arXiv subjects

Li Shen

Publications and source records attributed to Li Shen.

At least 235 records · Page 13Linked to original sources

arXiv2024

Is C4 Dataset Optimal for Pruning? An Investigation of Calibration Data for LLM Pruning

Network pruning has emerged as a potential solution to make LLMs cheaper to deploy. However, existing LLM pruning approaches universally rely on the C4 dataset as the calibration data for calculating pruning scores, leaving its optimality unexplored. In this study, we evaluate the choice of calibration data on LLM pruning, across a wide range of datasets that are most commonly used in LLM training and evaluation, including four pertaining datasets as well as three categories of downstream tasks encompassing nine datasets. Each downstream dataset is prompted with In-Context Learning (ICL) and Chain-of-Thought (CoT), respectively. Besides the already intriguing observation that the choice of calibration data significantly impacts the performance of pruned LLMs, our results also uncover several subtle and often unexpected findings, summarized as follows: (1) C4 is not the optimal choice for LLM pruning, even among commonly used pre-training datasets; (2) arithmetic datasets, when used as calibration data, performs on par or even better than pre-training datasets; (3) pruning with downstream datasets does not necessarily help the corresponding downstream task, compared to pre-training data; (4) ICL is widely beneficial to all data categories, whereas CoT is only useful on certain tasks. Our findings shed light on the importance of carefully selecting calibration data for LLM pruning and pave the way for more efficient deployment of these powerful models in real-world applications. We release our code at: https://github.com/abx393/llm-pruning-calibration-data.

cs.CL↗

arXiv2024

Clustering Alzheimer's Disease Subtypes via Similarity Learning and Graph Diffusion

Alzheimer's disease (AD) is a complex neurodegenerative disorder that affects millions of people worldwide. Due to the heterogeneous nature of AD, its diagnosis and treatment pose critical challenges. Consequently, there is a growing research interest in identifying homogeneous AD subtypes that can assist in addressing these challenges in recent years. In this study, we aim to identify subtypes of AD that represent distinctive clinical features and underlying pathology by utilizing unsupervised clustering with graph diffusion and similarity learning. We adopted SIMLR, a multi-kernel similarity learning framework, and graph diffusion to perform clustering on a group of 829 patients with AD and mild cognitive impairment (MCI, a prodromal stage of AD) based on their cortical thickness measurements extracted from magnetic resonance imaging (MRI) scans. Although the clustering approach we utilized has not been explored for the task of AD subtyping before, it demonstrated significantly better performance than several commonly used clustering methods. Specifically, we showed the power of graph diffusion in reducing the effects of noise in the subtype detection. Our results revealed five subtypes that differed remarkably in their biomarkers, cognitive status, and some other clinical features. To evaluate the resultant subtypes further, a genetic association study was carried out and successfully identified potential genetic underpinnings of different AD subtypes. Our source code is available at: https://github.com/PennShenLab/AD-SIMLR.

cs.LG↗

arXiv2024

Source-Free Domain Adaptation Guided by Vision and Vision-Language Pre-Training

Source-free domain adaptation (SFDA) aims to adapt a source model trained on a fully-labeled source domain to a related but unlabeled target domain. While the source model is a key avenue for acquiring target pseudolabels, the generated pseudolabels may exhibit source bias. In the conventional SFDA pipeline, a large data (e.g. ImageNet) pre-trained feature extractor is used to initialize the source model at the start of source training, and subsequently discarded. Despite having diverse features important for generalization, the pre-trained feature extractor can overfit to the source data distribution during source training and forget relevant target domain knowledge. Rather than discarding this valuable knowledge, we introduce an integrated framework to incorporate pre-trained networks into the target adaptation process. The proposed framework is flexible and allows us to plug modern pre-trained networks into the adaptation process to leverage their stronger representation learning capabilities. For adaptation, we propose the Co-learn algorithm to improve target pseudolabel quality collaboratively through the source model and a pre-trained feature extractor. Building on the recent success of the vision-language model CLIP in zero-shot image recognition, we present an extension Co-learn++ to further incorporate CLIP's zero-shot classification decisions. We evaluate on 4 benchmark datasets and include more challenging scenarios such as open-set, partial-set and open-partial SFDA. Experimental results demonstrate that our proposed strategy improves adaptation performance and can be successfully integrated with existing SFDA methods. Project code is available at https://github.com/zwenyu/colearn-plus.

cs.CV↗

arXiv2024

Meta-TTT: A Meta-learning Minimax Framework For Test-Time Training

Test-time domain adaptation is a challenging task that aims to adapt a pre-trained model to limited, unlabeled target data during inference. Current methods that rely on self-supervision and entropy minimization underperform when the self-supervised learning (SSL) task does not align well with the primary objective. Additionally, minimizing entropy can lead to suboptimal solutions when there is limited diversity within minibatches. This paper introduces a meta-learning minimax framework for test-time training on batch normalization (BN) layers, ensuring that the SSL task aligns with the primary task while addressing minibatch overfitting. We adopt a mixed-BN approach that interpolates current test batch statistics with the statistics from source domains and propose a stochastic domain synthesizing method to improve model generalization and robustness to domain shifts. Extensive experiments demonstrate that our method surpasses state-of-the-art techniques across various domain adaptation and generalization benchmarks, significantly enhancing the pre-trained model's robustness on unseen domains.

cs.LG↗

arXiv2024

Causality-based Subject and Task Fingerprints using fMRI Time-series Data

Recently, there has been a revived interest in system neuroscience causation models due to their unique capability to unravel complex relationships in multi-scale brain networks. In this paper, our goal is to verify the feasibility and effectiveness of using a causality-based approach for fMRI fingerprinting. Specifically, we propose an innovative method that utilizes the causal dynamics activities of the brain to identify the unique cognitive patterns of individuals (e.g., subject fingerprint) and fMRI tasks (e.g., task fingerprint). The key novelty of our approach stems from the development of a two-timescale linear state-space model to extract 'spatio-temporal' (aka causal) signatures from an individual's fMRI time series data. To the best of our knowledge, we pioneer and subsequently quantify, in this paper, the concept of 'causal fingerprint.' Our method is well-separated from other fingerprint studies as we quantify fingerprints from a cause-and-effect perspective, which are then incorporated with a modal decomposition and projection method to perform subject identification and a GNN-based (Graph Neural Network) model to perform task identification. Finally, we show that the experimental results and comparisons with non-causality-based methods demonstrate the effectiveness of the proposed methods. We visualize the obtained causal signatures and discuss their biological relevance in light of the existing understanding of brain functionalities. Collectively, our work paves the way for further studies on causal fingerprints with potential applications in both healthy controls and neurodegenerative diseases.

cs.LG↗

arXiv2024

Continual Learning From a Stream of APIs

Continual learning (CL) aims to learn new tasks without forgetting previous tasks. However, existing CL methods require a large amount of raw data, which is often unavailable due to copyright considerations and privacy risks. Instead, stakeholders usually release pre-trained machine learning models as a service (MLaaS), which users can access via APIs. This paper considers two practical-yet-novel CL settings: data-efficient CL (DECL-APIs) and data-free CL (DFCL-APIs), which achieve CL from a stream of APIs with partial or no raw data. Performing CL under these two new settings faces several challenges: unavailable full raw data, unknown model parameters, heterogeneous models of arbitrary architecture and scale, and catastrophic forgetting of previous APIs. To overcome these issues, we propose a novel data-free cooperative continual distillation learning framework that distills knowledge from a stream of APIs into a CL model by generating pseudo data, just by querying APIs. Specifically, our framework includes two cooperative generators and one CL model, forming their training as an adversarial game. We first use the CL model and the current API as fixed discriminators to train generators via a derivative-free method. Generators adversarially generate hard and diverse synthetic data to maximize the response gap between the CL model and the API. Next, we train the CL model by minimizing the gap between the responses of the CL model and the black-box API on synthetic data, to transfer the API's knowledge to the CL model. Furthermore, we propose a new regularization term based on network similarity to prevent catastrophic forgetting of previous APIs.Our method performs comparably to classic CL with full raw data on the MNIST and SVHN in the DFCL-APIs setting. In the DECL-APIs setting, our method achieves 0.97x, 0.75x and 0.69x performance of classic CL on CIFAR10, CIFAR100, and MiniImageNet.

cs.LG↗

arXiv2024

$\mathbb{USCD}$: Improving Code Generation of LLMs by Uncertainty-Aware Selective Contrastive Decoding

Large language models (LLMs) have shown remarkable capabilities in code generation. However, the effects of hallucinations (e.g., output noise) make it particularly challenging for LLMs to generate high-quality code in one pass. In this work, we propose a simple and effective \textbf{u}ncertainty-aware \textbf{s}elective \textbf{c}ontrastive \textbf{d}ecoding ($\mathbb{USCD}$) mechanism to improve the quality of one-pass code generation in LLMs and reduce the impact of output noise. To be specific, we first elaborately designed a negative prompt (namely lame prompt) to output noise by removing input-output examples from the standard few-shot prompt. Our preliminary study shows that the Jensen-Shannon divergence (JS divergence) between token distribution uncertainty and the output noise is relatively low (approximately $0.25$), indicating their high relevance. Then, we selectively eliminate output noise induced by lame prompts based on the uncertainty of the prediction distribution from the standard prompt. Notably, our proposed plug-and-play mechanism is an inference-only method, enjoying appealing flexibility. Extensive experiments on widely used benchmarks, e.g., HumanEval, MBPP, and MultiPL-E, upon several LLMs (i.e., Inocder-6b, CodeLlama-7b, WizardCoder-15b, StarCoder, and Llama2-7b), demonstrate that our proposed USCD significantly improves one-pass code generation, with an average \textit{pass@$1$} scores increase of 16.59\%. We will release code and data on GitHub.

cs.SE↗

arXiv2024

Diversifying the Mixture-of-Experts Representation for Language Models with Orthogonal Optimizer

The Mixture of Experts (MoE) has emerged as a highly successful technique in deep learning, based on the principle of divide-and-conquer to maximize model capacity without significant additional computational cost. Even in the era of large-scale language models (LLMs), MoE continues to play a crucial role, as some researchers have indicated that GPT-4 adopts the MoE structure to ensure diverse inference results. However, MoE is susceptible to performance degeneracy, particularly evident in the issues of imbalance and homogeneous representation among experts. While previous studies have extensively addressed the problem of imbalance, the challenge of homogeneous representation remains unresolved. In this study, we shed light on the homogeneous representation problem, wherein experts in the MoE fail to specialize and lack diversity, leading to frustratingly high similarities in their representations (up to 99\% in a well-performed MoE model). This problem restricts the expressive power of the MoE and, we argue, contradicts its original intention. To tackle this issue, we propose a straightforward yet highly effective solution: OMoE, an orthogonal expert optimizer. Additionally, we introduce an alternating training strategy that encourages each expert to update in a direction orthogonal to the subspace spanned by other experts. Our algorithm facilitates MoE training in two key ways: firstly, it explicitly enhances representation diversity, and secondly, it implicitly fosters interaction between experts during orthogonal weights computation. Through extensive experiments, we demonstrate that our proposed optimization algorithm significantly improves the performance of fine-tuning the MoE model on the GLUE benchmark, SuperGLUE benchmark, question-answering task, and name entity recognition tasks.

cs.CL↗

arXiv2024

Divide, Conquer and Combine: A Training-Free Framework for High-Resolution Image Perception in Multimodal Large Language Models

Multimodal large language models (MLLMs) have experienced significant advancements recently, but still struggle to recognize and interpret intricate details in high-resolution (HR) images effectively. While state-of-the-art (SOTA) MLLMs claim to process images at 4K resolution, existing MLLM benchmarks only support up to 2K, leaving the capabilities of SOTA models on true HR images largely untested. Furthermore, existing methods for enhancing HR image perception in MLLMs rely on computationally expensive visual instruction tuning. To address these limitations, we introduce HR-Bench, the first deliberately designed benchmark to rigorously evaluate MLLM performance on 4K&8K images. Through extensive experiments, we demonstrate that while downsampling HR images leads to vision information loss, leveraging complementary modalities, e.g., text, can effectively compensate for this loss. Building upon this insight, we propose Divide, Conquer and Combine (DC$^2$), a novel training-free framework for enhancing MLLM perception of HR images. DC$^2$ follows a three-staged approach: 1) Divide: recursively partitioning the HR image into patches and merging similar patches to minimize computational overhead, 2) Conquer: leveraging the MLLM to generate accurate textual descriptions for each image patch, and 3) Combine: utilizing the generated text descriptions to enhance the MLLM's understanding of the overall HR image. Extensive experiments show that: 1) the SOTA MLLM achieves 63% accuracy, which is markedly lower than the 87% accuracy achieved by humans on HR-Bench; 2) our DC$^2$ brings consistent and significant improvements (a relative increase of +6% on HR-Bench and +8% on general multimodal benchmarks). The benchmark and code will be released to facilitate the multimodal R&D community.

cs.CV↗

arXiv2024

SMILE: Zero-Shot Sparse Mixture of Low-Rank Experts Construction From Pre-Trained Foundation Models

Deep model training on extensive datasets is increasingly becoming cost-prohibitive, prompting the widespread adoption of deep model fusion techniques to leverage knowledge from pre-existing models. From simple weight averaging to more sophisticated methods like AdaMerging, model fusion effectively improves model performance and accelerates the development of new models. However, potential interference between parameters of individual models and the lack of interpretability in the fusion progress remain significant challenges. Existing methods often try to resolve the parameter interference issue by evaluating attributes of parameters, such as their magnitude or sign, or by parameter pruning. In this study, we begin by examining the fine-tuning of linear layers through the lens of subspace analysis and explicitly define parameter interference as an optimization problem to shed light on this subject. Subsequently, we introduce an innovative approach to model fusion called zero-shot Sparse MIxture of Low-rank Experts (SMILE) construction, which allows for the upscaling of source models into an MoE model without extra data or further training. Our approach relies on the observation that fine-tuning mostly keeps the important parts from the pre-training, but it uses less significant or unused areas to adapt to new tasks. Also, the issue of parameter interference, which is intrinsically intractable in the original parameter space, can be managed by expanding the dimensions. We conduct extensive experiments across diverse scenarios, such as image classification and text generation tasks, using full fine-tuning and LoRA fine-tuning, and we apply our method to large language models (CLIP models, Flan-T5 models, and Mistral-7B models), highlighting the adaptability and scalability of SMILE. Code is available at https://github.com/tanganke/fusion_bench

cs.LG↗

arXiv2024

Mayer-homology learning prediction of protein-ligand binding affinities

Artificial intelligence-assisted drug design is revolutionizing the pharmaceutical industry. Effective molecular features are crucial for accurate machine learning predictions, and advanced mathematics plays a key role in designing these features. Persistent homology theory, which equips topological invariants with persistence, provides valuable insights into molecular structures. The calculation of Betti numbers is based on differential that typically satisfy $d^2 = 0$. Our recent work has extended this concept by employing Mayer homology with a generalized differential that satisfies $d^N = 0$ for $N \geq 2$, leading to the development of persistent Mayer homology (PMH) theory and richer topological information across various scales. In this study, we utilize PMH to create a novel multiscale topological vectorization for molecular representation, offering valuable tools for descriptive and predictive analysis in molecular data and machine learning prediction. Specifically, benchmark tests on established protein-ligand datasets, including PDBbind-2007, PDBbind-2013, and PDBbind-2016, demonstrate the superior performance of our Mayer homology models in predicting protein-ligand binding affinities.

q-bio.BM↗

arXiv2024

Sequential Federated Learning in Hierarchical Architecture on Non-IID Datasets

In a real federated learning (FL) system, communication overhead for passing model parameters between the clients and the parameter server (PS) is often a bottleneck. Hierarchical federated learning (HFL) that poses multiple edge servers (ESs) between clients and the PS can partially alleviate communication pressure but still needs the aggregation of model parameters from multiple ESs at the PS. To further reduce communication overhead, we bring sequential FL (SFL) into HFL for the first time, which removes the central PS and enables the model training to be completed only through passing the global model between two adjacent ESs for each iteration, and propose a novel algorithm adaptive to such a combinational framework, referred to as Fed-CHS. Convergence results are derived for strongly convex and non-convex loss functions under various data heterogeneity setups, which show comparable convergence performance with the algorithms for HFL or SFL solely. Experimental results provide evidence of the superiority of our proposed Fed-CHS on both communication overhead saving and test accuracy over baseline methods.

cs.LG↗

arXiv2024

Nanoscale Surfactant Transport: Bridging Molecular and Continuum Models

Surfactant transport is central to a diverse range of natural phenomena, and for many practical applications in physics and engineering. Surprisingly, this process remains relatively poorly understood at the molecular scale. This study investigates the mechanism behind the transport of surfactant monolayers on flat and curved liquid vapor interfaces using nonequilibrium molecular dynamics simulations, which are compared with the continuum transport model. This approach not only provides fresh molecular level insight into surfactant dynamics, but also confirms the nanoscale mechanism of the lateral migration of surfactant molecules along a thin film that continuously deforms as surfactants spread. By connecting the continuum model where the long wave approximations prevail, to the molecular details where such approximations break down, we establish that the transport equation preserves substantial accuracy in capturing the underlying physics. Moreover, the relative importance of the different mechanisms of the transport process are identified. Consequently, we derive a novel, exact molecular equation for surfactant transport along a deforming surface. Finally, our findings demonstrate that the spreading of surfactants at the molecular scale adheres to expected scaling laws and aligns well with experimental observations.

cond-mat.soft↗

arXiv2024

Unmasking Bias in Diffusion Model Training

Denoising diffusion models have emerged as a dominant approach for image generation, however they still suffer from slow convergence in training and color shift issues in sampling. In this paper, we identify that these obstacles can be largely attributed to bias and suboptimality inherent in the default training paradigm of diffusion models. Specifically, we offer theoretical insights that the prevailing constant loss weight strategy in $ε$-prediction of diffusion models leads to biased estimation during the training phase, hindering accurate estimations of original images. To address the issue, we propose a simple but effective weighting strategy derived from the unlocked biased part. Furthermore, we conduct a comprehensive and systematic exploration, unraveling the inherent bias problem in terms of its existence, impact and underlying reasons. These analyses contribute to advancing the understanding of diffusion models. Empirical results demonstrate that our method remarkably elevates sample quality and displays improved efficiency in both training and sampling processes, by only adjusting loss weighting strategy. The code is released publicly at \url{https://github.com/yuhuUSTC/Debias}

cs.CV↗

arXiv2024

SDoH-GPT: Using Large Language Models to Extract Social Determinants of Health (SDoH)

Extracting social determinants of health (SDoH) from unstructured medical notes depends heavily on labor-intensive annotations, which are typically task-specific, hampering reusability and limiting sharing. In this study we introduced SDoH-GPT, a simple and effective few-shot Large Language Model (LLM) method leveraging contrastive examples and concise instructions to extract SDoH without relying on extensive medical annotations or costly human intervention. It achieved tenfold and twentyfold reductions in time and cost respectively, and superior consistency with human annotators measured by Cohen's kappa of up to 0.92. The innovative combination of SDoH-GPT and XGBoost leverages the strengths of both, ensuring high accuracy and computational efficiency while consistently maintaining 0.90+ AUROC scores. Testing across three distinct datasets has confirmed its robustness and accuracy. This study highlights the potential of leveraging LLMs to revolutionize medical note classification, demonstrating their capability to achieve highly accurate classifications with significantly reduced time and cost.

cs.CL↗

arXiv2024

A principled framework to assess the information-theoretic fitness of brain functional sub-circuits

In systems and network neuroscience, many common practices in brain connectomic analysis are often not properly scrutinized. One such practice is mapping a predetermined set of sub-circuits, like functional networks (FNs), onto subjects' functional connectomes (FCs) without adequately assessing the information-theoretic appropriateness of the partition. Another practice that goes unchallenged is thresholding weighted FCs to remove spurious connections without justifying the chosen threshold. This paper leverages recent theoretical advances in Stochastic Block Models (SBMs) to formally define and quantify the information-theoretic fitness (e.g., prominence) of a predetermined set of FNs when mapped to individual FCs under different fMRI task conditions. Our framework allows for evaluating any combination of FC granularity, FN partition, and thresholding strategy, thereby optimizing these choices to preserve important topological features of the human brain connectomes. By applying to the Human Connectome Project with Schaefer parcellations at multiple levels of granularity, the framework showed that the common thresholding value of 0.25 was indeed information-theoretically valid for group-average FCs despite its previous lack of justification. Our results pave the way for the proper use of FNs and thresholding methods and provide insights for future research in individualized parcellations.

q-bio.NC↗

arXiv2024

Volume-optimal persistence homological scaffolds of hemodynamic networks covary with MEG theta-alpha aperiodic dynamics

Higher-order properties of functional magnetic resonance imaging (fMRI) induced connectivity have been shown to unravel many exclusive topological and dynamical insights beyond pairwise interactions. Nonetheless, whether these fMRI-induced higher-order properties play a role in disentangling other neuroimaging modalities' insights remains largely unexplored and poorly understood. In this work, by analyzing fMRI data from the Human Connectome Project Young Adult dataset using persistent homology, we discovered that the volume-optimal persistence homological scaffolds of fMRI-based functional connectomes exhibited conservative topological reconfigurations from the resting state to attentional task-positive state. Specifically, while reflecting the extent to which each cortical region contributed to functional cycles following different cognitive demands, these reconfigurations were constrained such that the spatial distribution of cavities in the connectome is relatively conserved. Most importantly, such level of contributions covaried with powers of aperiodic activities mostly within the theta-alpha (4-12 Hz) band measured by magnetoencephalography (MEG). This comprehensive result suggests that fMRI-induced hemodynamics and MEG theta-alpha aperiodic activities are governed by the same functional constraints specific to each cortical morpho-structure. Methodologically, our work paves the way toward an innovative computing paradigm in multimodal neuroimaging topological learning.

q-bio.NC↗

arXiv2024

Subject-Adaptive Transfer Learning Using Resting State EEG Signals for Cross-Subject EEG Motor Imagery Classification

Electroencephalography (EEG) motor imagery (MI) classification is a fundamental, yet challenging task due to the variation of signals between individuals i.e., inter-subject variability. Previous approaches try to mitigate this using task-specific (TS) EEG signals from the target subject in training. However, recording TS EEG signals requires time and limits its applicability in various fields. In contrast, resting state (RS) EEG signals are a viable alternative due to ease of acquisition with rich subject information. In this paper, we propose a novel subject-adaptive transfer learning strategy that utilizes RS EEG signals to adapt models on unseen subject data. Specifically, we disentangle extracted features into task- and subject-dependent features and use them to calibrate RS EEG signals for obtaining task information while preserving subject characteristics. The calibrated signals are then used to adapt the model to the target subject, enabling the model to simulate processing TS EEG signals of the target subject. The proposed method achieves state-of-the-art accuracy on three public benchmarks, demonstrating the effectiveness of our method in cross-subject EEG MI classification. Our findings highlight the potential of leveraging RS EEG signals to advance practical brain-computer interface systems. The code is available at https://github.com/SionAn/MICCAI2024-ResTL.

eess.SP↗