Searcharxiv⌕ Search

arXiv subjects

Yong Huang

Publications and source records attributed to Yong Huang.

At least 55 records · Page 3Linked to original sources
arXiv2025

Molecule Generation for Target Protein Binding with Hierarchical Consistency Diffusion Model

Effective generation of molecular structures, or new chemical entities, that bind to target proteins is crucial for lead identification and optimization in drug discovery. Despite advancements in atom- and motif-wise deep learning models for 3D molecular generation, current methods often struggle with validity and reliability. To address these issues, we develop the Atom-Motif Consistency Diffusion Model (AMDiff), utilizing a joint-training paradigm for multi-view learning. This model features a hierarchical diffusion architecture that integrates both atom- and motif-level views of molecules, allowing for comprehensive exploration of complementary information. By leveraging classifier-free guidance and incorporating binding site features as conditional inputs, AMDiff ensures robust molecule generation across diverse targets. Compared to existing approaches, AMDiff exhibits superior validity and novelty in generating molecules tailored to fit various protein pockets. Case studies targeting protein kinases, including Anaplastic Lymphoma Kinase (ALK) and Cyclin-dependent kinase 4 (CDK4), demonstrate the model's capability in structure-based de novo drug design. Overall, AMDiff bridges the gap between atom-view and motif-view drug discovery and speeds up the process of target-aware molecular generation.

cs.LG↗
arXiv2025

Minkowski Problems for Geometric Measures

This paper describes the theory of Minkowski problems for geometric measures in convex geometric analysis. The theory goes back to Minkowski and Aleksandrov and has been developed extensively in recent years. The paper surveys classical and new Minkowski problems studied in convex geometry, PDEs, and harmonic analysis, and structured in a conceptual framework of the Brunn-Minkowski theory, its extensions, and related subjects.

math.MG↗
arXiv2025

Geometric measures in the dual Brunn-Minkowski theory and their associated Minkowski problems

A longstanding question in the dual Brunn-Minkowski theory is what are the dual analogues of Federer's curvature measures for convex bodies. The answer to this is provided. This leads naturally to dual versions of Minkowski-type problems, which answer the question of what are necessary and sufficient conditions for a Borel measure to be a dual curvature measure of a convex body. Sufficient conditions, involving measure concentration, are established for the existence of solutions to these problems.

math.MG↗
arXiv2024

MoR: Mixture of Ranks for Low-Rank Adaptation Tuning

Low-Rank Adaptation (LoRA) drives research to align its performance with full fine-tuning. However, significant challenges remain: (1) Simply increasing the rank size of LoRA does not effectively capture high-rank information, which leads to a performance bottleneck.(2) MoE-style LoRA methods substantially increase parameters and inference latency, contradicting the goals of efficient fine-tuning and ease of application. To address these challenges, we introduce Mixture of Ranks (MoR), which learns rank-specific information for different tasks based on input and efficiently integrates multi-rank information. We firstly propose a new framework that equates the integration of multiple LoRAs to expanding the rank of LoRA. Moreover, we hypothesize that low-rank LoRA already captures sufficient intrinsic information, and MoR can derive high-rank information through mathematical transformations of the low-rank components. Thus, MoR can reduces the learning difficulty of LoRA and enhances its multi-task capabilities. MoR achieves impressive results, with MoR delivering a 1.31\% performance improvement while using only 93.93\% of the parameters compared to baseline methods.

cs.LG↗
arXiv2024

MolNexTR: A Generalized Deep Learning Model for Molecular Image Recognition

In the field of chemical structure recognition, the task of converting molecular images into machine-readable data formats such as SMILES string stands as a significant challenge, primarily due to the varied drawing styles and conventions prevalent in chemical literature. To bridge this gap, we proposed MolNexTR, a novel image-to-graph deep learning model that collaborates to fuse the strengths of ConvNext, a powerful Convolutional Neural Network variant, and Vision-TRansformer. This integration facilitates a more detailed extraction of both local and global features from molecular images. MolNexTR can predict atoms and bonds simultaneously and understand their layout rules. It also excels at flexibly integrating symbolic chemistry principles to discern chirality and decipher abbreviated structures. We further incorporate a series of advanced algorithms, including an improved data augmentation module, an image contamination module, and a post-processing module for getting the final SMILES output. These modules cooperate to enhance the model's robustness to diverse styles of molecular images found in real literature. In our test sets, MolNexTR has demonstrated superior performance, achieving an accuracy rate of 81-97%, marking a significant advancement in the domain of molecular structure recognition.

cs.CV↗
arXiv2024

Eavesdropping Mobile Apps and Actions through Wireless Traffic in the Open World

While smartphones and WiFi networks are bringing many positive changes to people's lives, they are susceptible to traffic analysis attacks, which infer user's private information from encrypted traffic. Existing traffic analysis attacks mainly target TCP/IP layers or are limited to the closed-world assumption, where all possible apps and actions have been involved in the model training. To overcome these limitations, we propose MACPrint, a novel system that infers mobile apps and in-app actions based on WiFi MAC layer traffic in the open-world setting. MACPrint first extracts rich statistical and contextual features of encrypted wireless traffic. Then, we develop Label Recorder, an automatic traffic labeling app, to improve labeling accuracy in the training phase. Finally, TCN models with OpenMax functions are used to recognize mobile apps and actions in the open world accurately. To evaluate our system, we collect MAC layer traffic data over 125 hours from more than 40 apps. The experimental results show that MAC-Print can achieve an accuracy of over 96% for recognizing apps and actions in the closed-world setting, and obtains an accuracy of over 86% in the open-world setting.

cs.CR↗
arXiv2024

Improving WiFi CSI Fingerprinting with IQ Samples

Identity authentication is crucial for ensuring the information security of wireless communication. Radio frequency (RF) fingerprinting techniques provide a prom-ising supplement to cryptography-based authentication approaches but rely on dedicated equipment to capture in-phase and quadrature (IQ) samples, hindering their wide adoption. Recent advances advocate easily obtainable channel state in-formation (CSI) by commercial WiFi devices for lightweight RF fingerprinting, but they mainly focus on eliminating channel interference and cannot address the challenges of coarse granularity and information loss of CSI measurements. To overcome these challenges, we propose CSI2Q, a novel CSI fingerprinting sys-tem that achieves comparable performance to IQ-based approaches. Instead of ex-tracting fingerprints directly from raw CSI measurements, CSI2Q first transforms them into time-domain signals that share the same feature space with IQ samples. Then, the distinct advantages of an IQ fingerprinting model in feature extraction are transferred to its CSI counterpart via an auxiliary training strategy. Finally, the trained CSI fingerprinting model is used to decide which device the sample under test comes from. We evaluate CSI2Q on both synthetic and real CSI datasets. On the synthetic dataset, our system can improve the recognition accuracy from 76% to 91%. On the real dataset, CSI2Q boosts the accuracy from 67% to 82%.

cs.CR↗
arXiv2024

ChunkAttention: Efficient Self-Attention with Prefix-Aware KV Cache and Two-Phase Partition

Self-attention is an essential component of large language models (LLM) but a significant source of inference latency for long sequences. In multi-tenant LLM serving scenarios, the compute and memory operation cost of self-attention can be optimized by using the probability that multiple LLM requests have shared system prompts in prefixes. In this paper, we introduce ChunkAttention, a prefix-aware self-attention module that can detect matching prompt prefixes across multiple requests and share their key/value tensors in memory at runtime to improve the memory utilization of KV cache. This is achieved by breaking monolithic key/value tensors into smaller chunks and structuring them into the auxiliary prefix tree. Consequently, on top of the prefix-tree based KV cache, we design an efficient self-attention kernel, where a two-phase partition algorithm is implemented to improve the data locality during self-attention computation in the presence of shared system prompts. Experiments show that ChunkAttention can speed up the self-attention kernel by 3.2-4.8$\times$ compared to the state-of-the-art implementation, with the length of the system prompt ranging from 1024 to 4096.

cs.LG↗
arXiv2024

Low-Resource Multi-Granularity Academic Function Recognition Based on Multiple Prompt Knowledge

Fine-tuning pre-trained language models (PLMs), e.g., SciBERT, generally requires large numbers of annotated data to achieve state-of-the-art performance on a range of NLP tasks in the scientific domain. However, obtaining the fine-tune data for scientific NLP task is still challenging and expensive. Inspired by recent advancement in prompt learning, in this paper, we propose the Mix Prompt Tuning (MPT), which is a semi-supervised method to alleviate the dependence on annotated data and improve the performance of multi-granularity academic function recognition tasks with a small number of labeled examples. Specifically, the proposed method provides multi-perspective representations by combining manual prompt templates with automatically learned continuous prompt templates to help the given academic function recognition task take full advantage of knowledge in PLMs. Based on these prompt templates and the fine-tuned PLM, a large number of pseudo labels are assigned to the unlabeled examples. Finally, we fine-tune the PLM using the pseudo training set. We evaluate our method on three academic function recognition tasks of different granularity including the citation function, the abstract sentence function, and the keyword function, with datasets from computer science domain and biomedical domain. Extensive experiments demonstrate the effectiveness of our method and statistically significant improvements against strong baselines. In particular, it achieves an average increase of 5% in Macro-F1 score compared with fine-tuning, and 6% in Macro-F1 score compared with other semi-supervised method under low-resource settings. In addition, MPT is a general method that can be easily applied to other low-resource scientific classification tasks.

cs.CL↗
arXiv2024

Let's Learn Step by Step: Enhancing In-Context Learning Ability with Curriculum Learning

Demonstration ordering, which is an important strategy for in-context learning (ICL), can significantly affects the performance of large language models (LLMs). However, most of the current approaches of ordering require high computational costs to introduce the priori knowledge. In this paper, inspired by the human learning process, we propose a simple but effective demonstration ordering method for ICL, named the few-shot In-Context Curriculum Learning (ICCL). The ICCL implies gradually increasing the complexity of prompt demonstrations during the inference process. The difficulty can be assessed by human experts or LLMs-driven metrics, such as perplexity. Then we design extensive experiments to discuss the effectiveness of the ICCL at both corpus-level and instance-level. Moreover, we also investigate the formation mechanism of LLM's ICCL capability. Experimental results demonstrate that ICCL, developed during the instruction-tuning stage, is effective for representative open-source LLMs. To facilitate further research and applications by other scholars, we make the code publicly available.

cs.CL↗
arXiv2024

On Laplacian eigenvalue equation with constant Neumann boundary data

Let $Ω$ be a bounded Lipshcitz domain in $\mathbb{R}^n$ and we study boundary behaviors of solutions to the Laplacian eigenvalue equation with constant Neumann data. \begin{align} \label{cequation0} \begin{cases} -Δu=cu\quad &\mbox{in $Ω$}\\ \frac{\partial u}{\partial ν}=-1\quad &\mbox{on $\partial Ω$}. \end{cases} \end{align}First, by using properties of Bessel functions and proving new inequalities on elementary symmetric polynomials, we obtain the following inequality for rectangular boxes, balls and equilateral triangles: \begin{align} \label{bbb} \lim_{c\rightarrow μ_2^-}c\int_{\partial Ω}u_c\, dσ\ge \frac{n-1}{n}\frac{P^2(Ω)}{|Ω|}, \end{align}with equality achieved only at cubes and balls. In the above, $u_c$ is the solution to the eigenvalue equation and $μ_2$ is the second Neumann Laplacian eigenvalue. Second, let $κ_1$ be the best constant for the Poincaré inequality with mean zero on $\partial Ω$, and we prove that $κ_1\le μ_2$, with equality holds if and only if $\int_{\partial Ω}u_c\, dσ>0$ for any $c\in (0,μ_2)$. As a consequence, $κ_1=μ_2$ on balls, rectangular boxes and equilateral triangles, and balls maximize $κ_1$ over all Lipschitz domains with fixed volume. As an application, we extend the symmetry breaking results from ball domains obtained in Bucur-Buttazzo-Nitsch[J. Math. Pures Appl., 2017], to wider class of domains, and give quantitative estimates for the precise breaking threshold at balls and rectangular boxes. It is a direct consequence that for domains with $κ_1<μ_2$, the above boundary limit inequality is never true, while whether it is valid for domains on which $κ_1=μ_2$ remains open.

math.AP↗
arXiv2024

Spontaneous gap opening and potential excitonic states in an ideal Dirac semimetal Ta$_2$Pd$_3$Te$_5$

The opening of an energy gap in the electronic structure generally indicates the presence of interactions. In materials with low carrier density and short screening length, long-range Coulomb interaction favors the spontaneous formation of electron-hole pairs, so-called excitons, opening an excitonic gap at the Fermi level. Excitonic materials host unique phenomenons associated with pair excitations. However, there is still no generally recognized single-crystal material with excitonic order, which is, therefore, awaited in condensed matter physics. Here, we show that excitonic states may exist in the quasi-one-dimensional material Ta$_2$Pd$_3$Te$_5$, which has an almost ideal Dirac-like band structure, with Dirac point located exactly at Fermi level. We find that an energy gap appears at 350 K, and it grows with decreasing temperature. The spontaneous gap opening is absent in a similar material Ta$_2$Ni$_3$Te$_5$. Intriguingly, the gap is destroyed by the potassium deposition on the crystal, likely due to extra-doped carriers. Furthermore, we observe a pair of in-gap flat bands, which is an analog of the impurity states in a superconducting gap. All these observations can be properly explained by an excitonic order, providing Ta$_2$Pd$_3$Te$_5$ as a new and promising candidate realizing excitonic states.

cond-mat.mtrl-sci↗
arXiv2024

Optimizing Warfarin Dosing Using Contextual Bandit: An Offline Policy Learning and Evaluation Method

Warfarin, an anticoagulant medication, is formulated to prevent and address conditions associated with abnormal blood clotting, making it one of the most prescribed drugs globally. However, determining the suitable dosage remains challenging due to individual response variations, and prescribing an incorrect dosage may lead to severe consequences. Contextual bandit and reinforcement learning have shown promise in addressing this issue. Given the wide availability of observational data and safety concerns of decision-making in healthcare, we focused on using exclusively observational data from historical policies as demonstrations to derive new policies; we utilized offline policy learning and evaluation in a contextual bandit setting to establish the optimal personalized dosage strategy. Our learned policies surpassed these baseline approaches without genotype inputs, even when given a suboptimal demonstration, showcasing promising application potential.

cs.LG↗
arXiv2024

Doppler Tracking Data of Martian Mission Tianwen-I and Upper Limit of Stochastic Gravitational Wave Background

Two way ranging data for spacecraft tracking of China's first Martian mission Tianwen-I is analysed. Shortly before the spacecraft entered the Mars parking orbit, the two way coherent microwave link between the spacecraft and the Earth resembles a long arm gravitational wave interferometer, with both the spacecraft and the Earth regarded as in an approximate free falling state. By carefully selecting and analysing data segments of the time series of the two way ranging data during this time span, a parametric statistical model is built for the data segments and an upper limit for the stochastic gravitational waves background (SGWB) is then estimated within the frequency window 0.1Hz to 0.1 mHz. The upper bound improves considerably on those obtained before. In particular, around the deci-Hz band, there is a three orders improvement on the bound obtained previously by the two way ranging data of the Chang e 3 mission. Scientific applications of the upper bound is then considered and a weak upper bound is worked out for axions which is a promising candidate for ultra light dark matter.

gr-qc↗
arXiv2023

Dual curvature measures for log-concave functions

We introduce dual curvature measures for log-concave functions, which in the case of characteristic functions recover the dual curvature measures for convex bodies introduced by Huang-Lutwak-Yang-Zhang in 2016. Variational formulas are shown. The associated Minkowski problem for these dual curvature measures is considered and sufficient conditions in the symmetric setting are demonstrated.

math.MG↗
arXiv2023

Resolution Improvement for OpticalCoherence Tomography based on Sparse Continuous Deconvolution

We propose an image resolution improvement method for optical coherence tomography (OCT) based on sparse continuous deconvolution. Traditional deconvolution techniques such as Lucy-Richardson deconvolution suffers from the artifact convergence problem after a small number of iterations, which brings limitation to practical applications. In this work, we take advantage of the prior knowledge about the sample sparsity and continuity to constrain the deconvolution iteration. Sparsity is used to achieve the resolution improvement through the resolution preserving regularization term. And the continuity based on the correlation of the grayscale values in different directions is introduced to mitigate excessive image sparsity and noise reduction through the continuity regularization term. The Bregman splitting technique is then used to solve the resulting optimization problem. Both the numerical simulation study and experimental study on phantoms and biological samples show that our method can suppress artefacts of traditional deconvolution techniques effectively. Meanwhile, clear resolution improvement is demonstrated. It achieved nearly twofold resolution improvement for phantom beads image that can be quantitatively evaluated

physics.bio-ph↗
arXiv2023

Concentration breaking on two optimization problems

In the present paper, we study the boundary concentration breaking phenomena on two thermal insulation problems considered on Lipschitz domains, based on Serrin's overdetermined results, perturbation argument and comparison of Laplacian eigenvalues with different boundary conditions. Since neither of the functionals in the two problems is $C^1$, another key ingredient is to obtain the global Hölder regularity of minimizers to both problems on Lipschitz domains. Also, exact dependence on domain of breaking thresholds is also given in the first problem, and the breaking values are obtained in the second problem on ball domains, which are related to $2π$ in dimension $2$.

math.AP↗