latent space of the human brain. BrainHarmonix achieves strong generalization across diverse downstream tasks, including neurodevelopmental and neurodegenerative disorder classification and cognition prediction - consistently outperforming previous approaches. Our models - pretrained on 8 H100 GPUs - aim to catalyze a new era of AI-driven neuroscience powered by large-scale multimodal neuroimaging.

q-bio.NC↗

arXiv2025

A System-Level Analysis of Conference Peer Review

The conference peer review process involves three constituencies with different objectives: authors want their papers accepted at prestigious venues (and quickly), conferences want to present a program with many high-quality and few low-quality papers, and reviewers want to avoid being overburdened by reviews. These objectives are far from aligned, primarily because the evaluation of a submission is inherently noisy. Over the years, conferences have experimented with numerous policies to navigate the tradeoffs. These experiments include setting various bars for acceptance, varying the number of reviews per submission, requiring prior reviews to be included with resubmissions, and others. In this work, we investigate, both analytically and empirically, how well various policies work, and more importantly, why they do or do not work. We model the conference-author interactions as a Stackelberg game in which a prestigious conference commits to an acceptance policy; the authors best-respond by (re)submitting or not (re)submitting to the conference in each round of review, the alternative being a "sure accept" (such as a lightly refereed venue). Our main results include the following observations: 1) the conference should typically set a higher acceptance threshold than the actual desired quality; we call this the "resubmission gap". 2) the reviewing load is heavily driven by resubmissions of borderline papers - therefore, a judicious choice of acceptance threshold may lead to fewer reviews while incurring an acceptable loss in conference quality. 3) conference prestige, reviewer inaccuracy, and author patience increase the resubmission gap, and thus increase the review load for a fixed level of conference quality. For robustness, we further consider different models of paper quality and compare our theoretical results to simulations based on plausible parameters estimated from real data.

cs.GT↗

arXiv2025

Beyond Quantity: Distribution-Aware Labeling for Visual Grounding

Visual grounding requires large and diverse region-text pairs. However, manual annotation is costly and fixed vocabularies restrict scalability and generalization. Existing pseudo-labeling pipelines often overfit to biased distributions and generate noisy or redundant samples. Through our systematic analysis of data quality and distributional coverage, we find that performance gains come less from raw data volume and more from effective distribution expansion. Motivated by this insight, we propose DAL, a distribution-aware labeling framework for visual grounding. The proposed method first employs a dual-driven annotation module, where a closed-set path provides reliable pseudo labels and an open-set path enriches vocabulary and introduces novel concepts; meanwhile, it further performs explicit out-of-distribution (OOD) expression expansion to broaden semantic coverage. We then propose a consistency- and distribution-aware filtering module to discard noisy or redundant region-text pairs and rebalance underrepresented linguistic and visual content, thereby improving both data quality and training efficiency. Extensive experiments on three benchmarks demonstrate that our method consistently outperforms strong baselines and achieves state-of-the-art results, underscoring the critical role of distribution-aware labeling in building scalable and robust visual grounding datasets.

cs.CV↗