arXiv subjects

Yanxi Chen

Publications and source records attributed to Yanxi Chen.

34 records · Page 2Linked to original sources

arXiv2025

Enhancing Latent Computation in Transformers with Latent Tokens

Augmenting large language models (LLMs) with auxiliary tokens has emerged as a promising strategy for enhancing model performance. In this work, we introduce a lightweight method termed latent tokens; these are dummy tokens that may be non-interpretable in natural language but steer the autoregressive decoding process of a Transformer-based LLM via the attention mechanism. The proposed latent tokens can be seamlessly integrated with a pre-trained Transformer, trained in a parameter-efficient manner, and applied flexibly at inference time, while adding minimal complexity overhead to the existing infrastructure of standard Transformers. We propose several hypotheses about the underlying mechanisms of latent tokens and design synthetic tasks accordingly to verify them. Numerical results confirm that the proposed method noticeably outperforms the baselines, particularly in the out-of-distribution generalization scenarios, highlighting its potential in improving the adaptability of LLMs.

cs.LG↗

arXiv2025

RetinalGPT: A Retinal Clinical Preference Conversational Assistant Powered by Large Vision-Language Models

Recently, Multimodal Large Language Models (MLLMs) have gained significant attention for their remarkable ability to process and analyze non-textual data, such as images, videos, and audio. Notably, several adaptations of general-domain MLLMs to the medical field have been explored, including LLaVA-Med. However, these medical adaptations remain insufficiently advanced in understanding and interpreting retinal images. In contrast, medical experts emphasize the importance of quantitative analyses for disease detection and interpretation. This underscores a gap between general-domain and medical-domain MLLMs: while general-domain MLLMs excel in broad applications, they lack the specialized knowledge necessary for precise diagnostic and interpretative tasks in the medical field. To address these challenges, we introduce \textit{RetinalGPT}, a multimodal conversational assistant for clinically preferred quantitative analysis of retinal images. Specifically, we achieve this by compiling a large retinal image dataset, developing a novel data pipeline, and employing customized visual instruction tuning to enhance both retinal analysis and enrich medical knowledge. In particular, RetinalGPT outperforms MLLM in the generic domain by a large margin in the diagnosis of retinal diseases in 8 benchmark retinal datasets. Beyond disease diagnosis, RetinalGPT features quantitative analyses and lesion localization, representing a pioneering step in leveraging LLMs for an interpretable and end-to-end clinical research framework. The code is available at https://github.com/Retinal-Research/RetinalGPT

cs.CV↗

arXiv2025

Plasma-CycleGAN: Plasma Biomarker-Guided MRI to PET Cross-modality Translation Using Conditional CycleGAN

Cross-modality translation between MRI and PET imaging is challenging due to the distinct mechanisms underlying these modalities. Blood-based biomarkers (BBBMs) are revolutionizing Alzheimer's disease (AD) detection by identifying patients and quantifying brain amyloid levels. However, the potential of BBBMs to enhance PET image synthesis remains unexplored. In this paper, we performed a thorough study on the effect of incorporating BBBM into deep generative models. By evaluating three widely used cross-modality translation models, we found that BBBMs integration consistently enhances the generative quality across all models. By visual inspection of the generated results, we observed that PET images generated by CycleGAN exhibit the best visual fidelity. Based on these findings, we propose Plasma-CycleGAN, a novel generative model based on CycleGAN, to synthesize PET images from MRI using BBBMs as conditions. This is the first approach to integrate BBBMs in conditional cross-modality translation between MRI and PET.

cs.CV↗

arXiv2024

Many-MobileNet: Multi-Model Augmentation for Robust Retinal Disease Classification

In this work, we propose Many-MobileNet, an efficient model fusion strategy for retinal disease classification using lightweight CNN architecture. Our method addresses key challenges such as overfitting and limited dataset variability by training multiple models with distinct data augmentation strategies and different model complexities. Through this fusion technique, we achieved robust generalization in data-scarce domains while balancing computational efficiency with feature extraction capabilities.

cs.CV↗

arXiv2024

CUNSB-RFIE: Context-aware Unpaired Neural Schrödinger Bridge in Retinal Fundus Image Enhancement

Retinal fundus photography is significant in diagnosing and monitoring retinal diseases. However, systemic imperfections and operator/patient-related factors can hinder the acquisition of high-quality retinal images. Previous efforts in retinal image enhancement primarily relied on GANs, which are limited by the trade-off between training stability and output diversity. In contrast, the Schrödinger Bridge (SB), offers a more stable solution by utilizing Optimal Transport (OT) theory to model a stochastic differential equation (SDE) between two arbitrary distributions. This allows SB to effectively transform low-quality retinal images into their high-quality counterparts. In this work, we leverage the SB framework to propose an image-to-image translation pipeline for retinal image enhancement. Additionally, previous methods often fail to capture fine structural details, such as blood vessels. To address this, we enhance our pipeline by introducing Dynamic Snake Convolution, whose tortuous receptive field can better preserve tubular structures. We name the resulting retinal fundus image enhancement framework the Context-aware Unpaired Neural Schrödinger Bridge (CUNSB-RFIE). To the best of our knowledge, this is the first endeavor to use the SB approach for retinal image enhancement. Experimental results on a large-scale dataset demonstrate the advantage of the proposed method compared to several state-of-the-art supervised and unsupervised methods in terms of image quality and performance on downstream tasks.The code is available at https://github.com/Retinal-Research/CUNSB-RFIE .

eess.IV↗

arXiv2024

AMG: Avatar Motion Guided Video Generation

Human video generation task has gained significant attention with the advancement of deep generative models. Generating realistic videos with human movements is challenging in nature, due to the intricacies of human body topology and sensitivity to visual artifacts. The extensively studied 2D media generation methods take advantage of massive human media datasets, but struggle with 3D-aware control; whereas 3D avatar-based approaches, while offering more freedom in control, lack photorealism and cannot be harmonized seamlessly with background scene. We propose AMG, a method that combines the 2D photorealism and 3D controllability by conditioning video diffusion models on controlled rendering of 3D avatars. We additionally introduce a novel data processing pipeline that reconstructs and renders human avatar movements from dynamic camera videos. AMG is the first method that enables multi-person diffusion video generation with precise control over camera positions, human motions, and background style. We also demonstrate through extensive evaluation that it outperforms existing human video generation methods conditioned on pose sequences or driving videos in terms of realism and adaptability.

cs.CV↗

arXiv2024

Fast Computation of Optimal Transport via Entropy-Regularized Extragradient Methods

Efficient computation of the optimal transport distance between two distributions serves as an algorithm subroutine that empowers various applications. This paper develops a scalable first-order optimization-based method that computes optimal transport to within $\varepsilon$ additive accuracy with runtime $\widetilde{O}( n^2/\varepsilon)$, where $n$ denotes the dimension of the probability distributions of interest. Our algorithm achieves the state-of-the-art computational guarantees among all first-order methods, while exhibiting favorable numerical performance compared to classical algorithms like Sinkhorn and Greenkhorn. Underlying our algorithm designs are two key elements: (a) converting the original problem into a bilinear minimax problem over probability distributions; (b) exploiting the extragradient idea -- in conjunction with entropy regularization and adaptive learning rates -- to accelerate convergence.

cs.LG↗

arXiv2024

EE-LLM: Large-Scale Training and Inference of Early-Exit Large Language Models with 3D Parallelism

We present EE-LLM, a framework for large-scale training and inference of early-exit large language models (LLMs). While recent works have shown preliminary evidence for the efficacy of early exiting in accelerating LLM inference, EE-LLM makes a foundational step towards scaling up early-exit LLMs by supporting their training and inference with massive 3D parallelism. Built upon Megatron-LM, EE-LLM implements a variety of algorithmic innovations and performance optimizations tailored to early exiting, including a lightweight method that facilitates backpropagation for the early-exit training objective with pipeline parallelism, techniques of leveraging idle resources in the original pipeline schedule for computation related to early-exit layers, and two approaches of early-exit inference that are compatible with KV caching for autoregressive generation. Our analytical and empirical study shows that EE-LLM achieves great training efficiency with negligible computational overhead compared to standard LLM training, as well as outstanding inference speedup without compromising output quality. To facilitate further research and adoption, we release EE-LLM at https://github.com/pan-x-c/EE-LLM.

cs.LG↗

arXiv2024

Clustering Mixtures of Discrete Distributions: A Note on Mitra's Algorithm

In this note, we provide a refined analysis of Mitra's algorithm \cite{mitra2008clustering} for classifying general discrete mixture distribution models. Built upon spectral clustering \cite{mcsherry2001spectral}, this algorithm offers compelling conditions for probability distributions. We enhance this analysis by tailoring the model to bipartite stochastic block models, resulting in more refined conditions. Compared to those derived in \cite{mitra2008clustering}, our improved separation conditions are obtained.

cs.LG↗

arXiv2024

Boosting Single Positive Multi-label Classification with Generalized Robust Loss

Multi-label learning (MLL) requires comprehensive multi-semantic annotations that is hard to fully obtain, thus often resulting in missing labels scenarios. In this paper, we investigate Single Positive Multi-label Learning (SPML), where each image is associated with merely one positive label. Existing SPML methods only focus on designing losses using mechanisms such as hard pseudo-labeling and robust losses, mostly leading to unacceptable false negatives. To address this issue, we first propose a generalized loss framework based on expected risk minimization to provide soft pseudo labels, and point out that the former losses can be seamlessly converted into our framework. In particular, we design a novel robust loss based on our framework, which enjoys flexible coordination between false positives and false negatives, and can additionally deal with the imbalance between positive and negative samples. Extensive experiments show that our approach can significantly improve SPML performance and outperform the vast majority of state-of-the-art methods on all the four benchmarks.

cs.LG↗

arXiv2024

EE-Tuning: An Economical yet Scalable Solution for Tuning Early-Exit Large Language Models

This work introduces EE-Tuning, a lightweight and economical solution to training/tuning early-exit large language models (LLMs). In contrast to the common approach of full-parameter pre-training, EE-Tuning augments any pre-trained (and possibly fine-tuned) standard LLM with additional early-exit layers that are tuned in a parameter-efficient manner, which requires significantly less computational resources and training data. Our implementation of EE-Tuning achieves outstanding training efficiency via extensive performance optimizations, as well as scalability due to its full compatibility with 3D parallelism. Results of systematic experiments validate the efficacy of EE-Tuning, confirming that effective early-exit LLM inference can be achieved with a limited training budget. In hope of making early-exit LLMs accessible to the community, we release the source code of our implementation of EE-Tuning at https://github.com/pan-x-c/EE-LLM.

cs.LG↗

arXiv2023

Ranking from Pairwise Comparisons in General Graphs and Graphs with Locality

This technical report studies the problem of ranking from pairwise comparisons in the classical Bradley-Terry-Luce (BTL) model, with a focus on score estimation. For general graphs, we show that, with sufficiently many samples, maximum likelihood estimation (MLE) achieves an entrywise estimation error matching the Cramér-Rao lower bound, which can be stated in terms of effective resistances; the key to our analysis is a connection between statistical estimation and iterative optimization by preconditioned gradient descent. We are also particularly interested in graphs with locality, where only nearby items can be connected by edges; our analysis identifies conditions under which locality does not hurt, i.e. comparing the scores between a pair of items that are far apart in the graph is nearly as easy as comparing a pair of nearby items. We further explore divide-and-conquer algorithms that can provably achieve similar guarantees even in the regime with the sparsest samples, while enjoying certain computational advantages. Numerical results validate our theory and confirm the efficacy of the proposed algorithms.

stat.ML↗

arXiv2023

A Surface-Based Federated Chow Test Model for Integrating APOE Status, Tau Deposition Measure, and Hippocampal Surface Morphometry

Background: Alzheimer's Disease (AD) is the most common type of age-related dementia, affecting 6.2 million people aged 65 or older according to CDC data. It is commonly agreed that discovering an effective AD diagnosis biomarker could have enormous public health benefits, potentially preventing or delaying up to 40% of dementia cases. Tau neurofibrillary tangles are the primary driver of downstream neurodegeneration and subsequent cognitive impairment in AD, resulting in structural deformations such as hippocampal atrophy that can be observed in magnetic resonance imaging (MRI) scans. Objective: To build a surface-based model to 1) detect differences between APOE subgroups in patterns of tau deposition and hippocampal atrophy, and 2) use the extracted surface-based features to predict cognitive decline. Methods: Using data obtained from different institutions, we develop a surface-based federated Chow test model to study the synergistic effects of APOE, a previously reported significant risk factor of AD, and tau on hippocampal surface morphometry. Results: We illustrate that the APOE-specific morphometry features correlate with AD progression and better predict future AD conversion than other MRI biomarkers. For example, a strong association between atrophy and abnormal tau was identified in hippocampal subregion cornu ammonis 1 (CA1 subfield) and subiculum in e4 homozygote cohort. Conclusion: Our model allows for identifying MRI biomarkers for AD and cognitive decline prediction and may uncover a corner of the neural mechanism of the influence of APOE and tau deposition on hippocampal morphology.

physics.med-ph↗

arXiv2022

Learning Mixtures of Linear Dynamical Systems

We study the problem of learning a mixture of multiple linear dynamical systems (LDSs) from unlabeled short sample trajectories, each generated by one of the LDS models. Despite the wide applicability of mixture models for time-series data, learning algorithms that come with end-to-end performance guarantees are largely absent from existing literature. There are multiple sources of technical challenges, including but not limited to (1) the presence of latent variables (i.e. the unknown labels of trajectories); (2) the possibility that the sample trajectories might have lengths much smaller than the dimension $d$ of the LDS models; and (3) the complicated temporal dependence inherent to time-series data. To tackle these challenges, we develop a two-stage meta-algorithm, which is guaranteed to efficiently recover each ground-truth LDS model up to error $\tilde{O}(\sqrt{d/T})$, where $T$ is the total sample size. We validate our theoretical studies with numerical experiments, confirming the efficacy of the proposed algorithm.

stat.ML↗

arXiv2021

Learning Mixtures of Low-Rank Models

We study the problem of learning mixtures of low-rank models, i.e. reconstructing multiple low-rank matrices from unlabelled linear measurements of each. This problem enriches two widely studied settings -- low-rank matrix sensing and mixed linear regression -- by bringing latent variables (i.e. unknown labels) and structural priors (i.e. low-rank structures) into consideration. To cope with the non-convexity issues arising from unlabelled heterogeneous data and low-complexity structure, we develop a three-stage meta-algorithm that is guaranteed to recover the unknown matrices with near-optimal sample and computational complexities under Gaussian designs. In addition, the proposed algorithm is provably stable against random noise. We complement the theoretical studies with empirical evidence that confirms the efficacy of our algorithm.

stat.ML↗

arXiv2017

Active Orthogonal Matching Pursuit for Sparse Subspace Clustering

Sparse Subspace Clustering (SSC) is a state-of-the-art method for clustering high-dimensional data points lying in a union of low-dimensional subspaces. However, while $\ell_1$ optimization-based SSC algorithms suffer from high computational complexity, other variants of SSC, such as Orthogonal Matching Pursuit-based SSC (OMP-SSC), lose clustering accuracy in pursuit of improving time efficiency. In this letter, we propose a novel Active OMP-SSC, which improves clustering accuracy of OMP-SSC by adaptively updating data points and randomly dropping data points in the OMP process, while still enjoying the low computational complexity of greedy pursuit algorithms. We provide heuristic analysis of our approach, and explain how these two active steps achieve a better tradeoff between connectivity and separation. Numerical results on both synthetic data and real-world data validate our analyses and show the advantages of the proposed active algorithm.

cs.LG↗