Tianlong Chen

Junjie Yang, Tianlong Chen, Mingkang Zhu et al.

Learning to optimize (L2O) has gained increasing popularity, which automates the design of optimizers by data-driven approaches. However, current L2O methods often suffer from poor generalization performance in at least two folds: (i) applying the L2O-learned optimizer to unseen optimizees, in terms of lowering their loss function values (optimizer generalization, or ``generalizable learning of optimizers"); and (ii) the test performance of an optimizee (itself as a machine learning model), trained by the optimizer, in terms of the accuracy over unseen data (optimizee generalization, or ``learning to generalize"). While the optimizer generalization has been recently studied, the optimizee generalization (or learning to generalize) has not been rigorously studied in the L2O context, which is the aim of this paper. We first theoretically establish an implicit connection between the local entropy and the Hessian, and hence unify their roles in the handcrafted design of generalizable optimizers as equivalent metrics of the landscape flatness of loss functions. We then propose to incorporate these two metrics as flatness-aware regularizers into the L2O framework in order to meta-train optimizers to learn to generalize, and theoretically show that such generalization ability can be learned during the L2O meta-training process and then transformed to the optimizee loss function. Extensive experiments consistently validate the effectiveness of our proposals with substantially improved generalization on multiple sophisticated L2O models and diverse optimizees. Our code is available at: https://github.com/VITA-Group/Open-L2O/tree/main/Model_Free_L2O/L2O-Entropy.

Junjie Yang, Xuxi Chen, Tianlong Chen et al.

Learning to Optimize (L2O) has drawn increasing attention as it often remarkably accelerates the optimization procedure of complex tasks by ``overfitting" specific task type, leading to enhanced performance compared to analytical optimizers. Generally, L2O develops a parameterized optimization method (i.e., ``optimizer") by learning from solving sample problems. This data-driven procedure yields L2O that can efficiently solve problems similar to those seen in training, that is, drawn from the same ``task distribution". However, such learned optimizers often struggle when new test problems come with a substantially deviation from the training task distribution. This paper investigates a potential solution to this open challenge, by meta-training an L2O optimizer that can perform fast test-time self-adaptation to an out-of-distribution task, in only a few steps. We theoretically characterize the generalization of L2O, and further show that our proposed framework (termed as M-L2O) provably facilitates rapid task adaptation by locating well-adapted initial points for the optimizer weight. Empirical observations on several classic tasks like LASSO and Quadratic, demonstrate that M-L2O converges significantly faster than vanilla L2O with only $5$ steps of adaptation, echoing our theoretical results. Codes are available in https://github.com/VITA-Group/M-L2O.

Yun Zhu, Nevan Wichers, Chu-Cheng Lin et al.

Parameter Efficient Tuning has been an prominent approach to adapt the Large Language Model to downstream tasks. Most previous works considers adding the dense trainable parameters, where all parameters are used to adapt certain task. We found this less effective empirically using the example of LoRA that introducing more trainable parameters does not help. Motivated by this we investigate the importance of leveraging "sparse" computation and propose SiRA: sparse mixture of low rank adaption. SiRA leverages the Sparse Mixture of Expert(SMoE) to boost the performance of LoRA. Specifically it enforces the top $k$ experts routing with a capacity limit restricting the maximum number of tokens each expert can process. We propose a novel and simple expert dropout on top of gating network to reduce the over-fitting issue. Through extensive experiments, we verify SiRA performs better than LoRA and other mixture of expert approaches across different single tasks and multitask settings.

Xuxi Chen, Zhendong Wang, Daouda Sow et al.

In the rapidly advancing arena of large language models (LLMs), a key challenge is to enhance their capabilities amid a looming shortage of high-quality training data. Our study starts from an empirical strategy for the light continual training of LLMs using their original pre-training data sets, with a specific focus on selective retention of samples that incur moderately high losses. These samples are deemed informative and beneficial for model refinement, contrasting with the highest-loss samples, which would be discarded due to their correlation with data noise and complexity. We then formalize this strategy into a principled framework of Instance-Reweighted Distributionally Robust Optimization (IR-DRO). IR-DRO is designed to dynamically prioritize the training focus on informative samples through an instance reweighting mechanism, streamlined by a closed-form solution for straightforward integration into established training protocols. Through rigorous experimentation with various models and datasets, our findings indicate that our sample-targeted methods significantly improve LLM performance across multiple benchmarks, in both continual pre-training and instruction tuning scenarios. Our codes are available at https://github.com/VITA-Group/HardFocusTraining.

Jiayi Xin, Sukwon Yun, Jie Peng et al.

Modality fusion is a cornerstone of multimodal learning, enabling information integration from diverse data sources. However, vanilla fusion methods are limited by (1) inability to account for heterogeneous interactions between modalities and (2) lack of interpretability in uncovering the multimodal interactions inherent in the data. To this end, we propose I2MoE (Interpretable Multimodal Interaction-aware Mixture of Experts), an end-to-end MoE framework designed to enhance modality fusion by explicitly modeling diverse multimodal interactions, as well as providing interpretation on a local and global level. First, I2MoE utilizes different interaction experts with weakly supervised interaction losses to learn multimodal interactions in a data-driven way. Second, I2MoE deploys a reweighting model that assigns importance scores for the output of each interaction expert, which offers sample-level and dataset-level interpretation. Extensive evaluation of medical and general multimodal datasets shows that I2MoE is flexible enough to be combined with different fusion techniques, consistently improves task performance, and provides interpretation across various real-world scenarios. Code is available at https://github.com/Raina-Xin/I2MoE.

Chi-Jane Chen, Yuhang Chen, Sukwon Yun et al.

Image mass cytometry (IMC) enables high-dimensional spatial profiling by combining mass cytometry's analytical power with spatial distributions of cell phenotypes. Recent studies leverage large language models (LLMs) to extract cell states by translating gene or protein expression into biological context. However, existing single-cell LLMs face two major challenges: (1) Integration of spatial information: they struggle to generalize spatial coordinates and effectively encode spatial context as text, and (2) Treating each cell independently: they overlook cell-cell interactions, limiting their ability to capture biological relationships. To address these limitations, we propose Spatial2Sentence, a novel framework that integrates single-cell expression and spatial information into natural language using a multi-sentence approach. Spatial2Sentence constructs expression similarity and distance matrices, pairing spatially adjacent and expressionally similar cells as positive pairs while using distant and dissimilar cells as negatives. These multi-sentence representations enable LLMs to learn cellular interactions in both expression and spatial contexts. Equipped with multi-task learning, Spatial2Sentence outperforms existing single-cell LLMs on preprocessed IMC datasets, improving cell-type classification by 5.98% and clinical status prediction by 4.18% on the diabetes dataset while enhancing interpretability. The source code can be found here: https://github.com/UNITES-Lab/Spatial2Sentence.

Huaizhi Qu, Xiao Wang, Gengwei Zhang et al.

Cryo-electron microscopy (cryo-EM) has become a central tool for high-resolution structural biology, yet the massive scale of datasets (often exceeding 100k particle images) renders 3D reconstruction both computationally expensive and memory intensive. Traditional Fourier-space methods are efficient but lose fidelity due to repeated transforms, while recent real-space approaches based on neural radiance fields (NeRFs) improve accuracy but incur cubic memory and computation overhead. Therefore, we introduce GEM, a novel cryo-EM reconstruction framework built on 3D Gaussian Splatting (3DGS) that operates directly in real-space while maintaining high efficiency. Instead of modeling the entire density volume, GEM represents proteins with compact 3D Gaussians, each parameterized by only 11 values. To further improve the training efficiency, we designed a novel gradient computation to 3D Gaussians that contribute to each voxel. This design substantially reduced both memory footprint and training cost. On standard cryo-EM benchmarks, GEM achieves up to 48% faster training and 12% lower memory usage compared to state-of-the-art methods, while improving local resolution by as much as 38.8%. These results establish GEM as a practical and scalable paradigm for cryo-EM reconstruction, unifying speed, efficiency, and high-resolution accuracy. Our code is available at https://github.com/UNITES-Lab/GEM.

Yining Jiao, Sreekalyani Bhamidi, Huaizhi Qu et al.

The goal of this work is to develop principled techniques to extract information from high dimensional data sets with complex dependencies in areas such as medicine that can provide insight into individual as well as population level variation. We develop $\texttt{LucidAtlas}$, an approach that can represent spatially varying information, and can capture the influence of covariates as well as population uncertainty. As a versatile atlas representation, $\texttt{LucidAtlas}$ offers robust capabilities for covariate interpretation, individualized prediction, population trend analysis, and uncertainty estimation, with the flexibility to incorporate prior knowledge. Additionally, we discuss the trustworthiness and potential risks of neural additive models for analyzing dependent covariates and then introduce a marginalization approach to explain the dependence of an individual predictor on the models' response (the atlas). To validate our method, we demonstrate its generalizability on two medical datasets. Our findings underscore the critical role of by-construction interpretable models in advancing scientific discovery. Our code will be publicly available upon acceptance.

Junjie Yang, Tianlong Chen, Xuxi Chen et al.

Neural networks have demonstrated success in various domains, yet their performance can be significantly degraded by even a small input perturbation. Consequently, the construction of such perturbations, known as adversarial attacks, has gained significant attention, many of which fall within "white-box" scenarios where we have full access to the neural network. Existing attack algorithms, such as the projected gradient descent (PGD), commonly take the sign function on the raw gradient before updating adversarial inputs, thereby neglecting gradient magnitude information. In this paper, we present a theoretical analysis of how such sign-based update algorithm influences step-wise attack performance, as well as its caveat. We also interpret why previous attempts of directly using raw gradients failed. Based on that, we further propose a new raw gradient descent (RGD) algorithm that eliminates the use of sign. Specifically, we convert the constrained optimization problem into an unconstrained one, by introducing a new hidden variable of non-clipped perturbation that can move beyond the constraint. The effectiveness of the proposed RGD algorithm has been demonstrated extensively in experiments, outperforming PGD and other competitors in various settings, without incurring any additional computational overhead. The codes is available in https://github.com/JunjieYang97/RGD.

Guibin Zhang, Xiangguo Sun, Yanwei Yue et al.

Graph Neural Networks (GNNs) have demonstrated superior performance across various graph learning tasks but face significant computational challenges when applied to large-scale graphs. One effective approach to mitigate these challenges is graph sparsification, which involves removing non-essential edges to reduce computational overhead. However, previous graph sparsification methods often rely on a single global sparsity setting and uniform pruning criteria, failing to provide customized sparsification schemes for each node's complex local context. In this paper, we introduce Mixture-of-Graphs (MoG), leveraging the concept of Mixture-of-Experts (MoE), to dynamically select tailored pruning solutions for each node. Specifically, MoG incorporates multiple sparsifier experts, each characterized by unique sparsity levels and pruning criteria, and selects the appropriate experts for each node. Subsequently, MoG performs a mixture of the sparse graphs produced by different experts on the Grassmann manifold to derive an optimal sparse graph. One notable property of MoG is its entirely local nature, as it depends on the specific circumstances of each individual node. Extensive experiments on four large-scale OGB datasets and two superpixel datasets, equipped with five GNN backbones, demonstrate that MoG (I) identifies subgraphs at higher sparsity levels ($8.67\%\sim 50.85\%$), with performance equal to or better than the dense graph, (II) achieves $1.47-2.62\times$ speedup in GNN inference with negligible performance drop, and (III) boosts ``top-student'' GNN performance ($1.02\%\uparrow$ on RevGNN+\textsc{ogbn-proteins} and $1.74\%\uparrow$ on DeeperGCN+\textsc{ogbg-ppa}).

Guibin Zhang, Yanwei Yue, Kun Wang et al.

Graph Neural Networks (GNNs) excel in various graph learning tasks but face computational challenges when applied to large-scale graphs. A promising solution is to remove non-essential edges to reduce the computational overheads in GNN. Previous literature generally falls into two categories: topology-guided and semantic-guided. The former maintains certain graph topological properties yet often underperforms on GNNs due to low integration with neural network training. The latter performs well at lower sparsity on GNNs but faces performance collapse at higher sparsity levels. With this in mind, we take the first step to propose a new research line and concept termed Graph Sparse Training (GST), which dynamically manipulates sparsity at the data level. Specifically, GST initially constructs a topology & semantic anchor at a low training cost, followed by performing dynamic sparse training to align the sparse graph with the anchor. We introduce the Equilibria Sparsification Principle to guide this process, effectively balancing the preservation of both topological and semantic information. Ultimately, GST produces a sparse graph with maximum topological integrity and no performance degradation. Extensive experiments on 6 datasets and 5 backbones showcase that GST (I) identifies subgraphs at higher graph sparsity levels (1.67%~15.85% $\uparrow$) than state-of-the-art sparsification methods, (II) preserves more key spectral properties, (III) achieves 1.27-3.42$\times$ speedup in GNN inference and (IV) successfully helps graph adversarial defense and graph lottery tickets.

Zhen Tan, Song Wang, Yifan Li et al.

Post-hoc explanation methods provide interpretation by attributing predictions to input features. Natural explanations are expected to interpret how the inputs lead to the predictions. Thus, a fundamental question arises: Do these explanations unintentionally reverse the natural relationship between inputs and outputs? Specifically, are the explanations rationalizing predictions from the output rather than reflecting the true decision process? To investigate such explanatory inversion, we propose Inversion Quantification (IQ), a framework that quantifies the degree to which explanations rely on outputs and deviate from faithful input-output relationships. Using the framework, we demonstrate on synthetic datasets that widely used methods such as LIME and SHAP are prone to such inversion, particularly in the presence of spurious correlations, across tabular, image, and text domains. Finally, we propose Reproduce-by-Poking (RBP), a simple and model-agnostic enhancement to post-hoc explanation methods that integrates forward perturbation checks. We further show that under the IQ framework, RBP theoretically guarantees the mitigation of explanatory inversion. Empirically, for example, on the synthesized data, RBP can reduce the inversion by 1.8% on average across iconic post-hoc explanation approaches and domains.