arXiv subjects

Jiaxing He

Publications and source records attributed to Jiaxing He.

8 recordsLinked to original sources

arXiv2026

G-LoG Bi-filtration for Medical Image Classification

Building practical filtrations on objects to detect topological and geometric features is an important task in the field of Topological Data Analysis (TDA). In this paper, leveraging the ability of the Laplacian of Gaussian operator to enhance the boundaries of medical images, we define the G-LoG (Gaussian-Laplacian of Gaussian) bi-filtration to generate the features more suitable for multi-parameter persistence module. By modeling volumetric images as bounded functions, then we prove the interleaving distance on the persistence modules obtained from our bi-filtrations on the bounded functions is stable with respect to the maximum norm of the bounded functions. Finally, we conduct experiments on the MedMNIST dataset, comparing our bi-filtration against single-parameter filtration and the established deep learning baselines, including Google AutoML Vision, ResNet, AutoKeras and auto-sklearn. Experiments results demonstrate that our bi-filtration significantly outperforms single-parameter filtration. Notably, a simple Multi-Layer Perceptron (MLP) trained on the topological features generated by our bi-filtration achieves performance comparable to complex deep learning models trained on the original dataset.

cs.CV↗

arXiv2025

Persistence modules induced by inner functions

As well-known, inner functions play an important role in the study of bounded analytic function theory. In recent years, persistence module theory, as a main tool applied to Topological Data Analysis, has received widespread attention. In this paper, we aim to use persistence module theory to study inner functions. We introduce the persistence modules arised from the level sets of inner functions. Some properties of these persistence modules are shown. In particular, we prove that the persistence modules (potentially not of locally finite type) induced by a class of inner functions have interval module decompositions. Furthermore, we demonstrate that the interleaving distance of the persistence modules is continuous with respect to the supremum norm for a class of Blaschke products, which could be used to discuss the path-connectedness of Blaschke products. As an example, we provide an explicit formula for the interleaving distance of the persistence modules induced by the Blaschke products with order two.

math.AT↗

arXiv2025

Graph Generative Pre-trained Transformer

Graph generation is a critical task in numerous domains, including molecular design and social network analysis, due to its ability to model complex relationships and structured data. While most modern graph generative models utilize adjacency matrix representations, this work revisits an alternative approach that represents graphs as sequences of node set and edge set. We advocate for this approach due to its efficient encoding of graphs and propose a novel representation. Based on this representation, we introduce the Graph Generative Pre-trained Transformer (G2PT), an auto-regressive model that learns graph structures via next-token prediction. To further exploit G2PT's capabilities as a general-purpose foundation model, we explore fine-tuning strategies for two downstream applications: goal-oriented generation and graph property prediction. We conduct extensive experiments across multiple datasets. Results indicate that G2PT achieves superior generative performance on both generic graph and molecule datasets. Furthermore, G2PT exhibits strong adaptability and versatility in downstream tasks from molecular design to property prediction. Code available at https://github.com/tufts-ml/G2PT,

cs.LG↗

arXiv2025

Large Language Model is Secretly a Protein Sequence Optimizer

We consider the protein sequence engineering problem, which aims to find protein sequences with high fitness levels, starting from a given wild-type sequence. Directed evolution has been a dominating paradigm in this field which has an iterative process to generate variants and select via experimental feedback. We demonstrate large language models (LLMs), despite being trained on massive texts, are secretly protein sequence optimizers. With a directed evolutionary method, LLM can perform protein engineering through Pareto and experiment-budget constrained optimization, demonstrating success on both synthetic and experimental fitness landscapes.

cs.LG↗

arXiv2024

Mix-GENEO: A Flexible Filtration for Multiparameter Persistent Homology Detects Digital Images

Two important tasks in the field of Topological Data Analysis are building practical multifiltrations on objects and using TDA to detect the geometry. Motivated by the tasks, we build multiparameter filtrations by operators on images named multi-GENEO, multi-DGENEO and mix-GENEO, and we prove the stability of both the interleaving distance and multiparameter persistence landscape of multi-GENEO with respect to the pseudometric on bounded functions. We also give the estimations of upper bound for multi-DGENEO and mix-GENEO. In practical applications, we regard image as a discrete function space, and then we build multifiltrations on the discrete function space. Finally, we construct comparable experiment on MNIST dataset to demonstrate our bifiltrations are superior to 1-parameter filtrations including lower-star filtration and upper-star filtration. For instance, 6 and 9 can be distinguished by our bifiltrations, while they cannot be distinguished by 1-parameter filtrations. The experiment results demonstrate our bifiltrations have ability to detect geometric and topological differences of digital images.

cs.CV↗

arXiv2024

Stable Similarity Comparison of Persistent Homology Groups

Classification in the sense of similarity is an important issue. In this paper, we study similarity classification in Topological Data Analysis. We define a pseudometric $d_{S}^{(p)}$ to measure the distance between barcodes generated by persistent homology groups of topological spaces, and we provide that our pseudometric $d_{S}^{(2)}$ is a similarity invariant. Thereby, we establish a connection between Operator Theory and Topological Data Analysis. We give the calculation formula of the pseudometric $d_{S}^{(2)}$ $(d_{S}^{(1)})$ by arranging all eigenvalues of matrices determined by barcodes in descending order to get the infimum over all matchings. Since conformal linear transformation is one representative type of similarity transformations, we construct comparative experiments on both synthetic datasets and waves from an online platform to demonstrate that our pseudometric $d_{S}^{(2)}$ $(d_{S}^{(1)})$ is stable under conformal linear transformations, whereas the bottleneck and Wasserstein distances are not. In particular, our pseudometric on waves is only related to the waveform but is independent on the frequency and amplitude. Furthermore, the computation time for $d_{S}^{(2)}$ $(d_{S}^{(1)})$ is significantly less than the computation time for bottleneck distance and is comparable to the computation time for accelerated Wasserstein distance between barcodes.

math.AT↗

arXiv2024

GraphCroc: Cross-Correlation Autoencoder for Graph Structural Reconstruction

Graph-structured data is integral to many applications, prompting the development of various graph representation methods. Graph autoencoders (GAEs), in particular, reconstruct graph structures from node embeddings. Current GAE models primarily utilize self-correlation to represent graph structures and focus on node-level tasks, often overlooking multi-graph scenarios. Our theoretical analysis indicates that self-correlation generally falls short in accurately representing specific graph features such as islands, symmetrical structures, and directional edges, particularly in smaller or multiple graph contexts. To address these limitations, we introduce a cross-correlation mechanism that significantly enhances the GAE representational capabilities. Additionally, we propose GraphCroc, a new GAE that supports flexible encoder architectures tailored for various downstream tasks and ensures robust structural reconstruction, through a mirrored encoding-decoding process. This model also tackles the challenge of representation bias during optimization by implementing a loss-balancing strategy. Both theoretical analysis and numerical evaluations demonstrate that our methodology significantly outperforms existing self-correlation-based GAEs in graph structure reconstruction.

cs.LG↗

arXiv2023

Efficient and Degree-Guided Graph Generation via Discrete Diffusion Modeling

Diffusion-based generative graph models have been proven effective in generating high-quality small graphs. However, they need to be more scalable for generating large graphs containing thousands of nodes desiring graph statistics. In this work, we propose EDGE, a new diffusion-based generative graph model that addresses generative tasks with large graphs. To improve computation efficiency, we encourage graph sparsity by using a discrete diffusion process that randomly removes edges at each time step and finally obtains an empty graph. EDGE only focuses on a portion of nodes in the graph at each denoising step. It makes much fewer edge predictions than previous diffusion-based models. Moreover, EDGE admits explicitly modeling the node degrees of the graphs, further improving the model performance. The empirical study shows that EDGE is much more efficient than competing methods and can generate large graphs with thousands of nodes. It also outperforms baseline models in generation quality: graphs generated by our approach have more similar graph statistics to those of the training graphs.

cs.LG↗