Gilad Lerman

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35ranked-venue papers
3as first author
12since 2021 · last 2025
0000-0003-4624-3115ORCID · verified

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

Artificial intelligence and machine learning · 29 · 11 since 2021Graphics, computer vision, multimedia, augmented reality and games · 12 · 1 first-author · 5 since 2021Applied, interdisciplinary, general and emerging computing · 2 · 2 first-author
YearPublicationVenuePosition
2025 Cycle-Sync: Robust Global Camera Pose Estimation through Enhanced Cycle-Consistent Synchronization
abstract
We introduce Cycle-Sync, a robust and global framework for estimating camera poses (both rotations and locations). Our core innovation is a location solver that adapts message-passing least squares (MPLS) - originally developed for group synchronization - to the camera localization setting. We modify MPLS to emphasize cycle-consistent information, redefine cycle consistencies using estimated distances from previous iterations, and incorporate a Welsch-type robust loss. We establish the strongest known deterministic exact-recovery guarantee for camera location estimation, demonstrating that cycle consistency alone enables the lowest sample complexity to date. To further boost robustness, we introduce a plug-and-play outlier rejection module inspired by robust subspace recovery, and we fully integrate cycle consistency into MPLS for rotation averaging. Our global approach avoids the need for bundle adjustment. Experiments on synthetic and real datasets show that Cycle-Sync consistently outperforms leading pose estimators, including full structure-from-motion pipelines with bundle adjustment.
Shaohan Li, Yunpeng Shi, Gilad Lerman
NeurIPS3
2024 The effect of Leaky ReLUs on the training and generalization of overparameterized networks
abstract
We investigate the training and generalization errors of overparameterized neural networks (NNs) with a wide class of leaky rectified linear unit (ReLU) functions. More specifically, we carefully upper bound both the convergence rate of the training error and the generalization error of such NNs and investigate the dependence of these bounds on the Leaky ReLU parameter, $\alpha$. We show that $\alpha =-1$, which corresponds to the absolute value activation function, is optimal for the training error bound. Furthermore, in special settings, it is also optimal for the generalization error bound. Numerical experiments empirically support the practical choices guided by the theory.
Yinglong Guo, Shaohan Li, Gilad Lerman
AISTATS3
2024 Efficient Detection of Long Consistent Cycles and its Application to Distributed Synchronization
abstract
Group synchronization plays a crucial role in global pipelines for Structure from Motion (SfM). Its formulation is nonconvex and it is faced with highly corrupted measurements. Cycle consistency has been effective in addressing these challenges. However, computationally efficient solutions are needed for cycles longer than three, especially in practical scenarios where 3-cycles are unavailable. To overcome this computational bottleneck, we propose an algorithm for group synchronization that leverages information from cycles of lengths ranging from three to six with a time complexity of order O(n3) (or O(n2.373) when using a faster matrix multiplication algorithm). We establish non-trivial theory for this and related methods that achieves competitive sample complexity, assuming the uniform corruption model. To advocate the practical need for our method, we consider distributed group synchronization, which requires at least 4-cycles, and we illustrate state-of-the-art performance by our method in this context.
Shaohan Li, Yunpeng Shi, Gilad Lerman
CVPR3
2024 A Subspace-Constrained Tyler's Estimator and its Applications to Structure from Motion
abstract
We present the subspace-constrained Tyler's estimator (STE) designed for recovering a low-dimensional subspace within a dataset that may be highly corrupted with outliers. STE is a fusion of the Tyler's M-estimator (TME) and a variant of the fast median subspace. Our theoretical analysis suggests that, under a common inlier-outlier model, STE can effectively recover the underlying subspace, even when it contains a smaller fraction of inliers relative to other methods in the field of robust subspace recovery. We apply STE in the context of Structure from Motion (SfM) in two ways: for robust estimation of the fundamental matrix and for the removal of outlying cameras, enhancing the robustness of the SfM pipeline. Numerical experiments confirm the state-of-the-art performance of our method in these applications. This research makes significant contributions to the field of robust subspace recovery, particularly in the context of computer vision and 3D reconstruction.
Feng Yu 0016, Teng Zhang 0002, Gilad Lerman
CVPR3
2024 Improving Hyperbolic Representations via Gromov-Wasserstein Regularization
Yifei Yang 0001, Wonjun Lee 0004, Dongmian Zou, Gilad Lerman
ECCV (82)4
2024 Tensor-Based Synchronization and the Low-Rankness of the Block Trifocal Tensor
abstract
The block tensor of trifocal tensors provides crucial geometric information on the three-view geometry of a scene. The underlying synchronization problem seeks to recover camera poses (locations and orientations up to a global transformation) from the block trifocal tensor. We establish an explicit Tucker factorization of this tensor, revealing a low multilinear rank of $(6,4,4)$ independent of the number of cameras under appropriate scaling conditions. We prove that this rank constraint provides sufficient information for camera recovery in the noiseless case. The constraint motivates a synchronization algorithm based on the higher-order singular value decomposition of the block trifocal tensor. Experimental comparisons with state-of-the-art global synchronization methods on real datasets demonstrate the potential of this algorithm for significantly improving location estimation accuracy. Overall this work suggests that higher-order interactions in synchronization problems can be exploited to improve performance, beyond the usual pairwise-based approaches.
Daniel Miao, Gilad Lerman, Joe Kileel 0001
NeurIPS2
2023 An Unpooling Layer for Graph Generation
abstract
We propose a novel and trainable graph unpooling layer for effective graph generation. The unpooling layer receives an input graph with features and outputs an enlarged graph with desired structure and features. We prove that the output graph of the unpooling layer remains connected and for any connected graph there exists a series of unpooling layers that can produce it from a 3-node graph. We apply the unpooling layer within the generator of a generative adversarial network as well as the decoder of a variational autoencoder. We give extensive experimental evidence demonstrating the competitive performance of our proposed method on synthetic and real data.
Yinglong Guo, Dongmian Zou, Gilad Lerman
AISTATS3
2023 Robust Variational Autoencoding with Wasserstein Penalty for Novelty Detection
abstract
We propose a new method for novelty detection that can tolerate high corruption of the training points, whereas previous works assumed either no or very low corruption. Our method trains a robust variational autoencoder (VAE), which aims to generate a model for the uncorrupted training points. To gain robustness to high corruption, we incorporate the following four changes to the common VAE: 1. Extracting crucial features of the latent code by a carefully designed dimension reduction component for distributions; 2. Modeling the latent distribution as a mixture of Gaussian low-rank inliers and full-rank outliers, where the testing only uses the inlier model; 3. Applying the Wasserstein-1 metric for regularization, instead of the Kullback-Leibler (KL) divergence; and 4. Using a robust error for reconstruction. We establish both robustness to outliers and suitability to low-rank modeling of the Wasserstein metric as opposed to the KL divergence. We illustrate state-of-the-art results on standard benchmarks.
Chieh-Hsin Lai, Dongmian Zou, Gilad Lerman
AISTATS3
2023 Depth Descent Synchronization in ${{\,\mathrm{\text {SO}}\,}}(D)$
Tyler Maunu, Gilad Lerman
Int. J. Comput. Vis.2
2022 Fast, Accurate and Memory-Efficient Partial Permutation Synchronization
abstract
Previous partial permutation synchronization (PPS) algorithms, which are commonly used for multi-object matching, often involve computation-intensive and memory-demanding matrix operations. These operations become intractable for large scale structure-from-motion datasets. For pure permutation synchronization, the recent Cycle-Edge Message Passing (CEMP) framework suggests a memory-efficient and fast solution. Here we overcome the restriction of CEMP to compact groups and propose an improved algorithm, CEMP-Partial, for estimating the corruption levels of the observed partial permutations. It allows us to subsequently implement a nonconvex weighted projected power method without the need of spectral initialization. The resulting new PPS algorithm, MatchFAME (Fast, Accurate and Memory-Efficient Matching), only involves sparse matrix operations, and thus enjoys lower time and space complexities in comparison to previous PPS algorithms. We prove that under adversarial corruption, though without additive noise and with certain assumptions, CEMP-Partial is able to exactly classify corrupted and clean partial permutations. We demonstrate the state-of-the-art accuracy, speed and memory efficiency of our method on both synthetic and real datasets.
Shaohan Li, Yunpeng Shi, Gilad Lerman
CVPR3
2022 Robust Group Synchronization via Quadratic Programming
abstract
We propose a novel quadratic programming formulation for estimating the corruption levels in group synchronization, and use these estimates to solve this problem. Our objective function exploits the cycle consistency of the group and we thus refer to our method as detection and estimation of structural consistency (DESC). This general framework can be extended to other algebraic and geometric structures. Our formulation has the following advantages: it can tolerate corruption as high as the information-theoretic bound, it does not require a good initialization for the estimates of group elements, it has a simple interpretation, and under some mild conditions the global minimum of our objective function exactly recovers the corruption levels. We demonstrate the competitive accuracy of our approach on both synthetic and real data experiments of rotation averaging.
Yunpeng Shi, Cole Wyeth, Gilad Lerman
ICML3
2021 Scalable Cluster-Consistency Statistics for Robust Multi-Object Matching
abstract
We develop new statistics for robustly filtering corrupted keypoint matches in the structure from motion pipeline. The statistics are based on consistency constraints that arise within the clustered structure of the graph of keypoint matches. The statistics are designed to give smaller values to corrupted matches and than uncorrupted matches. These new statistics are combined with an iterative reweighting scheme to filter keypoints, which can then be fed into any standard structure from motion pipeline. This filtering method can be efficiently implemented and scaled to massive datasets as it only requires sparse matrix multiplication. We demonstrate the efficacy of this method on synthetic and real structure from motion datasets and show that it achieves state-of-the-art accuracy and speed in these tasks.
Yunpeng Shi, Shaohan Li, Tyler Maunu, Gilad Lerman
3DV4
2020 Robust Subspace Recovery Layer for Unsupervised Anomaly Detection
Chieh-Hsin Lai, Dongmian Zou, Gilad Lerman
ICLR3
2020 Message Passing Least Squares Framework and its Application to Rotation Synchronization
abstract
We propose an efficient algorithm for solving group synchronization under high levels of corruption and noise, while we focus on rotation synchronization. We first describe our recent theoretically guaranteed message passing algorithm that estimates the corruption levels of the measured group ratios. We then propose a novel reweighted least squares method to estimate the group elements, where the weights are initialized and iteratively updated using the estimated corruption levels. We demonstrate the superior performance of our algorithm over state-of-the-art methods for rotation synchronization using both synthetic and real data.
Yunpeng Shi, Gilad Lerman
ICML2
2020 Robust Multi-Object Matching via Iterative Reweighting of the Graph Connection Laplacian
abstract
We propose an efficient and robust iterative solution to the multi-object matching problem. We first clarify serious limitations of current methods as well as the inappropriateness of the standard iteratively reweighted least squares procedure. In view of these limitations, we suggest a novel and more reliable iterative reweighting strategy that incorporates information from higher-order neighborhoods by exploiting the graph connection Laplacian. We demonstrate the superior performance of our procedure over state-of-the-art methods using both synthetic and real datasets.
Yunpeng Shi, Shaohan Li, Gilad Lerman
NeurIPS3
2020 Solving Jigsaw Puzzles by the Graph Connection Laplacian
abstract
We propose a novel mathematical framework to address the problem of automatically solving large jigsaw puzzles. This problem assumes a large image, which is cut into equal square pieces that are arbitrarily rotated and shuffled, and asks to recover the original image given the transformed pieces. The main contribution of this work is a method for recovering the rotations of the pieces when both shuffles and rotations are unknown. A major challenge of this procedure is estimating the graph connection Laplacian without the knowledge of shuffles. A careful combination of our proposed method for estimating rotations with any existing method for estimating shuffles results in a practical solution for the jigsaw puzzle problem. Our theory guarantees, in a clean setting, that our basic idea of recovering rotations is robust to some corruption of the connection graph. Numerical experiments demonstrate the competitive accuracy of this solution, its robustness to corruption, and its computational advantage for large puzzles.
Vahan Huroyan, Gilad Lerman, Hau-Tieng Wu
SIAM J. Imaging Sci.2
2019 Encoding robust representation for graph generation
abstract
Generative networks have made it possible to generate meaningful signals such as images and texts from simple noise. Recently, generative methods based on GAN and VAE were developed for graphs and graph signals. However, the mathematical properties of these methods are unclear, and training good generative models is difficult. This work proposes a graph generation model that uses a recent adaptation of Mallat's scattering transform to graphs. The proposed model is naturally composed of an encoder and a decoder. The encoder is a Gaussianized graph scattering transform, which is robust to signal and graph manipulation. The decoder is a simple fully connected network that is adapted to specific tasks, such as link prediction, signal generation on graphs and full graph and signal generation. The training of our proposed system is efficient since it is only applied to the decoder and the hardware requirements are moderate. Numerical results demonstrate state-of-the-art performance of the proposed system for both link prediction and graph and signal generation.
Dongmian Zou, Gilad Lerman
IJCNN2
2019 A Well-Tempered Landscape for Non-convex Robust Subspace Recovery
abstract
We present a mathematical analysis of a non-convex energy landscape for robust subspace recovery. We prove that an underlying subspace is the only stationary point and local minimizer in a specified neighborhood under a deterministic condition on a dataset. If the deterministic condition is satisfied, we further show that a geodesic gradient descent method over the Grassmannian manifold can exactly recover the underlying subspace when the method is properly initialized. Proper initialization by principal component analysis is guaranteed with a simple deterministic condition. Under slightly stronger assumptions, the gradient descent method with a piecewise constant step-size scheme achieves linear convergence. The practicality of the deterministic condition is demonstrated on some statistical models of data, and the method achieves almost state-of-the-art recovery guarantees on the Haystack Model for different regimes of sample size and ambient dimension. In particular, when the ambient dimension is fixed and the sample size is large enough, we show that our gradient method can exactly recover the underlying subspace for any fixed fraction of outliers (less than 1).
Tyler Maunu, Teng Zhang 0002, Gilad Lerman
J. Mach. Learn. Res.3
2018 Estimation of Camera Locations in Highly Corrupted Scenarios: All About That Base, No Shape Trouble
abstract
We propose a strategy for improving camera location estimation in structure from motion. Our setting assumes highly corrupted pairwise directions (i.e., normalized relative location vectors), so there is a clear room for improving current state-of-the-art solutions for this problem. Our strategy identifies severely corrupted pairwise directions by using a geometric consistency condition. It then selects a cleaner set of pairwise directions as a preprocessing step for common solvers. We theoretically guarantee the successful performance of a basic version of our strategy under a synthetic corruption model. Numerical results on artificial and real data demonstrate the significant improvement obtained by our strategy.
Yunpeng Shi, Gilad Lerman
CVPR2
2018 An Overview of Robust Subspace Recovery
abstract
This paper will serve as an introduction to the body of work on robust subspace recovery. Robust subspace recovery involves finding an underlying low-dimensional subspace in a data set that is possibly corrupted with outliers. While this problem is easy to state, it has been difficult to develop optimal algorithms due to its underlying nonconvexity. This work emphasizes advantages and disadvantages of proposed approaches and unsolved problems in the area.
Gilad Lerman, Tyler Maunu
Proc. IEEE1
2018 Exact Camera Location Recovery by Least Unsquared Deviations
abstract
We establish exact recovery for the Least Unsquared Deviations (LUD) algorithm of Özyeşil and Singer. More precisely, we show that for sufficiently many cameras with given corrupted pairwise directions, where both camera locations and pairwise directions are generated by a special probabilistic model, the LUD algorithm exactly recovers the camera locations with high probability. A similar exact recovery guarantee for camera locations was established for the ShapeFit algorithm by Hand, Lee, and Voroninski, but with typically less corruption.
Gilad Lerman, Yunpeng Shi, Teng Zhang 0002
SIAM J. Imaging Sci.1
2017 Spectral Clustering Based on Local PCA
abstract
We propose a spectral clustering method based on local principal components analysis (PCA). After performing local PCA in selected neighborhoods, the algorithm builds a nearest neighbor graph weighted according to a discrepancy between the principal subspaces in the neighborhoods, and then applies spectral clustering. As opposed to standard spectral methods based solely on pairwise distances between points, our algorithm is able to resolve intersections. We establish theoretical guarantees for simpler variants within a prototypical mathematical framework for multi-manifold clustering, and evaluate our algorithm on various simulated data sets.
Ery Arias-Castro, Gilad Lerman, Teng Zhang 0002
J. Mach. Learn. Res.2
2016 Enhancing feature tracking with gyro regularization
Bryan Poling, Gilad Lerman
Image Vis. Comput.2
2015 Multi-Manifold Modeling in Non-Euclidean spaces
abstract
This paper advocates a novel framework for segmenting a dataset on a Riemannian manifold M into clusters lying around low-dimensional submanifolds of M. Important examples of M, for which the proposed algorithm is computationally efficient, include the sphere, the set of positive definite matrices, and the Grassmannian. The proposed algorithm constructs a data-affinity matrix by thoroughly exploiting the intrinsic geometry and then applies spectral clustering. Local geometry is encoded by sparse coding and directional information of local tangent spaces and geodesics, which is important in resolving intersecting clusters and establishing the theoretical guarantees for a simplified variant of the algorithm. To avoid complication, these guarantees assume that the underlying submanifolds are geodesic. Extensive validation on synthetic and real data demonstrates the resiliency of the proposed method against deviations from the theoretical (geodesic) model as well as its superior performance over state-of-the-art techniques.
Xu Wang 0066, Konstantinos Slavakis, Gilad Lerman
AISTATS3
2014 Robust Stochastic Principal Component Analysis
abstract
We consider the problem of finding lower dimensional subspaces in the presence of outliers and noise in the online setting. In particular, we extend previous batch formulations of robust PCA to the stochastic setting with minimal storage requirements and runtime complexity. We introduce three novel stochastic approximation algorithms for robust PCA that are extensions of standard algorithms for PCA - the stochastic power method, incremental PCA and online PCA using matrix-exponentiated-gradient (MEG) updates. For robust online PCA we also give a sub-linear convergence guarantee. Our numerical results demonstrate the superiority of the the robust online method over the other robust stochastic methods and the advantage of robust methods over their non-robust counterparts in the presence of outliers in artificial and real scenarios.
John Goes, Teng Zhang 0002, Raman Arora, Gilad Lerman
AISTATS4
2014 Better Feature Tracking through Subspace Constraints
abstract
Feature tracking in video is a crucial task in computer vision. Usually, the tracking problem is handled one feature at a time, using a single-feature tracker like the Kanade-Lucas-Tomasi algorithm, or one of its derivatives. While this approach works quite well when dealing with high-quality video and "strong" features, it often falters when faced with dark and noisy video containing low-quality features. We present a framework for jointly tracking a set of features, which enables sharing information between the different features in the scene. We show that our method can be employed to track features for both rigid and non-rigid motions (possibly of few moving bodies) even when some features are occluded. Furthermore, it can be used to significantly improve tracking results in poorly-lit scenes (where there is a mix of good and bad features). Our approach does not require direct modeling of the structure or the motion of the scene, and runs in real time on a single CPU core.
Bryan Poling, Gilad Lerman, Arthur Szlam
CVPR2
2014 A New Approach to Two-View Motion Segmentation Using Global Dimension Minimization
Bryan Poling, Gilad Lerman
Int. J. Comput. Vis.2
2014 A novel M-estimator for robust PCA
Teng Zhang 0002, Gilad Lerman
J. Mach. Learn. Res.2
2013 Fast Subspace Search via Grassmannian Based Hashing
abstract
The problem of efficiently deciding which of a database of models is most similar to a given input query arises throughout modern computer vision. Motivated by applications in recognition, image retrieval and optimization, there has been significant recent interest in the variant of this problem in which the database models are linear subspaces and the input is either a point or a subspace. Current approaches to this problem have poor scaling in high dimensions, and may not guarantee sub linear query complexity. We present a new approach to approximate nearest subspace search, based on a simple, new locality sensitive hash for subspaces. Our approach allows point-to-subspace query for a database of subspaces of arbitrary dimension d, in a time that depends sub linearly on the number of subspaces in the database. The query complexity of our algorithm is linear in the ambient dimension D, allowing it to be directly applied to high-dimensional imagery data. Numerical experiments on model problems in image repatching and automatic face recognition confirm the advantages of our algorithm in terms of both speed and accuracy.
Xu Wang 0066, Stefan Atev, John Wright 0001, Gilad Lerman
ICCV4
2013 Robust Locally Linear Analysis with Applications to Image Denoising and Blind Inpainting
abstract
We study the related problems of denoising images corrupted by impulsive noise and blind inpainting (i.e., inpainting when the deteriorated region is unknown). Our basic approach is to model the set of patches of pixels in an image as a union of low-dimensional subspaces, corrupted by sparse but perhaps large magnitude noise. For this purpose, we develop a robust and iterative method for single subspace modeling and extend it to an iterative algorithm for modeling multiple subspaces. We prove convergence for both algorithms and carefully compare our methods with other recent ideas for such robust modeling. We demonstrate state-of-the-art performance of our method for both imaging problems.
Yi Wang 0009, Arthur Szlam, Gilad Lerman
SIAM J. Imaging Sci.3
2012 On the Sample Complexity of Robust PCA
abstract
We estimate the sample complexity of a recent robust estimator for a generalized version of the inverse covariance matrix. This estimator is used in a convex algorithm for robust subspace recovery (i.e., robust PCA). Our model assumes a sub-Gaussian underlying distribution and an i.i.d.~sample from it. Our main result shows with high probability that the norm of the difference between the generalized inverse covariance of the underlying distribution and its estimator from an i.i.d.~sample of size $N$ is of order $O(N^{-0.5+\eps})$ for arbitrarily small $\eps>0$ (affecting the probabilistic estimate); this rate of convergence is close to one of direct covariance and inverse covariance estimation, i.e., $O(N^{-0.5})$. Our precise probabilistic estimate implies for some natural settings that the sample complexity of the generalized inverse covariance estimation when using the Frobenius norm is $O(D^{2+\delta})$ for arbitrarily small $\delta>0$ (whereas the sample complexity of direct covariance estimation with Frobenius norm is $O(D^{2})$). These results provide similar rates of convergence and sample complexity for the corresponding robust subspace recovery algorithm, which are close to those of PCA. To the best of our knowledge, this is the only work analyzing the sample complexity of any robust PCA algorithm.
Matthew Coudron, Gilad Lerman
NIPS2
2012 Hybrid Linear Modeling via Local Best-Fit Flats
abstract
We present a simple and fast geometric method for modeling data by a union of affine subspaces. The method begins by forming a collection of local best-fit affine subspaces, i.e., subspaces approximating the data in local neighborhoods. The correct sizes of the local neighborhoods are determined automatically by the Jones’ β 2 numbers (we prove under certain geometric conditions that our method finds the optimal local neighborhoods). The collection of subspaces is further processed by a greedy selection procedure or a spectral method to generate the final model. We discuss applications to tracking-based motion segmentation and clustering of faces under different illuminating conditions. We give extensive experimental evidence demonstrating the state of the art accuracy and speed of the suggested algorithms on these problems and also on synthetic hybrid linear data as well as the MNIST handwritten digits data; and we demonstrate how to use our algorithms for fast determination of the number of affine subspaces.
Teng Zhang 0002, Arthur Szlam, Yi Wang 0009, Gilad Lerman
Int. J. Comput. Vis.4
2010 Randomized hybrid linear modeling by local best-fit flats
abstract
The hybrid linear modeling problem is to identify a set of d-dimensional affine sets in RD. It arises, for example, in object tracking and structure from motion. The hybrid linear model can be considered as the second simplest (behind linear) manifold model of data. In this paper we will present a very simple geometric method for hybrid linear modeling based on selecting a set of local best fit flats that minimize a global ℓ1error measure. The size of the local neighborhoods is determined automatically by the Jones' β2numbers; it is proven under certain geometric conditions that good local neighborhoods exist and are found by our method. We also demonstrate how to use this algorithm for fast determination of the number of affine subspaces. We give extensive experimental evidence demonstrating the state of the art accuracy and speed of the algorithm on synthetic and real hybrid linear data.
Teng Zhang 0002, Arthur Szlam, Yi Wang 0009, Gilad Lerman
CVPR4
2009 Spectral Curvature Clustering (SCC)
abstract
This paper presents novel techniques for improving the performance of a multi-way spectral clustering framework (Govindu in Proceedings of the 2005 IEEE Computer Society Conference on Computer Vision and Pattern Recognition (CVPR’05), vol. 1, pp. 1150–1157, 2005; Chen and Lerman, 2007, preprint in the supplementary webpage) for segmenting affine subspaces. Specifically, it suggests an iterative sampling procedure to improve the uniform sampling strategy, an automatic scheme of inferring the tuning parameter from the data, a precise initialization procedure for K-means, as well as a simple strategy for isolating outliers. The resulting algorithm, Spectral Curvature Clustering (SCC), requires only linear storage and takes linear running time in the size of the data. It is supported by theory which both justifies its successful performance and guides our practical choices. We compare it with other existing methods on a few artificial instances of affine subspaces. Application of the algorithm to several real-world problems is also discussed.
Guangliang Chen, Gilad Lerman
Int. J. Comput. Vis.2
2007 Functional genomics via multiscale analysis: application to gene expression and ChIP-on-chip data
abstract
UNLABELLED: We present a fast, versatile and adaptive-multiscale algorithm for analyzing a wide-variety of DNA microarray data. Its primary application is in normalization of array data as well as subsequent identification of 'enriched targets', e.g. differentially expressed genes in expression profiling arrays and enriched sites in ChIP-on-chip experimental data. We show how to accommodate the unique characteristics of ChIP-on-chip data, where the set of 'enriched targets' is large, asymmetric and whose proportion to the whole data varies locally. SUPPLEMENTARY INFORMATION: Supplementary figures, related preprint, free software as well as our raw DNA microarray data with PCR validations are available at http://www.math.umn.edu/~lerman/supp/bioinfo06 as well as Bioinformatics online.
Gilad Lerman, Joseph McQuown, Alexandre Blais, Brian D. Dynlacht, Guangliang Chen, Bud Mishra
Bioinform.1