Researcher profile

Zelin Zang

Zelin Zang contributes to research discovery and scholarly infrastructure.

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Machine Learning Artificial Intelligence Biomolecules eess.SP Software Engineering

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preprint2026arXiv

CellScientist: Dual-Space Hierarchical Orchestration for Closed-Loop Refinement of Virtual Cell Models

Virtual Cell Modeling (VCM) requires models that not only predict perturbation responses, but also support targeted revision when predictions fail. Current LLM-assisted modeling workflows face a refinement-routing problem: prediction discrepancies are observed through executable implementations, but the relevant revision may involve the modeling assumption, representation design, implementation, or task constraint. Without structured feedback propagation across these levels, iterative refinement may repair code while failing to revise the assumption responsible for the discrepancy. We propose CellScientist, a dual-space hierarchical framework that couples a high-level hypothesis space with a low-level executable implementation space. CellScientist represents modeling decisions as structured states, realizes them as admissible programs under task and interface constraints, and routes execution discrepancies back to targeted hypothesis or implementation updates. This enables a closed Hypothesis -> Implementation -> Hypothesis loop where failures become structured signals for model refinement rather than debugging events. Across morphology and transcriptomic benchmarks, with additional single-cell perturbation evaluations, the final executable models selected by CellScientist improve over reference baselines under fixed split and evaluation protocols, while the workflow produces auditable refinement traces.

preprint2026arXiv

scHelix: Asymmetric Dual-Stream Integration via Explicit Gene-Level Disentanglement

A critical challenge in single-cell RNA sequencing (scRNA-seq) integration is resolving the tension between eliminating batch effects and maintaining biological fidelity. While recent evidence indicates that batch effects manifest heterogeneously across genes, most existing methods process the transcriptome uniformly, frequently resulting in over-correction and loss of subtle biological signals. To address this, we present scHelix, a dataset-adaptive framework that fundamentally changes how features are processed by explicitly partitioning genes into domain-invariant Anchors and domain-sensitive Variants at the input level. scHelix utilizes a dual-stream sparse diffusion encoder equipped with stop-gradient graph caching to efficiently learn multi-scale structural representations. The core of our approach is a novel asymmetric Align-Refine-Fuse protocol: the unstable Variant stream is first aligned to the robust topology of the Anchor stream, followed by a conservative refinement phase where the Anchor stream absorbs denoised details via bounded residual gating. This divide-and-conquer architecture prevents shortcut learning and ensures robust batch removal without compromising the integrity of biological clusters. Extensive benchmarking demonstrates that scHelix outperforms state-of-the-art methods.

preprint2024arXiv

Graph-level Protein Representation Learning by Structure Knowledge Refinement

This paper focuses on learning representation on the whole graph level in an unsupervised manner. Learning graph-level representation plays an important role in a variety of real-world issues such as molecule property prediction, protein structure feature extraction, and social network analysis. The mainstream method is utilizing contrastive learning to facilitate graph feature extraction, known as Graph Contrastive Learning (GCL). GCL, although effective, suffers from some complications in contrastive learning, such as the effect of false negative pairs. Moreover, augmentation strategies in GCL are weakly adaptive to diverse graph datasets. Motivated by these problems, we propose a novel framework called Structure Knowledge Refinement (SKR) which uses data structure to determine the probability of whether a pair is positive or negative. Meanwhile, we propose an augmentation strategy that naturally preserves the semantic meaning of the original data and is compatible with our SKR framework. Furthermore, we illustrate the effectiveness of our SKR framework through intuition and experiments. The experimental results on the tasks of graph-level classification demonstrate that our SKR framework is superior to most state-of-the-art baselines.

preprint2022arXiv

DLME: Deep Local-flatness Manifold Embedding

Manifold learning (ML) aims to seek low-dimensional embedding from high-dimensional data. The problem is challenging on real-world datasets, especially with under-sampling data, and we find that previous methods perform poorly in this case. Generally, ML methods first transform input data into a low-dimensional embedding space to maintain the data's geometric structure and subsequently perform downstream tasks therein. The poor local connectivity of under-sampling data in the former step and inappropriate optimization objectives in the latter step leads to two problems: structural distortion and underconstrained embedding. This paper proposes a novel ML framework named Deep Local-flatness Manifold Embedding (DLME) to solve these problems. The proposed DLME constructs semantic manifolds by data augmentation and overcomes the structural distortion problem using a smoothness constrained based on a local flatness assumption about the manifold. To overcome the underconstrained embedding problem, we design a loss and theoretically demonstrate that it leads to a more suitable embedding based on the local flatness. Experiments on three types of datasets (toy, biological, and image) for various downstream tasks (classification, clustering, and visualization) show that our proposed DLME outperforms state-of-the-art ML and contrastive learning methods.

preprint2022arXiv

Surrogate Representation Learning with Isometric Mapping for Gray-box Graph Adversarial Attacks

Gray-box graph attacks aim at disrupting the performance of the victim model by using inconspicuous attacks with limited knowledge of the victim model. The parameters of the victim model and the labels of the test nodes are invisible to the attacker. To obtain the gradient on the node attributes or graph structure, the attacker constructs an imaginary surrogate model trained under supervision. However, there is a lack of discussion on the training of surrogate models and the robustness of provided gradient information. The general node classification model loses the topology of the nodes on the graph, which is, in fact, an exploitable prior for the attacker. This paper investigates the effect of representation learning of surrogate models on the transferability of gray-box graph adversarial attacks. To reserve the topology in the surrogate embedding, we propose Surrogate Representation Learning with Isometric Mapping (SRLIM). By using Isometric mapping method, our proposed SRLIM can constrain the topological structure of nodes from the input layer to the embedding space, that is, to maintain the similarity of nodes in the propagation process. Experiments prove the effectiveness of our approach through the improvement in the performance of the adversarial attacks generated by the gradient-based attacker in untargeted poisoning gray-box setups.

preprint2020arXiv

Machine Learning for Predictive Deployment of UAVs with Multiple Access

In this paper, a machine learning based deployment framework of unmanned aerial vehicles (UAVs) is studied. In the considered model, UAVs are deployed as flying base stations (BS) to offload heavy traffic from ground BSs. Due to time-varying traffic distribution, a long short-term memory (LSTM) based prediction algorithm is introduced to predict the future cellular traffic. To predict the user service distribution, a KEG algorithm, which is a joint K-means and expectation maximization (EM) algorithm based on Gaussian mixture model (GMM), is proposed for determining the service area of each UAV. Based on the predicted traffic, the optimal UAV positions are derived and three multi-access techniques are compared so as to minimize the total transmit power. Simulation results show that the proposed method can reduce up to 24\% of the total power consumption compared to the conventional method without traffic prediction. Besides, rate splitting multiple access (RSMA) has the lower required transmit power compared to frequency domain multiple access (FDMA) and time domain multiple access (TDMA).

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