Author name cluster

Yan Cui

Possible papers associated with this exact author name in Arrow. This page groups case-insensitive exact name matches and is not a full identity disambiguation profile.

6 papers

2 author rows

AAAI Conference 2026 Conference Paper

Gene Incremental Learning for Single-Cell Transcriptomics

Jiaxin Qi
Yan Cui
Jianqiang Huang
Gaogang Xie

Classes, as fundamental elements of Computer Vision, have been extensively studied within incremental learning frameworks. In contrast, tokens, which play essential roles in many research fields, exhibit similar characteristics of growth, yet investigations into their incremental learning remain significantly scarce. This research gap primarily stems from the holistic nature of tokens in language, which imposes significant challenges on the design of incremental learning frameworks for them. To overcome this obstacle, in this work, we turn to a type of token, gene, for a large-scale biological dataset—single-cell transcriptomics—to formulate a pipeline for gene incremental learning and establish corresponding evaluations. We found that the forgetting problem also exists in gene incremental learning, thus we adapted existing class incremental learning methods to mitigate the forgetting of genes. Through extensive experiments, we demonstrated the soundness of our framework design and evaluations, as well as the effectiveness of the method adaptations. Finally, we provide a complete benchmark for gene incremental learning in single-cell transcriptomics.

PDF Details DOI

AAAI Conference 2025 Conference Paper

A Simple and Comprehensive Benchmark for Single-Cell Transcriptomics

Jiaxin Qi
Yan Cui
Kailei Guo
Xiaomin Zhang
Jianqiang Huang
Gaogang Xie

Single-cell transcriptomics describes complex molecular features at the individual cell level, serving various roles in biological research, such as enhancing gene expression and predicting drug responses. Due to transcriptomic data structurally resembling sequential data, many researchers have trained numerous transformers on extensive transcriptomic datasets. However, they have consistently neglected to explore the intrinsic properties of the data and the appropriateness of their chosen model architecture. In this paper, we carefully investigate the nature of transcriptomics, identifying three overlooked problems: 1) long-tailed data problem, 2) model selection problem, and 3) evaluation problem. Consequently, by applying the weighted sampling strategy, we address the long-tailed data problem and achieve consistent improvement across all settings. By adapting different model structures to transcriptomic data, we discover that transformers are not the only option. By developing three downstream tasks and fair evaluation metrics, we establish a simple and comprehensive benchmark to validate the effectiveness of models for transcriptomics. Through extensive experiments, we clarify the misunderstandings in the traditional methods and provide competitive baselines, thereby paving the way for future research in this field.

PDF Details DOI

IROS Conference 2024 Conference Paper

Event-intensity Stereo with Cross-modal Fusion and Contrast

Yuanbo Wang
Shanglai Qu
Tianyu Meng
Yan Cui
Haiyin Piao
Xiaopeng Wei
Xin Yang 0011

For binocular stereo, traditional cameras excel in capturing fine details and texture information but are limited in terms of dynamic range and their ability to handle rapid motion. On the contrary, event cameras provide pixel-level intensity changes with low latency and a wide dynamic range, albeit at the cost of less detail in their output. It is natural to leverage the strengths of both modalities. We solve this problem by introducing a cross-modal fusion module that learns a visual representation from both sensor inputs. Additionally, we extract and compare dense event-intensity stereo pair features by contrasting “pairs of event-intensity pairs from different views and different modalities and different timestamps”. This provides the flexibility in masking hard negatives and enables networks to effectively combine event-intensity signals within a contrastive learning framework, leading to an improved matching accuracy and facilitating more accurate estimation of disparity. Experimental results validate the effectiveness of our model and the improvement of disparity estimation accuracy.

Details

YNIMG Journal 2021 Journal Article

Computational exploration of dynamic mechanisms of steady state visual evoked potentials at the whole brain level

Ge Zhang
Yan Cui
Yangsong Zhang
Hefei Cao
Guanyu Zhou
Haifeng Shu
Dezhong Yao
Yang Xia

Periodic visual stimulation can induce stable steady-state visual evoked potentials (SSVEPs) distributed in multiple brain regions and has potential applications in both neural engineering and cognitive neuroscience. However, the underlying dynamic mechanisms of SSVEPs at the whole-brain level are still not completely understood. Here, we addressed this issue by simulating the rich dynamics of SSVEPs with a large-scale brain model designed with constraints of neuroimaging data acquired from the human brain. By eliciting activity of the occipital areas using an external periodic stimulus, our model was capable of replicating both the spatial distributions and response features of SSVEPs that were observed in experiments. In particular, we confirmed that alpha-band (8–12 Hz) stimulation could evoke stronger SSVEP responses; this frequency sensitivity was due to nonlinear entrainment and resonance, and could be modulated by endogenous factors in the brain. Interestingly, the stimulus-evoked brain networks also exhibited significant superiority in topological properties near this frequency-sensitivity range, and stronger SSVEP responses were demonstrated to be supported by more efficient functional connectivity at the neural activity level. These findings not only provide insights into the mechanistic understanding of SSVEPs at the whole-brain level but also indicate a bright future for large-scale brain modeling in characterizing the complicated dynamics and functions of the brain.

Details DOI

YNIMG Journal 2021 Journal Article

State-independent and state-dependent patterns in the rat default mode network

Wei Jing
Yang Xia
Min Li
Yan Cui
Mingming Chen
Miaomiao Xue
Daqing Guo
Bharat B. Biswal

Resting-state studies have typically assumed constant functional connectivity (FC) between brain regions, and these parameters of interest provide meaningful descriptions of the functional organization of the brain. A number of studies have recently provided evidence pointing to dynamic FC fluctuations in the resting brain, especially in higher-order regions such as the default mode network (DMN). The neural activities underlying dynamic FC remain poorly understood. Here, we recorded electrophysiological signals from DMN regions in freely behaving rats. The dynamic FCs between signals within the DMN were estimated by the phase locking value (PLV) method with sliding time windows across vigilance states [quiet wakefulness (QW) and slow-wave and rapid eye movement sleep (SWS and REMS)]. Factor analysis was then performed to reveal the hidden patterns within the DMN. We identified distinct spatial FC patterns according to the similarities between their temporal dynamics. Interestingly, some of these patterns were vigilance state-dependent, while others were independent across states. The temporal contributions of these patterns fluctuated over time, and their interactive relationships were different across vigilance states. These spatial patterns with dynamic temporal contributions and combinations may offer a flexible framework for efficiently integrating information to support cognition and behavior. These findings provide novel insights into the dynamic functional organization of the rat DMN.

Details DOI

JBHI Journal 2019 Journal Article

Identifying Brain Networks at Multiple Time Scales via Deep Recurrent Neural Network

Yan Cui
Shijie Zhao
Han Wang
Li Xie
Yaowu Chen
Junwei Han
Lei Guo
Fan Zhou

For decades, task functional magnetic resonance imaging has been a powerful noninvasive tool to explore the organizational architecture of human brain function. Researchers have developed a variety of brain network analysis methods for task fMRI data, including the general linear model, independent component analysis, and sparse representation methods. However, these shallow models are limited in faithful reconstruction and modeling of the hierarchical and temporal structures of brain networks, as demonstrated in more and more studies. Recently, recurrent neural networks (RNNs) exhibit great ability of modeling hierarchical and temporal dependence features in the machine learning field, which might be suitable for task fMRI data modeling. To explore such possible advantages of RNNs for task fMRI data, we propose a novel framework of a deep recurrent neural network (DRNN) to model the functional brain networks from task fMRI data. Experimental results on the motor task fMRI data of Human Connectome Project 900 subjects release demonstrated that the proposed DRNN can not only faithfully reconstruct functional brain networks, but also identify more meaningful brain networks with multiple time scales which are overlooked by traditional shallow models. In general, this work provides an effective and powerful approach to identifying functional brain networks at multiple time scales from task fMRI data.

Details DOI