arXiv subjects

Zhihao Zhan

Publications and source records attributed to Zhihao Zhan.

23 records · Page 2Linked to original sources

arXiv2025

Overcoming Long-Context Limitations of State-Space Models via Context-Dependent Sparse Attention

Efficient long-context modeling remains a critical challenge for natural language processing (NLP), as the time complexity of the predominant Transformer architecture scales quadratically with the sequence length. While state-space models (SSMs) offer alternative sub-quadratic solutions, they struggle to capture long-range dependencies effectively. In this work, we focus on analyzing and improving the long-context modeling capabilities of SSMs. We show that the widely used synthetic task, associative recall, which requires a model to recall a value associated with a single key without context, insufficiently represents the complexities of real-world long-context modeling. To address this limitation, we extend the associative recall to a novel synthetic task, \emph{joint recall}, which requires a model to recall the value associated with a key given in a specified context. Theoretically, we prove that SSMs do not have the expressiveness to solve multi-query joint recall in sub-quadratic time complexity. To resolve this issue, we propose a solution based on integrating SSMs with Context-Dependent Sparse Attention (CDSA), which has the expressiveness to solve multi-query joint recall with sub-quadratic computation. To bridge the gap between theoretical analysis and real-world applications, we propose locality-sensitive Hashing Attention with sparse Key Selection (HAX), which instantiates the theoretical solution and is further tailored to natural language domains. Extensive experiments on both synthetic and real-world long-context benchmarks show that HAX consistently outperforms SSM baselines and SSMs integrated with context-independent sparse attention (CISA).

cs.LG↗

arXiv2025

A Multi-Sensor Fusion Approach for Rapid Orthoimage Generation in Large-Scale UAV Mapping

Rapid generation of large-scale orthoimages from Unmanned Aerial Vehicles (UAVs) has been a long-standing focus of research in the field of aerial mapping. A multi-sensor UAV system, integrating the Global Positioning System (GPS), Inertial Measurement Unit (IMU), 4D millimeter-wave radar and camera, can provide an effective solution to this problem. In this paper, we utilize multi-sensor data to overcome the limitations of conventional orthoimage generation methods in terms of temporal performance, system robustness, and geographic reference accuracy. A prior-pose-optimized feature matching method is introduced to enhance matching speed and accuracy, reducing the number of required features and providing precise references for the Structure from Motion (SfM) process. The proposed method exhibits robustness in low-texture scenes like farmlands, where feature matching is difficult. Experiments show that our approach achieves accurate feature matching orthoimage generation in a short time. The proposed drone system effectively aids in farmland detection and management.

cs.CV↗

arXiv2025

Cell-ontology guided transcriptome foundation model

Transcriptome foundation models TFMs hold great promises of deciphering the transcriptomic language that dictate diverse cell functions by self-supervised learning on large-scale single-cell gene expression data, and ultimately unraveling the complex mechanisms of human diseases. However, current TFMs treat cells as independent samples and ignore the taxonomic relationships between cell types, which are available in cell ontology graphs. We argue that effectively leveraging this ontology information during the TFM pre-training can improve learning biologically meaningful gene co-expression patterns while preserving TFM as a general purpose foundation model for downstream zero-shot and fine-tuning tasks. To this end, we present single cell, Cell-ontology guided TFM scCello. We introduce cell-type coherence loss and ontology alignment loss, which are minimized along with the masked gene expression prediction loss during the pre-training. The novel loss component guide scCello to learn the cell-type-specific representation and the structural relation between cell types from the cell ontology graph, respectively. We pre-trained scCello on 22 million cells from CellxGene database leveraging their cell-type labels mapped to the cell ontology graph from Open Biological and Biomedical Ontology Foundry. Our TFM demonstrates competitive generalization and transferability performance over the existing TFMs on biologically important tasks including identifying novel cell types of unseen cells, prediction of cell-type-specific marker genes, and cancer drug responses.

cs.LG↗

arXiv2025

Image Motion Blur Removal in the Temporal Dimension with Video Diffusion Models

Most motion deblurring algorithms rely on spatial-domain convolution models, which struggle with the complex, non-linear blur arising from camera shake and object motion. In contrast, we propose a novel single-image deblurring approach that treats motion blur as a temporal averaging phenomenon. Our core innovation lies in leveraging a pre-trained video diffusion transformer model to capture diverse motion dynamics within a latent space. It sidesteps explicit kernel estimation and effectively accommodates diverse motion patterns. We implement the algorithm within a diffusion-based inverse problem framework. Empirical results on synthetic and real-world datasets demonstrate that our method outperforms existing techniques in deblurring complex motion blur scenarios. This work paves the way for utilizing powerful video diffusion models to address single-image deblurring challenges.

eess.IV↗

arXiv2023

GraphVF: Controllable Protein-Specific 3D Molecule Generation with Variational Flow

Designing molecules that bind to specific target proteins is a fundamental task in drug discovery. Recent models leverage geometric constraints to generate ligand molecules that bind cohesively with specific protein pockets. However, these models cannot effectively generate 3D molecules with 2D skeletal curtailments and property constraints, which are pivotal to drug potency and development. To tackle this challenge, we propose GraphVF, a variational flow-based framework that combines 2D topology and 3D geometry, for controllable generation of binding 3D molecules. Empirically, our method achieves state-of-the-art binding affinity and realistic sub-structural layouts for protein-specific generation. In particular, GraphVF represents the first controllable geometry-aware, protein-specific molecule generation method, which can generate binding 3D molecules with tailored sub-structures and physio-chemical properties. Our code is available at https://github.com/Franco-Solis/GraphVF-code.

q-bio.BM↗