Yihang Gao

Jiarui Ouyang, Yihui Wang, Yihang Gao et al.

Spatial Transcriptomics (ST) offers spatially resolved gene expression but remains costly. Predicting expression directly from widely available Hematoxylin and Eosin (H&E) stained images presents a cost-effective alternative. However, most computational approaches (i) predict each gene independently, overlooking co-expression structure, and (ii) cast the task as continuous regression despite expression being discrete counts. This mismatch can yield biologically implausible outputs and complicate downstream analyses. We introduce GenAR, a multi-scale autoregressive framework that refines predictions from coarse to fine. GenAR clusters genes into hierarchical groups to expose cross-gene dependencies, models expression as codebook-free discrete token generation to directly predict raw counts, and conditions decoding on fused histological and spatial embeddings. From an information-theoretic perspective, the discrete formulation avoids log-induced biases and the coarse-to-fine factorization aligns with a principled conditional decomposition. Extensive experimental results on four Spatial Transcriptomics datasets across different tissue types demonstrate that GenAR achieves state-of-the-art performance, offering potential implications for precision medicine and cost-effective molecular profiling. Code is publicly available at https://github.com/oyjr/genar.

Chuanyang Zheng, Yihang Gao, Han Shi et al.

Positional encoding plays a crucial role in transformers, significantly impacting model performance and length generalization. Prior research has introduced absolute positional encoding (APE) and relative positional encoding (RPE) to distinguish token positions in given sequences. However, both APE and RPE remain fixed after model training regardless of input data, limiting their adaptability and flexibility. Hence, we expect that the desired positional encoding should be data-adaptive and can be dynamically adjusted with the given attention. In this paper, we propose a Data-Adaptive Positional Encoding (DAPE) method, which dynamically and semantically adjusts based on input context and learned fixed priors. Experimental validation on real-world datasets (Arxiv, Books3, and CHE) demonstrates that DAPE enhances model performances in terms of trained length and length generalization, where the improvements are statistically significant. The model visualization suggests that our model can keep both local and anti-local information. Finally, we successfully train the model on sequence length 128 and achieve better performance at evaluation sequence length 8192, compared with other static positional encoding methods, revealing the benefit of the adaptive positional encoding method.

Guoxuan Chen, Han Shi, Jiawei Li et al.

Large Language Models (LLMs) have exhibited exceptional performance across a spectrum of natural language processing tasks. However, their substantial sizes pose considerable challenges, particularly in computational demands and inference speed, due to their quadratic complexity. In this work, we have identified a key pattern: certain seemingly meaningless separator tokens (i.e., punctuations) contribute disproportionately to attention scores compared to semantically meaningful tokens. This observation suggests that information of the segments between these separator tokens can be effectively condensed into the separator tokens themselves without significant information loss. Guided by this insight, we introduce SepLLM, a plug-and-play framework that accelerates inference by compressing these segments and eliminating redundant tokens. Additionally, we implement efficient kernels for training acceleration. Experimental results across training-free, training-from-scratch, and post-training settings demonstrate SepLLM's effectiveness. Notably, using the Llama-3-8B backbone, SepLLM achieves over 50% reduction in KV cache on the GSM8K-CoT benchmark while maintaining comparable performance. Furthermore, in streaming settings, SepLLM effectively processes sequences of up to 4 million tokens or more while maintaining consistent language modeling capabilities.

Chuanyang Zheng, Yihang Gao, Guoxuan Chen et al.

The softmax function is crucial in Transformer attention, which normalizes each row of the attention scores with summation to one, achieving superior performances over other alternative functions. However, the softmax function can face a gradient vanishing issue when some elements of the attention scores approach extreme values, such as probabilities close to one or zero. In this paper, we propose Self-Adjust Softmax (SA-Softmax) to address this issue by modifying $softmax(x)$ to $x \cdot softmax(x)$ and its normalized variant $\frac{(x - min(x_{\min},0))}{max(0,x_{max})-min(x_{min},0)} \cdot softmax(x)$. We theoretically show that SA-Softmax provides enhanced gradient properties compared to the vanilla softmax function. Moreover, SA-Softmax Attention can be seamlessly integrated into existing Transformer models to their attention mechanisms with minor adjustments. We conducted experiments to evaluate the empirical performance of Transformer models using SA-Softmax compared to the vanilla softmax function. These experiments, involving models with up to 2.7 billion parameters, are conducted across diverse datasets, language tasks, and positional encoding methods.

Yihang Gao, Michael K. Ng, Vincent Y. F. Tan

Kolmogorov--Arnold networks (KANs) have demonstrated their potential as an alternative to multi-layer perceptions (MLPs) in various domains, especially for science-related tasks. However, transfer learning of KANs remains a relatively unexplored area. In this paper, inspired by Tucker decomposition of tensors and evidence on the low tensor-rank structure in KAN parameter updates, we develop low tensor-rank adaptation (LoTRA) for fine-tuning KANs. We study the expressiveness of LoTRA based on Tucker decomposition approximations. Furthermore, we provide a theoretical analysis to select the learning rates for each LoTRA component to enable efficient training. Our analysis also shows that using identical learning rates across all components leads to inefficient training, highlighting the need for an adaptive learning rate strategy. Beyond theoretical insights, we explore the application of LoTRA for efficiently solving various partial differential equations (PDEs) by fine-tuning KANs. Additionally, we propose Slim KANs that incorporate the inherent low-tensor-rank properties of KAN parameter tensors to reduce model size while maintaining superior performance. Experimental results validate the efficacy of the proposed learning rate selection strategy and demonstrate the effectiveness of LoTRA for transfer learning of KANs in solving PDEs. Further evaluations on Slim KANs for function representation and image classification tasks highlight the expressiveness of LoTRA and the potential for parameter reduction through low tensor-rank decomposition.

Yihang Gao, Michael K. Ng, Michael W. Mahoney et al.

We study online statistical inference for the solutions of stochastic optimization problems with equality and inequality constraints. Such problems are prevalent in statistics and machine learning, encompassing constrained $M$-estimation, physics-informed models, safe reinforcement learning, and algorithmic fairness. We develop a stochastic sequential quadratic programming (SSQP) method to solve these problems, where the step direction is computed by sequentially performing a quadratic approximation of the objective and a linear approximation of the constraints. Despite having access to unbiased estimates of population gradients, a key challenge in constrained stochastic problems lies in dealing with the bias in the step direction. As such, we apply a momentum-style gradient moving-average technique within SSQP to debias the step. We show that our method achieves global almost-sure convergence and exhibits local asymptotic normality with an optimal primal-dual limiting covariance matrix in the sense of Hájek and Le Cam. In addition, we provide a plug-in covariance matrix estimator for practical inference. To our knowledge, the proposed SSQP method is the first fully online method that attains primal-dual asymptotic minimax optimality without relying on projection operators onto the constraint set, which are generally intractable for nonlinear problems. Through extensive experiments on benchmark nonlinear problems, as well as on constrained generalized linear models and portfolio allocation problems using both synthetic and real data, we demonstrate superior performance of our method, showing that the method and its asymptotic behavior not only solve constrained stochastic problems efficiently but also provide valid and practical online inference in real-world applications.

Chuanyang Zheng, Jiankai Sun, Yihang Gao et al.

The attention mechanism is a core component of the Transformer architecture. Various methods have been developed to compute attention scores, including multi-head attention (MHA), multi-query attention, group-query attention and so on. We further analyze the MHA and observe that its performance improves as the number of attention heads increases, provided the hidden size per head remains sufficiently large. Therefore, increasing both the head count and hidden size per head with minimal parameter overhead can lead to significant performance gains at a low cost. Motivated by this insight, we introduce Simulated Attention Score (SAS), which maintains a compact model size while simulating a larger number of attention heads and hidden feature dimension per head. This is achieved by projecting a low-dimensional head representation into a higher-dimensional space, effectively increasing attention capacity without increasing parameter count. Beyond the head representations, we further extend the simulation approach to feature dimension of the key and query embeddings, enhancing expressiveness by mimicking the behavior of a larger model while preserving the original model size. To control the parameter cost, we also propose Parameter-Efficient Attention Aggregation (PEAA). Comprehensive experiments on a variety of datasets and tasks demonstrate the effectiveness of the proposed SAS method, achieving significant improvements over different attention variants.

Yihang Gao, Vincent Y. F. Tan

In this paper, we propose SubLoRA, a rank determination method for Low-Rank Adaptation (LoRA) based on submodular function maximization. In contrast to prior approaches, such as AdaLoRA, that rely on first-order (linearized) approximations of the loss function, SubLoRA utilizes second-order information to capture the potentially complex loss landscape by incorporating the Hessian matrix. We show that the linearization becomes inaccurate and ill-conditioned when the LoRA parameters have been well optimized, motivating the need for a more reliable and nuanced second-order formulation. To this end, we reformulate the rank determination problem as a combinatorial optimization problem with a quadratic objective. However, solving this problem exactly is NP-hard in general. To overcome the computational challenge, we introduce a submodular function maximization framework and devise a greedy algorithm with approximation guarantees. We derive a sufficient and necessary condition under which the rank-determination objective becomes submodular, and construct a closed-form projection of the Hessian matrix that satisfies this condition while maintaining computational efficiency. Our method combines solid theoretical foundations, second-order accuracy, and practical computational efficiency. We further extend SubLoRA to a joint optimization setting, alternating between LoRA parameter updates and rank determination under a rank budget constraint. Extensive experiments on fine-tuning physics-informed neural networks (PINNs) for solving partial differential equations (PDEs) demonstrate the effectiveness of our approach. Results show that SubLoRA outperforms existing methods in both rank determination and joint training performance.

Yihang Gao, Michael K. Ng

In this paper, we study a physics-informed algorithm for Wasserstein Generative Adversarial Networks (WGANs) for uncertainty quantification in solutions of partial differential equations. By using groupsort activation functions in adversarial network discriminators, network generators are utilized to learn the uncertainty in solutions of partial differential equations observed from the initial/boundary data. Under mild assumptions, we show that the generalization error of the computed generator converges to the approximation error of the network with high probability, when the number of samples are sufficiently taken. According to our established error bound, we also find that our physics-informed WGANs have higher requirement for the capacity of discriminators than that of generators. Numerical results on synthetic examples of partial differential equations are reported to validate our theoretical results and demonstrate how uncertainty quantification can be obtained for solutions of partial differential equations and the distributions of initial/boundary data. However, the quality or the accuracy of the uncertainty quantification theory in all the points in the interior is still the theoretical vacancy, and required for further research.

Yihang Gao, Michael K. Ng, Mingjie Zhou

Studied here are Wasserstein generative adversarial networks (WGANs) with GroupSort neural networks as their discriminators. It is shown that the error bound of the approximation for the target distribution depends on the width and depth (capacity) of the generators and discriminators and the number of samples in training. A quantified generalization bound is established for the Wasserstein distance between the generated and target distributions. According to the theoretical results, WGANs have a higher requirement for the capacity of discriminators than that of generators, which is consistent with some existing results. More importantly, the results with overly deep and wide (high-capacity) generators may be worse than those with low-capacity generators if discriminators are insufficiently strong. Numerical results obtained using Swiss roll and MNIST datasets confirm the theoretical results.