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Kai Yi

Publications and source records attributed to Kai Yi.

At least 19 recordsLinked to original sources

From a Long-standing Prediction to a New Family of Hadrons

Fully charmed tetraquarks have evolved from a long-standing theoretical prediction into one of the most active frontiers in hadron spectroscopy. This article reviews their development from early theoretical studies and experimental searches to the recent breakthroughs at the Large Hadron Collider, with particular emphasis on the contributions of the Nanjing Normal University (NNU) and Tsinghua University (THU) teams at the CMS experiment. We summarize the discovery of the fully charmed tetraquark family, the establishment of interference among resonances, and the first determination of their quantum numbers. These advances have transformed the search for a single exotic resonance into the study of a new family of hadrons and opened a promising avenue for exploring the nonperturbative dynamics of Quantum Chromodynamics.

hep-ex

DBMol: Design of High-Affinity, Target-Specific Small Molecules through Structure Prediction Models

Designing small molecule ligands that bind with high affinity to specific protein pockets is a fundamental goal in drug discovery, as small molecules constitute a major fraction of approved therapeutics. Recent breakthroughs in structure prediction, such as AlphaFold-3 and Boltz-2, enable accurate biomolecular interaction prediction and show promise as foundation models for downstream tasks, including binding affinity prediction. We propose to leverage these models and introduce DBMol, a new structure predictor-guided framework for de novo small molecule design. DBMol formulates an alternating optimization and projection process. In the optimization stage, DBMol starts from an initial molecule and uses gradient-based optimization to improve pocket-specific interactions and predicted binding affinity using a structure prediction model. In the projection stage, a flow-matching model maps the optimized molecular graph to discrete and chemically valid molecules. Experiments show that DBMol effectively optimizes the Boltz-2 affinity proxy and generates molecules with strong predicted affinity and specificity under Boltz-2 evaluation. To reduce self-confirmation bias, we further evaluate generated molecules using held-out metrics, including AF3-based evaluation. DBMol substantially improves pocket coverage while maintaining molecular diversity over unconditional generation, and is competitive under held-out metrics despite the absence of reference-ligand supervision. These results support the promise of structure prediction models as effective optimization signals for de novo molecular design.

cs.LG

A Characterization of the $2m-4$ Case of Highly Sorted Permutations

Let $s$ denote West's stack-sorting map. In 2020, Defant characterized and enumerated the set $s^{n-m}(S_n)$ for $n \geq 2m-3$. While $|s^{n-m}(S_n)| = B_m$ when $n \geq 2m-2$, where $B_m$ denotes the $m$th Bell number, there are additional permutations when $n = 2m-3$. In this paper, we explore the more complex $n = 2m-4$ case, with several forms of additional permutations. We characterize $s^{m-4}(S_{2m-4})$ and find that its size is \[B_m + \frac{m^2 + 7m - 28}{2}\] for $m \geq 5$. This answers Defant's question about the $2m-4$ case. Furthermore, we find some differences in the behavior of the $2m-5$ case compared to the $2m-3$ and $2m-4$ cases.

math.CO

JacQuant: STE-Free Quantization-Aware Training via Learned Jacobian Surrogates

Quantization-aware training (QAT) is widely deployed but typically relies on the Straight-Through Estimator (STE), which passes gradients through non-differentiable quantizers by fiat. This often makes training brittle near bin boundaries and weakly aligned with the actual behavior of the low-precision model. We introduce JacQuant, a QAT framework that learns a lightweight surrogate of the model's local sensitivity to parameter changes and uses it to stabilize and accelerate training within standard variance-reduced optimizers. The surrogate is inexpensive (diagonal or block-diagonal), data-driven, and compatible with common weight and activation quantizers. On code-preserving training phases, we prove convergence for non-convex objectives and obtain linear rates under a PL condition, and we relate the learned sensitivity to end-to-end output fidelity via a simple calibration argument. Across LLM benchmarks at $\leq 2$ bits, JacQuant consistently reaches higher accuracy than STE-based QAT, and the runtime analyses on various models show that the added cost remains negligible under practical group sizes. The method is drop-in and requires no changes to the forward quantizers; our empirical claims are scoped to ultra-low-bit LLM QAT.

cs.LG

WinQ: Accelerating Quantization-Aware Training of Language Models Around Saddle Points

Quantization-aware training (QAT) is widely adopted to quantize language models by training full-precision weights using gradients from the quantized model. The main bottleneck is its slow convergence and early performance plateau, particularly below 4-bit-widths. While this problem has been observed in prior work, its precise cause remains unclear. In this paper, we analyze the convergence of QAT by estimating the spectrum of the loss-surface Hessians. We find that the weights converge to flat regions around saddle points, where a large fraction of the Hessian eigenvalues are both positive and negative. During training, an increasing fraction of Hessian eigenvalues concentrates around zero, whose magnitude decreases. At lower bit-widths, the magnitude of eigenvalues in the Hessian spectrum is significantly smaller. To mitigate these issues, we propose an algorithm called WinQ to accelerate QAT, which involves: (1) periodically resetting weights to the linear interpolation of full-precision and quantized weights, reducing the distance to the quantization grid and increasing eigenvalue magnitude, and (2) computing gradients of noise-injected weights to regularize the Hessian. Extensive experiments show that WinQ accelerates QAT by up to 4 times across various quantization methods and models. Under the same training cost, WinQ improves state-of-the-art sub-4-bit quantization by up to 8.8%. These results are consistent across 16 settings with different language models, quantization methods, and bit widths.

cs.LG

Computational Approach to the $SC_{231}$ Consecutive-Pattern-Avoiding Stack Sort

Defant and Zheng introduced a consecutive-pattern-avoiding stack sort map $SC_{\sigma}$, where the stack must avoid a consecutive pattern $\sigma$. Seidel and Sun disproved a conjecture in Defant and Zheng's paper about the maximum sort-number of a length $n$ permutation under $SC_{231}$. In this paper, we compute sort-numbers for each permutation of length up to $14$, and we estimate the average sort-numbers up to length $1000$. Our results suggest the maximum and average sort-numbers grow faster than linear with respect to $n$ for the tested ranges, though the long-term behavior remains unclear. We also prove properties of $SC_{231}$ mathematically, such as a $n-1$ lower bound and a $\frac{(n+1)(n-2)}{2}$ upper bound for the maximum sort-number of length $n$ permutations.

math.CO

CARE: A Molecular-Guided Foundation Model with Adaptive Region Modeling for Whole Slide Image Analysis

Foundation models have recently achieved impressive success in computational pathology, demonstrating strong generalization across diverse histopathology tasks. However, existing models overlook the heterogeneous and non-uniform organization of pathological regions of interest (ROIs) because they rely on natural image backbones not tailored for tissue morphology. Consequently, they often fail to capture the coherent tissue architecture beyond isolated patches, limiting interpretability and clinical relevance. To address these challenges, we present Cross-modal Adaptive Region Encoder (CARE), a foundation model for pathology that automatically partitions WSIs into several morphologically relevant regions. Specifically, CARE employs a two-stage pretraining strategy: (1) a self-supervised unimodal pretraining stage that learns morphological representations from 34,277 whole-slide images (WSIs) without segmentation annotations, and (2) a cross-modal alignment stage that leverages RNA and protein profiles to refine the construction and representation of adaptive regions. This molecular guidance enables CARE to identify biologically relevant patterns and generate irregular yet coherent tissue regions, selecting the most representative area as ROI. CARE supports a broad range of pathology-related tasks, using either the ROI feature or the slide-level feature obtained by aggregating adaptive regions. Based on only one-tenth of the pretraining data typically used by mainstream foundation models, CARE achieves superior average performance across 33 downstream benchmarks, including morphological classification, molecular prediction, and survival analysis, and outperforms other foundation model baselines overall.

cs.CV

Experimental road of the $J/\psi\phi$ mass spectrum, current status, and implications

Inspired by the $X(4140)$ structure reported in the $J/\psi \phi$ system by the CDF experiment in 2009, a series of searches have been carried out in the $J/\psi \phi$ and $J/\psi K$ channels, leading to the claim of ten structures in the $B \rightarrow J/\psi \phi K$ system. This article provides a comprehensive review of experimental developments, from the initial evidence of $X(4140)$ at CDF to the amplitude analyses and diffractive process investigations by the LHCb experiment, as well as theoretical interpretations of these states. A triplet of $J^{PC} = 1^{++}$ states with relatively large mass splittings [about 200~MeV (natural units are adopted)] has been identified in the $J/\psi \phi$ system by LHCb. Their mass-squared values align approximately linearly with a possible radial quantum number, suggesting that the triplet may represent a radially excited family. For $X(4140)$, the first state in the triplet, its width reported by LHCb is inconsistent with that measured by other experiments, and possible reasons for this discrepancy are discussed. A potential connection between an excess at 4.35~GeV in the $J/\psi \phi$ mass spectrum reported by the Belle experiment through a two-photon process and a potential spin-2 excess in the LHCb data is also investigated. In addition, potential parallels between the $J/\psi \phi$ and $J/\psi J/\psi$ systems, both composed of two vector mesons, are discussed. The continued interest in, and complexity of, these systems underscore the necessity of further experimental exploration with increased statistical precision across a variety of experiments, particularly those with relatively flat efficiency across the Dalitz plot. The $J/\psi \omega$, $\phi \phi$, $\rho \omega$, and $\rho \phi$ systems are mentioned, and the prospects for the $J/\psi \Upsilon$ and $\Upsilon \Upsilon$ systems, are also highlighted.

hep-ex

Strategies for Improving Communication Efficiency in Distributed and Federated Learning: Compression, Local Training, and Personalization

Distributed and federated learning are essential paradigms for training models across decentralized data sources while preserving privacy, yet communication overhead remains a major bottleneck. This dissertation explores strategies to improve communication efficiency, focusing on model compression, local training, and personalization. We establish a unified framework for biased and unbiased compression operators with convergence guarantees, then propose adaptive local training strategies that incorporate personalization to accelerate convergence and mitigate client drift. In particular, Scafflix balances global and personalized objectives, achieving superior performance under both IID and non-IID settings. We further introduce privacy-preserving pruning frameworks that optimize sparsity while minimizing communication costs, with Cohort-Squeeze leveraging hierarchical aggregation to reduce cross-device overhead. Finally, SymWanda, a symmetric post-training pruning method, enhances robustness under high sparsity and maintains accuracy without retraining. Extensive experiments on benchmarks and large-scale language models demonstrate favorable trade-offs among accuracy, convergence, and communication, offering theoretical and practical insights for scalable, efficient distributed learning.

cs.LG

A Lightweight Convolution and Vision Transformer integrated model with Multi-scale Self-attention Mechanism

Vision Transformer (ViT) has prevailed in computer vision tasks due to its strong long-range dependency modelling ability. \textcolor{blue}{However, its large model size and weak local feature modeling ability hinder its application in real scenarios. To balance computation efficiency and performance in downstream vision tasks, we propose an efficient ViT model with sparse attention (dubbed SAEViT) and convolution blocks. Specifically, a Sparsely Aggregated Attention (SAA) module has been proposed to perform adaptive sparse sampling and recover the feature map via deconvolution operation,} which significantly reduces the computational complexity of attention operations. In addition, a Channel-Interactive Feed-Forward Network (CIFFN) layer is developed to enhance inter-channel information exchange through feature decomposition and redistribution, which mitigates the redundancy in traditional feed-forward networks (FFN). Finally, a hierarchical pyramid structure with embedded depth-wise separable convolutional blocks (DWSConv) is devised to further strengthen convolutional features. Extensive experiments on mainstream datasets show that SAEViT achieves Top-1 accuracies of 76.3\% and 79.6\% on the ImageNet-1K classification task with only 0.8 GFLOPs and 1.3 GFLOPs, respectively, demonstrating a lightweight solution for fundamental vision tasks.

cs.CV

All-atom inverse protein folding through discrete flow matching

The recent breakthrough of AlphaFold3 in modeling complex biomolecular interactions, including those between proteins and ligands, nucleotides, or metal ions, creates new opportunities for protein design. In so-called inverse protein folding, the objective is to find a sequence of amino acids that adopts a target protein structure. Many inverse folding methods struggle to predict sequences for complexes that contain non-protein components, and perform poorly with complexes that adopt multiple structural states. To address these challenges, we present ADFLIP (All-atom Discrete FLow matching Inverse Protein folding), a generative model based on discrete flow-matching for designing protein sequences conditioned on all-atom structural contexts. ADFLIP progressively incorporates predicted amino acid side chains as structural context during sequence generation and enables the design of dynamic protein complexes through ensemble sampling across multiple structural states. Furthermore, ADFLIP implements training-free classifier guidance sampling, which allows the incorporation of arbitrary pre-trained models to optimise the designed sequence for desired protein properties. We evaluated the performance of ADFLIP on protein complexes with small-molecule ligands, nucleotides, or metal ions, including dynamic complexes for which structure ensembles were determined by nuclear magnetic resonance (NMR). Our model achieves state-of-the-art performance in single-structure and multi-structure inverse folding tasks, demonstrating excellent potential for all-atom protein design. The code is available at https://github.com/ykiiiiii/ADFLIP.

q-bio.BM

How Particle System Theory Enhances Hypergraph Message Passing

Hypergraphs effectively model higher-order relationships in natural phenomena, capturing complex interactions beyond pairwise connections. We introduce a novel hypergraph message passing framework inspired by interacting particle systems, where hyperedges act as fields inducing shared node dynamics. By incorporating attraction, repulsion, and Allen-Cahn forcing terms, particles of varying classes and features achieve class-dependent equilibrium, enabling separability through the particle-driven message passing. We investigate both first-order and second-order particle system equations for modeling these dynamics, which mitigate over-smoothing and heterophily thus can capture complete interactions. The more stable second-order system permits deeper message passing. Furthermore, we enhance deterministic message passing with stochastic element to account for interaction uncertainties. We prove theoretically that our approach mitigates over-smoothing by maintaining a positive lower bound on the hypergraph Dirichlet energy during propagation and thus to enable hypergraph message passing to go deep. Empirically, our models demonstrate competitive performance on diverse real-world hypergraph node classification tasks, excelling on both homophilic and heterophilic datasets.

cs.LG

Sparse-ProxSkip: Accelerated Sparse-to-Sparse Training in Federated Learning

In Federated Learning (FL), both client resource constraints and communication costs pose major problems for training large models. In the centralized setting, sparse training addresses resource constraints, while in the distributed setting, local training addresses communication costs. Recent work has shown that local training provably improves communication complexity through acceleration. In this work we show that in FL, naive integration of sparse training and acceleration fails, and we provide theoretical and empirical explanations of this phenomenon. We introduce Sparse-ProxSkip, addressing the issue and implementing the efficient technique of Straight-Through Estimator pruning into sparse training. We demonstrate the performance of Sparse-ProxSkip in extensive experiments.

cs.LG

Symmetric Pruning of Large Language Models

Popular post-training pruning methods such as Wanda and RIA are known for their simple, yet effective, designs that have shown exceptional empirical performance. Wanda optimizes performance through calibrated activations during pruning, while RIA emphasizes the relative, rather than absolute, importance of weight elements. Despite their practical success, a thorough theoretical foundation explaining these outcomes has been lacking. This paper introduces new theoretical insights that redefine the standard minimization objective for pruning, offering a deeper understanding of the factors contributing to their success. Our study extends beyond these insights by proposing complementary strategies that consider both input activations and weight significance. We validate these approaches through rigorous experiments, demonstrating substantial enhancements over existing methods. Furthermore, we introduce a novel training-free fine-tuning approach $R^2$-DSnoT that incorporates relative weight importance and a regularized decision boundary within a dynamic pruning-and-growing framework, significantly outperforming strong baselines and establishing a new state of the art.

cs.LG

Estimating Large Global Significances with a New Monte Carlo Extrapolation Method

In particle physics, it is needed to evaluate the possibility that excesses of events in mass spectra are due to statistical fluctuations as quantified by the standards of local and global significances. Without prior knowledge of a particle's mass, it is especially critical to estimate its global significance. The usual approach is to count the number of times a significance limit is exceeded in a collection of simulated Monte Carlo (MC) 'toy experiments.' To demonstrate this conventional method for global significance, we performed simulation studies according to a recent Compact Muon Solenoid (CMS) result to show its effectiveness. However, this counting method is not practical for computing large global significances. To address this problem, we developed a new 'extrapolation' method to evaluate the global significance. We compared the global significance estimated by our new method with that of the conventional approach, and verified its feasibility and effectiveness. This method is also applicable for cases where only small toy MC samples are available. In this approach, the significance is calculated based on p-values, assuming symmetrical Gaussian distributions.

hep-ex

Score-matching-based Structure Learning for Temporal Data on Networks

Causal discovery is a crucial initial step in establishing causality from empirical data and background knowledge. Numerous algorithms have been developed for this purpose. Among them, the score-matching method has demonstrated superior performance across various evaluation metrics, particularly for the commonly encountered Additive Nonlinear Causal Models. However, current score-matching-based algorithms are primarily designed to analyze independent and identically distributed (i.i.d.) data. More importantly, they suffer from high computational complexity due to the pruning step required for handling dense Directed Acyclic Graphs (DAGs). To enhance the scalability of score matching, we have developed a new parent-finding subroutine for leaf nodes in DAGs, significantly accelerating the most time-consuming part of the process: the pruning step. This improvement results in an efficiency-lifted score matching algorithm, termed Parent Identification-based Causal structure learning for both i.i.d. and temporal data on networKs, or PICK. The new score-matching algorithm extends the scope of existing algorithms and can handle static and temporal data on networks with weak network interference. Our proposed algorithm can efficiently cope with increasingly complex datasets that exhibit spatial and temporal dependencies, commonly encountered in academia and industry. The proposed algorithm can accelerate score-matching-based methods while maintaining high accuracy in real-world applications.

stat.ML

MANTA: A Large-Scale Multi-View and Visual-Text Anomaly Detection Dataset for Tiny Objects

We present MANTA, a visual-text anomaly detection dataset for tiny objects. The visual component comprises over 137.3K images across 38 object categories spanning five typical domains, of which 8.6K images are labeled as anomalous with pixel-level annotations. Each image is captured from five distinct viewpoints to ensure comprehensive object coverage. The text component consists of two subsets: Declarative Knowledge, including 875 words that describe common anomalies across various domains and specific categories, with detailed explanations for < what, why, how>, including causes and visual characteristics; and Constructivist Learning, providing 2K multiple-choice questions with varying levels of difficulty, each paired with images and corresponded answer explanations. We also propose a baseline for visual-text tasks and conduct extensive benchmarking experiments to evaluate advanced methods across different settings, highlighting the challenges and efficacy of our dataset.

cs.CV

A Regressor-Guided Graph Diffusion Model for Predicting Enzyme Mutations to Enhance Turnover Number

Enzymes are biological catalysts that can accelerate chemical reactions compared to uncatalyzed reactions in aqueous environments. Their catalytic efficiency is quantified by the turnover number (kcat), a parameter in enzyme kinetics. Enhancing enzyme activity is important for optimizing slow chemical reactions, with far-reaching implications for both research and industrial applications. However, traditional wet-lab methods for measuring and optimizing enzyme activity are often resource-intensive and time-consuming. To address these limitations, we introduce kcatDiffuser, a novel regressor-guided diffusion model designed to predict and improve enzyme turnover numbers. Our approach innovatively reformulates enzyme mutation prediction as a protein inverse folding task, thereby establishing a direct link between structural prediction and functional optimization. kcatDiffuser is a graph diffusion model guided by a regressor, enabling the prediction of amino acid mutations at multiple random positions simultaneously. Evaluations on BERENDA dataset shows that kcatDiffuser can achieve a Δ log kcat of 0.209, outperforming state-of-the-art methods like ProteinMPNN, PiFold, GraDe-IF in improving enzyme turnover numbers. Additionally, kcatDiffuser maintains high structural fidelity with a recovery rate of 0.716, pLDDT score of 92.515, RMSD of 3.764, and TM-score of 0.934, demonstrating its ability to generate enzyme variants with enhanced activity while preserving essential structural properties. Overall, kcatDiffuser represents a more efficient and targeted approach to enhancing enzyme activity. The code is available at https://github.com/xz32yu/KcatDiffuser.

q-bio.QM