Ruili Feng

dblp:20/9594 · DBLP profile ↗
← Back
20ranked-venue papers
7as first author
19since 2021 · last 2025
0000-0001-9463-8045ORCID · corroborated

Domains — the database's venue-derived domains; a paper can count in several

Artificial intelligence and machine learning · 19 · 7 first-author · 19 since 2021Graphics, computer vision, multimedia, augmented reality and games · 6 · 2 first-author · 6 since 2021Applied, interdisciplinary, general and emerging computing · 1
YearPublicationVenuePosition
2025 BACON: Improving Clarity of Image Captions via Bag-of-Concept Graphs
abstract
Advancements in large Vision-Language Models have brought precise, accurate image captioning, vital for advancing multi-modal image understanding and processing. Yet these captions often carry lengthy, intertwined contexts that are difficult to parse and frequently overlook essential cues, posing a great barrier for models like GroundingDINO and SDXL, which lack the strong text encoding and syntax analysis needed to fully leverage dense captions. To address this, we propose BACON, a prompting method that breaks down VLM-generated captions into disentangled, structured elements such as objects, relationships, styles, and themes. This approach not only minimizes confusion from handling complex contexts but also allows for efficient transfer into a JSON dictionary, enabling models without linguistic processing capabilities to easily access key information. We annotated 100,000 image-caption pairs using BACON with GPT-4V and trained an LLaVA captioner on this dataset, enabling it to produce BACON-style captions without relying on costly GPT-4V. Evaluations of overall quality, precision, and recall—as well as user studies—demonstrate that the resulting caption model consistently outperforms other SOTA VLM models in generating high-quality captions. Besides, we show that BACON-style captions exhibit better clarity when applied to various models, enabling them to accomplish previously unattainable tasks or surpass existing SOTA solutions without training. For example, BACON-style captions help GroundingDINO achieve 1.51× higher recall scores on open-vocabulary object detection tasks compared to leading methods.
Zhantao Yang, Ruili Feng, Huangji Wang, Zhicai Wang, Shangwen Zhu, Han Zhang 0010, Jie Xiao 0002, Pingyu Wu, Kai Zhu 0004, Jixuan Chen, Chen-Wei Xie, Hongyang Zhang 0001, Yu Liu 0063, Fan Cheng 0002
CVPR2
2025 The Matrix: Infinite-Horizon World Generation with Real-Time Moving Control
abstract
We present The Matrix, a foundational realistic world simulator capable of generating infinitely long 720p high-fidelity real-scene video streams with real-time, responsive control in both first- and third-person perspectives. Trained on limited supervised data from video games like Forza Horizon 5 and Cyberpunk 2077, complemented by large-scale unsupervised footage from real-world settings like Tokyo streets, The Matrix allows users to traverse diverse terrains—deserts, grasslands, water bodies, and urban landscapes—in continuous, uncut hour-long sequences. With speeds of up to 16 FPS, the system supports real-time interactivity and demonstrates zero-shot generalization, translating virtual game environments to real-world contexts where collecting continuous movement data is often infeasible. For example, The Matrix can simulate a BMW X3 driving through an office setting—an environment present in neither gaming data nor real-world sources. This approach showcases the potential of game data to advance robust world models, bridging the gap between simulations and real-world applications in scenarios with limited data.
Ruili Feng, Han Zhang 0010, Zhilei Shu, Zhantao Yang, Longxiang Tang, Zhicai Wang, Andy Zheng, Jie Xiao 0002, Ruihang Chu, Yu Liu 0063, Hongyang Zhang 0001
NeurIPS1
2024 DreamClean: Restoring Clean Image Using Deep Diffusion Prior
abstract
Image restoration poses a garners substantial interest due to the exponential surge in demands for recovering high-quality images from diverse mobile camera devices, adverse lighting conditions, suboptimal shooting environments, and frequent image compression for efficient transmission purposes. Yet this problem gathers significant challenges as people are blind to the type of restoration the images suffer, which, is usually the case in real-day scenarios and is most urgent to solve for this field. Current research, however, heavily relies on prior knowledge of the restoration type, either explicitly through rules or implicitly through the availability of degraded-clean image pairs to define the restoration process, and consumes considerable effort to collect image pairs of vast degradation types. This paper introduces DreamClean, a training-free method that needs no degradation prior knowledge but yields high-fidelity and generality towards various types of image degradation. DreamClean embeds the degraded image back to the latent of pre-trained diffusion models and re-sample it through a carefully designed diffusion process that mimics those generating clean images. Thanks to the rich image prior in diffusion models and our novel Variance Preservation Sampling (VPS) technique, DreamClean manages to handle various different degradation types at one time and reaches far more satisfied final quality than previous competitors. DreamClean relies on elegant theoretical supports to assure its convergence to clean image when VPS has appropriate parameters, and also enjoys superior experimental performance over various challenging tasks that could be overwhelming for previous methods when degradation prior is unavailable.
Jie Xiao 0002, Ruili Feng, Han Zhang 0010, Zhantao Yang, Yurui Zhu, Xueyang Fu, Kai Zhu 0004, Yu Liu 0063, Zhengjun Zha
ICLR2
2024 Lipschitz Singularities in Diffusion Models
abstract
Diffusion models, which employ stochastic differential equations to sample images through integrals, have emerged as a dominant class of generative models. However, the rationality of the diffusion process itself receives limited attention, leaving the question of whether the problem is well-posed and well-conditioned. In this paper, we uncover a vexing propensity of diffusion models: they frequently exhibit the infinite Lipschitz near the zero point of timesteps. We provide theoretical proofs to illustrate the presence of infinite Lipschitz constants and empirical results to confirm it. The Lipschitz singularities pose a threat to the stability and accuracy during both the training and inference processes of diffusion models. Therefore, the mitigation of Lipschitz singularities holds great potential for enhancing the performance of diffusion models. To address this challenge, we propose a novel approach, dubbed E-TSDM, which alleviates the Lipschitz singularities of the diffusion model near the zero point. Remarkably, our technique yields a substantial improvement in performance. Moreover, as a byproduct of our method, we achieve a dramatic reduction in the Fréchet Inception Distance of acceleration methods relying on network Lipschitz, including DDIM and DPM-Solver, by over 33\%. Extensive experiments on diverse datasets validate our theory and method. Our work may advance the understanding of the general diffusion process, and also provide insights for the design of diffusion models.
Zhantao Yang, Ruili Feng, Han Zhang 0010, Yujun Shen, Kai Zhu 0004, Lianghua Huang, Yu Liu 0063, Deli Zhao, Jingren Zhou 0001, Fan Cheng 0002
ICLR2
2024 CCM: Real-Time Controllable Visual Content Creation Using Text-to-Image Consistency Models
abstract
Consistency Models (CMs) have showed a promise in creating high-quality images with few steps. However, the way to add new conditional controls to the pre-trained CMs has not been explored. In this paper, we explore the pivotal subject of leveraging the generative capacity and efficiency of consistency models to facilitate controllable visual content creation via ControlNet. First, it is observed that ControlNet trained for diffusion models (DMs) can be directly applied to CMs for high-level semantic controls but sacrifice image low-level details and realism. To tackle with this issue, we develop a CMs-tailored training strategy for ControlNet using the consistency training. It is substantiated that ControlNet can be successfully established through the consistency training technique. Besides, a unified adapter can be trained utilizing the consistency training, which enhances the adaptation of DM’s ControlNet. We quantitatively and qualitatively evaluate all strategies across various conditional controls, including sketch, hed, canny, depth, human pose, low-resolution image and masked image, with the pre-trained text-to-image latent consistency models.
Jie Xiao 0002, Kai Zhu 0004, Han Zhang 0010, Yujun Shen, Zhantao Yang, Ruili Feng, Yu Liu 0063, Xueyang Fu, Zhengjun Zha
ICML7
2024 IBD-PSC: Input-level Backdoor Detection via Parameter-oriented Scaling Consistency
abstract
Deep neural networks (DNNs) are vulnerable to backdoor attacks, where adversaries can maliciously trigger model misclassifications by implanting a hidden backdoor during model training. This paper proposes a simple yet effective input-level backdoor detection (dubbed IBD-PSC) as a ‘firewall’ to filter out malicious testing images. Our method is motivated by an intriguing phenomenon, i.e., parameter-oriented scaling consistency (PSC), where the prediction confidences of poisoned samples are significantly more consistent than those of benign ones when amplifying model parameters. In particular, we provide theoretical analysis to safeguard the foundations of the PSC phenomenon. We also design an adaptive method to select BN layers to scale up for effective detection. Extensive experiments are conducted on benchmark datasets, verifying the effectiveness and efficiency of our IBD-PSC method and its resistance to adaptive attacks. Codes are available at https://github.com/THUYimingLi/BackdoorBox.
Linshan Hou, Ruili Feng, Zhongyun Hua, Wei Luo 0001, Leo Yu Zhang, Yiming Li 0004
ICML2
2023 Neural Dependencies Emerging from Learning Massive Categories
abstract
This work presents two astonishing findings on neural networks learned for large-scale image classification. 1) Given a well-trained model, the logits predicted for some category can be directly obtained by linearly combining the predictions of a few other categories, which we call neural dependency. 2) Neural dependencies exist not only within a single model, but even between two independently learned models, regardless of their architectures. Towards a theoretical analysis of such phenomena, we demonstrate that identifying neural dependencies is equivalent to solving the Covariance Lasso (CovLasso) regression problem proposed in this paper. Through investigating the properties of the problem solution, we confirm that neural dependency is guaranteed by a redundant logit covariance matrix, which condition is easily met given massive categories, and that neural dependency is highly sparse, implying that one category correlates to only a few others. We further empirically show the potential of neural dependencies in understanding internal data correlations, generalizing models to unseen categories, and improving model robustness with a dependency-derived regularizer. Code to reproduce the results in this paper is available at https://github.com/RuiLiFengiNeural-Dependencies.
Ruili Feng, Kecheng Zheng, Kai Zhu 0004, Yujun Shen, Jian Zhao 0018, Deli Zhao, Jingren Zhou 0001, Michael I. Jordan, Zhengjun Zha
CVPR1
2023 Dimensionality-Varying Diffusion Process
abstract
Diffusion models, which learn to reverse a signal destruction process to generate new data, typically require the signal at each step to have the same dimension. We argue that, considering the spatial redundancy in image signals, there is no need to maintain a high dimensionality in the evolution process, especially in the early generation phase. To this end, we make a theoretical generalization of the forward diffusion process via signal decomposition. Concretely, we manage to decompose an image into multiple orthogonal components and control the attenuation of each component when perturbing the image. That way, along with the noise strength increasing, we are able to diminish those inconsequential components and thus use a lower-dimensional signal to represent the source, barely losing information. Such a reformulation allows to vary dimensions in both training and inference of diffusion models. Extensive experiments on a range of datasets suggest that our approach substantially reduces the computational cost and achieves on-par or even better synthesis performance compared to baseline methods. We also show that our strategy facilitates high-resolution image synthesis and improves FID of diffusion model trained on FFHQ at$1024\times 1024$resolution from 52.40 to 10.46. Code is available at https://github.com/damo-vilab/dvdp.
Han Zhang 0010, Ruili Feng, Zhantao Yang, Lianghua Huang, Yu Liu 0063, Yujun Shen, Deli Zhao, Jingren Zhou 0001, Fan Cheng 0002
CVPR2
2023 Self-Organizing Pathway Expansion for Non-Exemplar Class-Incremental Learning
abstract
Non-exemplar class-incremental learning aims to recognize both the old and new classes without access to old class samples. The conflict between old and new class optimization is exacerbated since the shared neural pathways can only be differentiated by the incremental samples. To address this problem, we propose a novel self-organizing pathway expansion scheme. Our scheme consists of a class-specific pathway organization strategy that reduces the coupling of optimization pathway among different classes to enhance the independence of the feature representation, and a pathway-guided feature optimization mechanism to mitigate the update interference between the old and new classes. Extensive experiments on four datasets demonstrate significant performance gains, outperforming the state-of-the-art methods by a margin of 1%, 3%, 2% and 2%, respectively.
Kai Zhu 0004, Kecheng Zheng, Ruili Feng, Deli Zhao, Yang Cao 0010, Zhengjun Zha
ICCV3
2023 Regularized Mask Tuning: Uncovering Hidden Knowledge in Pre-trained Vision-Language Models
abstract
Prompt tuning and adapter tuning have shown great potential in transferring pre-trained vision-language models (VLMs) to various downstream tasks. In this work, we design a new type of tuning method, termed as regularized mask tuning, which masks the network parameters through a learnable selection. Inspired by neural pathways, we argue that the knowledge required by a downstream task already exists in the pre-trained weights but just gets concealed in the upstream pre-training stage. To bring the useful knowledge back into light, we first identify a set of parameters that are important to a given downstream task, then attach a binary mask to each parameter, and finally optimize these masks on the downstream data with the parameters frozen. When updating the mask, we introduce a novel gradient dropout strategy to regularize the parameter selection, in order to prevent the model from forgetting old knowledge and overfitting the downstream data. Experimental results on 11 datasets demonstrate the consistent superiority of our method over previous alternatives. It is noteworthy that we manage to deliver 18.73% performance improvement compared to the zero-shot CLIP via masking an average of only 2.56% parameters. Furthermore, our method is synergistic with most existing parameter-efficient tuning methods and can boost the performance on top of them. Project page can be found here.
Kecheng Zheng, Ruili Feng, Kai Zhu 0004, Jiawei Liu 0001, Deli Zhao, Zhengjun Zha, Wei Chen 0001, Yujun Shen
ICCV3
2023 Cones: Concept Neurons in Diffusion Models for Customized Generation
abstract
Human brains respond to semantic features of presented stimuli with different neurons. This raises the question of whether deep neural networks admit a similar behavior pattern. To investigate this phenomenon, this paper identifies a small cluster of neurons associated with a specific subject in a diffusion model. We call those neurons the concept neurons. They can be identified by statistics of network gradients to a stimulation connected with the given subject. The concept neurons demonstrate magnetic properties in interpreting and manipulating generation results. Shutting them can directly yield the related subject contextualized in different scenes. Concatenating multiple clusters of concept neurons can vividly generate all related concepts in a single image. Our method attains impressive performance for multi-subject customization, even four or more subjects. For large-scale applications, the concept neurons are environmentally friendly as we only need to store a sparse cluster of int index instead of dense float32 parameter values, reducing storage consumption by 90% compared with previous customized generation methods. Extensive qualitative and quantitative studies on diverse scenarios show the superiority of our method in interpreting and manipulating diffusion models.
Ruili Feng, Kai Zhu 0004, Kecheng Zheng, Yu Liu 0063, Deli Zhao, Jingren Zhou 0001, Yang Cao 0010
ICML2
2023 DIFFER: Decomposing Individual Reward for Fair Experience Replay in Multi-Agent Reinforcement Learning
abstract
Cooperative multi-agent reinforcement learning (MARL) is a challenging task, as agents must learn complex and diverse individual strategies from a shared team reward. However, existing methods struggle to distinguish and exploit important individual experiences, as they lack an effective way to decompose the team reward into individual rewards. To address this challenge, we propose DIFFER, a powerful theoretical framework for decomposing individual rewards to enable fair experience replay in MARL. By enforcing the invariance of network gradients, we establish a partial differential equation whose solution yields the underlying individual reward function. The individual TD-error can then be computed from the solved closed-form individual rewards, indicating the importance of each piece of experience in the learning task and guiding the training process. Our method elegantly achieves an equivalence to the original learning framework when individual experiences are homogeneous, while also adapting to achieve more muscular efficiency and fairness when diversity is observed. Our extensive experiments on popular benchmarks validate the effectiveness of our theory and method, demonstrating significant improvements in learning efficiency and fairness. Code is available in supplement material.
Xunhan Hu, Jian Zhao 0018, Wengang Zhou 0001, Ruili Feng, Houqiang Li
NeurIPS4
2023 Customizable Image Synthesis with Multiple Subjects
abstract
Synthesizing images with user-specified subjects has received growing attention due to its practical applications. Despite the recent success in single subject customization, existing algorithms suffer from high training cost and low success rate along with increased number of subjects. Towards controllable image synthesis with multiple subjects as the constraints, this work studies how to efficiently represent a particular subject as well as how to appropriately compose different subjects. We find that the text embedding regarding the subject token already serves as a simple yet effective representation that supports arbitrary combinations without any model tuning. Through learning a residual on top of the base embedding, we manage to robustly shift the raw subject to the customized subject given various text conditions. We then propose to employ layout, a very abstract and easy-to-obtain prior, as the spatial guidance for subject arrangement. By rectifying the activations in the cross-attention map, the layout appoints and separates the location of different subjects in the image, significantly alleviating the interference across them. Using cross-attention map as the intermediary, we could strengthen the signal of target subjects and weaken the signal of irrelevant subjects within a certain region, significantly alleviating the interference across subjects. Both qualitative and quantitative experimental results demonstrate our superiority over state-of-the-art alternatives under a variety of settings for multi-subject customization.
Yujun Shen, Kecheng Zheng, Kai Zhu 0004, Ruili Feng, Yu Liu 0063, Deli Zhao, Jingren Zhou 0001, Yang Cao 0010
NeurIPS6
2022 Weakly Supervised High-Fidelity Clothing Model Generation
abstract
The development of online economics arouses the demand of generating images of models on product clothes, to display new clothes and promote sales. However, the expensive proprietary model images challenge the existing image virtual try-on methods in this scenario, as most of them need to be trained on considerable amounts of model images accompanied with paired clothes images. In this paper, we propose a cheap yet scalable weakly-supervised method called Deep Generative Projection (DGP) to address this specific scenario. Lying in the heart of the proposed method is to imitate the process of human predicting the wearing effect, which is an unsupervised imagination based on life experience rather than computation rules learned from supervisions. Here a pretrained StyleGAN is used to capture the practical experience of wearing. Experiments show that projecting the rough alignment of clothing and body onto the StyleGAN space can yield photo-realistic wearing results. Experiments on real scene proprietary model images demonstrate the superiority of DGP over several state-of-the-art supervised methods when generating clothing model images.
Ruili Feng, Chengji Shen, Xin Gao 0032, Zhenjiang Liu, Kairi Ou, Deli Zhao, Zhengjun Zha
CVPR1
2022 Principled Knowledge Extrapolation with GANs
abstract
Human can extrapolate well, generalize daily knowledge into unseen scenarios, raise and answer counterfactual questions. To imitate this ability via generative models, previous works have extensively studied explicitly encoding Structural Causal Models (SCMs) into architectures of generator networks. This methodology, however, limits the flexibility of the generator as they must be carefully crafted to follow the causal graph, and demands a ground truth SCM with strong ignorability assumption as prior, which is a nontrivial assumption in many real scenarios. Thus, many current causal GAN methods fail to generate high fidelity counterfactual results as they cannot easily leverage state-of-the-art generative models. In this paper, we propose to study counterfactual synthesis from a new perspective of knowledge extrapolation, where a given knowledge dimension of the data distribution is extrapolated, but the remaining knowledge is kept indistinguishable from the original distribution. We show that an adversarial game with a closed-form discriminator can be used to address the knowledge extrapolation problem, and a novel principal knowledge descent method can efficiently estimate the extrapolated distribution through the adversarial game. Our method enjoys both elegant theoretical guarantees and superior performance in many scenarios.
Ruili Feng, Jie Xiao 0002, Kecheng Zheng, Deli Zhao, Jingren Zhou 0001, Qibin Sun, Zhengjun Zha
ICML1
2022 Rank Diminishing in Deep Neural Networks
abstract
The rank of neural networks measures information flowing across layers. It is an instance of a key structural condition that applies across broad domains of machine learning. In particular, the assumption of low-rank feature representations led to algorithmic developments in many architectures. For neural networks, however, the intrinsic mechanism that yields low-rank structures remains vague and unclear. To fill this gap, we perform a rigorous study on the behavior of network rank, focusing particularly on the notion of rank deficiency. We theoretically establish a universal monotone decreasing property of network ranks from the basic rules of differential and algebraic composition, and uncover rank deficiency of network blocks and deep function coupling. By virtue of our numerical tools, we provide the first empirical analysis of the per-layer behavior of network ranks in realistic settings, \ieno, ResNets, deep MLPs, and Transformers on ImageNet. These empirical results are in direct accord with our theory. Furthermore, we reveal a novel phenomenon of independence deficit caused by the rank deficiency of deep networks, where classification confidence of a given category can be linearly decided by the confidence of a handful of other categories. The theoretical results of this work, together with the empirical findings, may advance understanding of the inherent principles of deep neural networks. Code to detect the rank behavior of networks can be found in https://github.com/RuiLiFeng/Rank-Diminishing-in-Deep-Neural-Networks.
Ruili Feng, Kecheng Zheng, Deli Zhao, Michael I. Jordan, Zhengjun Zha
NeurIPS1
2021 Uncertainty Principles of Encoding GANs
abstract
The compelling synthesis results of Generative Adversarial Networks (GANs) demonstrate rich semantic knowledge in their latent codes. To obtain this knowledge for downstream applications, encoding GANs has been proposed to learn encoders, such that real world data can be encoded to latent codes, which can be fed to generators to reconstruct those data. However, despite the theoretical guarantees of precise reconstruction in previous works, current algorithms generally reconstruct inputs with non-negligible deviations from inputs. In this paper we study this predicament of encoding GANs, which is indispensable research for the GAN community. We prove three uncertainty principles of encoding GANs in practice: a) the ‘perfect’ encoder and generator cannot be continuous at the same time, which implies that current framework of encoding GANs is ill-posed and needs rethinking; b) neural networks cannot approximate the underlying encoder and generator precisely at the same time, which explains why we cannot get ‘perfect’ encoders and generators as promised in previous theories; c) neural networks cannot be stable and accurate at the same time, which demonstrates the difficulty of training and trade-off between fidelity and disentanglement encountered in previous works. Our work may eliminate gaps between previous theories and empirical results, promote the understanding of GANs, and guide network designs for follow-up works.
Ruili Feng, Zhouchen Lin, Jiapeng Zhu 0001, Deli Zhao, Jingren Zhou 0001, Zhengjun Zha
ICML1
2021 Understanding Noise Injection in GANs
abstract
Noise injection is an effective way of circumventing overfitting and enhancing generalization in machine learning, the rationale of which has been validated in deep learning as well. Recently, noise injection exhibits surprising effectiveness when generating high-fidelity images in Generative Adversarial Networks (GANs) (e.g. StyleGAN). Despite its successful applications in GANs, the mechanism of its validity is still unclear. In this paper, we propose a geometric framework to theoretically analyze the role of noise injection in GANs. First, we point out the existence of the adversarial dimension trap inherent in GANs, which leads to the difficulty of learning a proper generator. Second, we successfully model the noise injection framework with exponential maps based on Riemannian geometry. Guided by our theories, we propose a general geometric realization for noise injection. Under our novel framework, the simple noise injection used in StyleGAN reduces to the Euclidean case. The goal of our work is to make theoretical steps towards understanding the underlying mechanism of state-of-the-art GAN algorithms. Experiments on image generation and GAN inversion validate our theory in practice.
Ruili Feng, Deli Zhao, Zhengjun Zha
ICML1
2021 Low-Rank Subspaces in GANs
abstract
The latent space of a Generative Adversarial Network (GAN) has been shown to encode rich semantics within some subspaces. To identify these subspaces, researchers typically analyze the statistical information from a collection of synthesized data, and the identified subspaces tend to control image attributes globally (i.e., manipulating an attribute causes the change of an entire image). By contrast, this work introduces low-rank subspaces that enable more precise control of GAN generation. Concretely, given an arbitrary image and a region of interest (e.g., eyes of face images), we manage to relate the latent space to the image region with the Jacobian matrix and then use low-rank factorization to discover steerable latent subspaces. There are three distinguishable strengths of our approach that can be aptly called LowRankGAN. First, compared to analytic algorithms in prior work, our low-rank factorization of Jacobians is able to find the low-dimensional representation of attribute manifold, making image editing more precise and controllable. Second, low-rank factorization naturally yields a null space of attributes such that moving the latent code within it only affects the outer region of interest. Therefore, local image editing can be simply achieved by projecting an attribute vector into the null space without relying on a spatial mask as existing methods do. Third, our method can robustly work with a local region from one image for analysis yet well generalize to other images, making it much easy to use in practice. Extensive experiments on state-of-the-art GAN models (including StyleGAN2 and BigGAN) trained on various datasets demonstrate the effectiveness of our LowRankGAN.
Jiapeng Zhu 0001, Ruili Feng, Yujun Shen, Deli Zhao, Zhengjun Zha, Jingren Zhou 0001, Qifeng Chen 0001
NeurIPS2
2011 CASCADE_SCAN: mining signal transduction network from high-throughput data based on steepest descent method
abstract
BACKGROUND: Signal transduction is an essential biological process involved in cell response to environment changes, by which extracellular signaling initiates intracellular signaling. Many computational methods have been generated in mining signal transduction networks with the increasing of high-throughput genomic and proteomic data. However, more effective means are still needed to understand the complex mechanisms of signaling pathways. RESULTS: We propose a new approach, namely CASCADE_SCAN, for mining signal transduction networks from high-throughput data based on the steepest descent method using indirect protein-protein interactions (PPIs). This method is useful for actual biological application since the given proteins utilized are no longer confined to membrane receptors or transcription factors as in existing methods. The precision and recall values of CASCADE_SCAN are comparable with those of other existing methods. Moreover, functional enrichment analysis of the network components supported the reliability of the results. CONCLUSIONS: CASCADE_SCAN is a more suitable method than existing methods for detecting underlying signaling pathways where the membrane receptors or transcription factors are unknown, providing significant insight into the mechanism of cellular signaling in growth, development and cancer. A new tool based on this method is freely available at http://www.genomescience.com.cn/CASCADE_SCAN/.
Kai Wang 0084, Fuyan Hu, Kejia Xu, Ruili Feng, Tieqiao Wen
BMC Bioinform.6