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sparse matrix inverse python 2020

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# sparse matrix inverse python

sparse matrix inverse python

This makes it potentially easier to interface with the python scientific stack. The approach used to generate random problem is very simple and could be improved in order to generate harder sparse LPs. A preconditioner M for a matrix A is an “approximate inverse” i.e. We would like to solve the following equation: \[\begin{equation} AX = B \end{equation}\] where \(A\), \(X\), and \(B\) are also sparse matrices. M @ A is close to the identity. We use essential cookies to perform essential website functions, e.g. This make it easier to pin down which constraint is causing problem. By converting a dense matrix into a sparse matrix it can be made to fit in the RAM. we provide an implementation of Mehrotra's Predictor-Corrector Pimal-Dual Interior Point method translated to python from, implement some presolve methods to avoid singular matrices in the interior point methods (for example, OSQP. We use optional third-party analytics cookies to understand how you use GitHub.com so we can build better products. Is it true that you want element-by-element multiplication of u' and u as opposed to normal matrix multiplication? There are primarily two types of sparse matrices that we use: CSC - Compressed Sparse Column. (Above is the printable version of this cheat sheet) Python for Data-Science Cheat Sheet : SciPy - Linear Algebra We could implement the approach used in section 6.2.1 in https://arxiv.org/pdf/1404.6770v3.pdf to generate random problems with the matlab code available here, [1] Sparse Linear Programming via Primal and Dual Augmented Coordinate Descent Ian En-Hsu Yen, Kai Zhong, Cho-Jui Hsieh, Pradeep K Ravikumar, Inderjit S Dhillon , NIPS 2015. code, [2] Diagonal preconditioning for first order primal-dual algorithms in convex optimization T. Pock and A.Chambolle ICCV 2011, [3] Distributed Optimization and Statistical Learning via the Alternating Direction Method of Multipliers Stephen Boyd Foundations and Trends in Machine Learning 2010. So here we will learn about it and along with it, we will have a look at the algorithm and then code for the conversion of the matrix to a sparse matrix. Working with Sparse Matrices 5. To estimate a probabilistic model (e.g. This library provides a python class SparseLP (in SparseLP.py) that aims at making it easier to build linear programs from python. Here are the resulting segmentations obtain with the various LP solvers, with the same random data term with the optimizations limited to 15 seconds for each solver. Sparse Matrix: Sparse Matrix is … We take inspiration from this scikit-learn example here to generate samples of a gaussian with a sparse inverse covariance (precision) matrix. From the sample we compute the empirical covariance A and the we estimate a sparse inverse covariance (precision) matrix B from that empirical covariance using the LP formulation above. create a cython binding for LPsparse [1] using scipy.sparse matrices for the interface and adding the possibility to compute the convergence curve by providing the problem known solution to the solver or by adding the possibility to define a callback to a python function. tol : float. A matrix is a two-dimensional data object made of m rows and n columns, therefore having total m x n values. Pre-trained models and datasets built by Google and the community CSR - Compressed Sparse Row. We can use writeMM function to save the sparse matrix object into a file. paper here, [11] OSQP: An Operator Splitting Solver for Quadratic Programs. You would also like to save the sparse matrix and use it later. SciPy has a module, scipy.sparse that provides functions to deal with sparse data. In this page, I would like to describe a similar tool: the sparse matrix conjugate gradient. b : {array, matrix} Right hand side of the linear system. Python scipy.sparse.linalg.spsolve() Examples ... (M,M) ndarray or sparse matrix inverse of `A` Notes ----- This computes the sparse inverse of `A`. OSQP can be executde on GPU with, GPU implementation of OSQP (can be 2 order of magnitude faster). Let b=f(B) we have f(AB)=Mb with M=kron(A, Id) Introduction to Sparse Matrix in Python Sparse matrices are memory efficient data structures that enable us store large matrices with very few non-zero elements aka sparse matrices. 2013, [7] Multiblock ADMM Methods for Linear Programming. Since [math]B[/math] is symmetric, these two nonzero entries must be equal to [math]\alpha[/math], say. square matrix to be inverted. download the GitHub extension for Visual Studio, Adaptive Primal-Dual Hybrid Gradient Methods, http://www.cs.ubc.ca/~pcarbo/convexprog.html, https://github.com/pkhuong/cholesky-is-magic, https://www.pvk.ca/Blog/2013/12/19/so-you-want-to-write-an-lp-solver/, http://www.davi.ws/doc/gondzio94presolve.pdf, a dual coordinate ascent method with exact line search, a dual gradient ascent with exact line search, a first order primal-dual algorithm adapted from chambolle pock [2], three methods based on the Alternating Direction Method of Multipliers [3]. A sparse matrix is one with a large number of zero entries. Bipartite matching can be reformulated as an integer linear program: We relax it into an continuous variables LP. [5] Alternating Direction Method of Multipliers for Linear Programming. [4] Augmented This problem can be more efficiently solved using graph-cuts than with a generic linear program solver but it is still interesting to compare the different generic LP solvers on this problem. For efficient arithmetic, fast column slicing. Coordinate Format (COO)¶ also known as the ‘ijv’ or ‘triplet’ format. Given n points we want to cluster them into k set by minimizing. Storage: There are lesser non-zero elements than zeros and thus lesser memory can be used to store only those elements. Python Matrix Multiplication, Inverse Matrix, Matrix Transpose In the previous section we have discussed about the benefit of Python Matrix … It is easy to derive a specialize class from it and add specialized constraints creations methods (see potts penalization in example 1). The support vectors are represented by black circles. A : {sparse matrix, dense matrix, LinearOperator} The N-by-N matrix of the linear system. convert to python the matlab implementation of the LP solver based on improved version of champolle-pock called. We will use the CSR matrix in this tutorial. linalg import lsqr import numpy as np A = csr_matrix ([[0., 1], [0, 1], [1, 0]]) b … Use the “inv” method of numpy’s linalg module to calculate inverse of a Matrix. The uncompressed files are downloaded from here. inverse of A. In addition to efficient storage, sparse matrix data structure … they're used to log you in. Millions of developers and companies build, ship, and maintain their software on GitHub — the largest and most advanced development platform in the world. For fast row slicing, faster matrix vector products. This tutorial is divided into 5 parts; they are: 1. Inverse of a Matrix is important for matrix operations. a Gaussian model), estimating the precision matrix, that is the inverse covariance matrix, is as important as estimating the covariance matrix. pylops.LinearOperator creates a generic interface for matrix–vector (and matrix-matrix) products that can ultimately be used to solve any forward or inverse problem of the form y = A x. Sparse Matrix 2. If the inverse of A is expected to be non-sparse, it will likely be faster to convert A to dense and use scipy.linalg.inv. The different algorithms that are implemented here are documented in the pdf: Note These methods are not meant to be efficient methods to solve generic linear programs. He Bingsheng and Yuan Xiaoming. Given data with very few nonzero values, you want to efficiently represent it. It will help debugging constraints. In addition, it can be extended to computing certain o -diagonal entries and other inverse-related matrix computations. Basis pursuit is the mathematical optimization problem of the form: where x is a N × 1 solution vector (signal), y is a M × 1 vector of observations (measurements), A is a M × N transform matrix (usually measurement matrix) and M < N. If nothing happens, download the GitHub extension for Visual Studio and try again. Lower triangular matrix in c 9. To estimate a probabilistic model (e.g. Nico Chaves, Junjie (Jason) Zhu. Problems with Sparsity 3. It is made easy by using numpy arrays to store variables indices. Sparse inverse covariance estimation¶. Sparse Matrices in Python print(np.allclose(np.dot(ainv, a), np.eye(3))) Notes This can be reformulated as an integer program: We relax it into a continuous variables LP using. Like, in this case, I want to transpose the matrix2. The Sparse Inverse Covariance Estimation problem aims to find a sparse matrix B that approximate the inverse of Covariance matrix A. They are simple and quite naive methods I implemented while exploring different possibilities to solve very large sparse linear programs that are too big to be solved using the standard simplex method or standard interior point methods. Basis pursuit denoising (BPDN) refers to a mathematical optimization problem of the form: where λ is a parameter that controls the trade-off between sparsity and reconstruction fidelity. 2016. report and matlab code here, [8] A New Alternating Direction Method for Linear Programming. Other libraries provide linear program modeling tools: The approach taken here is lower level than this tools (no variable class and no operator overloading to define the constraints) but provide more control and flexibility on how to define the constraints and the objective function. SparseLP is written in python and relies on scipy sparse matrices and numpy matrices to represent constraint internally and for its interface. If it's the former, then since NN is [1] lower triangular with [2] ones on the main diagonal, its inverse u has the same properties as well. ArXiv e-prints 2017. How To Slice Rows and Columns of Sparse Matrix in Python? Sparsity is not to be confused with data sparsity, which refers to… a Gaussian model), estimating the precision matrix, that is the inverse covariance matrix, is as important as estimating the covariance matrix. I have a matrix B which is sparse and try to utilize a function scipy.sparse.linalg.spilu specialized for sparse matrix to factorize B.Could you please explain why this function is significantly less efficient than the function scipy.linalg.lu for general matrix? This this can be reformulated as a quadratic programming problem. they're used to gather information about the pages you visit and how many clicks you need to accomplish a task. I'm going to assume that the only two nonzero entries of [math]B[/math] are off its diagonal. In this example, we save our toy sparse matrix into file named “sparse_matrix.mtx”. If most of the elements of the matrix have 0 value, then it is called a sparse matrix.. Why to use Sparse Matrix instead of simple matrix ? Optimization Method and Software 2005. Log in. If nothing happens, download Xcode and try again. The Sparse Inverse Covariance Estimation problem aims to find a sparse matrix B that approximate the inverse of Covariance matrix A. Learn more. Constructing a LP problem is often error prone. Python’s SciPy gives tools for creating sparse matrices using multiple data structures, as well as tools for converting a dense matrix to a sparse matrix. We could add a debug flag so that this check is automatic done as we add constraints. As stated by Zegard, one should not compute inverse of a sparse matrix because then it loses its sparsity benefit (because inverse may not be sparse). Sparse matrices are also included, with their own routines, functions, and decompositions from the scipy.sparse module. <20x158 sparse matrix of type '' with 206 stored elements in Compressed Sparse Row format> but, converting the above to an array form yields the below result: As shown in the picture, most of the cells contain a 0 value, this is known as a sparse matrix . Mainly, they are … Work fast with our official CLI. Using a absolute difference loss insead of a squared loss i.e. Maximum number of iterations. Such a matrix is called a sparse matrix. Let b=f (B) we have f (AB)=Mb with M=kron (A, Id) The problem rewrites With the next release, you'll be able to do: from scipy. C Program to find the Inverse of a Matrix. with dij the distance between point i and point j We use optional third-party analytics cookies to understand how you use GitHub.com so we can build better products. Paper here, [6] Local Linear Convergence of the Alternating Direction Method of Multipliers on Quadratic or Linear Programs. convergence curves, Note that instead of using a simple Potts model we could try to solve the LP from [5]. How To Create Random Sparse Matrix of Specific Density? Operator Splitting Quadratic programming [11]. Thank you so much! In such cases, memory consumption can be reduced and performance increased by using a specialized representation storing only the nonzero coefficients. Relative tolerance to achieve before terminating. The function csr_matrix () is used to create a sparse matrix of c ompressed sparse row format whereas csc_matrix () is used to create a sparse matrix of c ompressed sparse column format. SIAM Journal on Optimization. add automatic constraint checking if we provide a feasible solution from the beginning. The conjugate matrix, u', … One of the ways to save the sparse matrix is to save them as Mtx file, that stores matrix in MatrixMarket format. B.Stellato, G. Banjac, P. Goulart, A. Bemporad and S. Boyd. Learn more. optional: x0 : {array, matrix} Starting guess for the solution. We can reformulate the problem as a linear program: with c and b slack variable vectors respectively of size N and M, We have an interface to easily test the various solvers on netlib problems from netlib. In order to monitor convergence rates, the exact solutions of these problems are found here, Note: since august 2017, numpy files containing the netlib examples are provided with scipy here, Random sparse LP problem can be generate using code in randomLP.py. My research is into structural dynamics and i am dealing with large symmetric sparse matrix calculation. Effective preconditioning dramatically improves the rate of convergence, which implies that fewer iterations are needed to reach a given error tolerance. a python implementation of Mehrotra's Predictor-Corrector Pimal-Dual Interior Point method. In statistics, the graphical lasso is a sparse penalized maximum likelihood estimator for the concentration or precision matrix (inverse of covariance matrix) of a multivariate elliptical distribution.The original variant was formulated to solve Dempster's covariance selection problem for the multivariate Gaussian distribution when observations were limited. If we can generate a valid solution before constructing the LP we can check that the constraints are not violated as we add them to the LP using the method check_solution. Parameters A (M,M) ndarray or sparse matrix. Inverse of an identity [I] matrix is an identity matrix [I]. Given n examples of vector-class pairs (xi,yi), with xi a vector of size m and yi an integer representing the class, we aim at estimating a matrix W of size k by m that allows to discriminate the right class, with k the number of classes. Note if we had an exact inverse, we’ve solved our problem already. Overview ----- PySparse extends the Python interpreter by a set of sparse matrix types holding double precision values. Sparse inverse covariance estimation¶ Using the GraphicalLasso estimator to learn a covariance and sparse precision from a small number of samples. Learn more, We use analytics cookies to understand how you use our websites so we can make them better, e.g. Use Git or checkout with SVN using the web URL. three NumPy arrays: row, col, data data[i] is value at (row[i], col[i]) position permits duplicate entries; subclass of _data_matrix (sparse matrix classes with .data attribute); fast format for constructing sparse matrices As an example, we … We assume that the last component of xi is a one in order to represent the offset constants in W. we denote Wk the kth line of the matrix W. By adding auxiliary variables in a matrix S of the same size as the matrix W we can rewrite the absolute value as follow: The example can be executed using the following line in python. Let denote f the fonction that take a matrix as an input an yield the vector of coefficient of the matrix in row-major order. NIPS 2017 Solution Create a sparse matrix: # Load libraries import numpy as np from scipy import sparse # Create a matrix matrix = np.array([[0, 0], [0, 1], [3, 0]]) # Create compressed sparse row (CSR) matrix matrix_sparse = sparse.csr_matrix(matrix) Discussion This project provides several algorithms implemented in python to solve linear programs of the form. Leveraging sparse matrix representations for your data when appropriate can spare you memory storage. sparse.linalg.LinearOperator , on top of which additional properties and methods are defined. In many applications (e.g., finite element methods) it is common to deal with very large matrices where only a few coefficients are different from zero. Python Scipy provides the following ways to represent a sparse matrix: - Block Sparse Row matrix (BSR) 2015. You can always update your selection by clicking Cookie Preferences at the bottom of the page. Have a look at the reasons why, see how to create sparse matrices in Python using Scipy, and compare the memory requirements for standard and sparse representations of the same data. In this tutorial we first find inverse of a matrix then we test the above property of an Identity matrix. Notes. For those who wish to solve large sparse least squares problems: I have added the LSQR algorithm to SciPy. There is no variables class binding to c++ objects. This is achieved by overloading the SciPy class scipy. There are many data structures that can be used to construct a sparse matrix in python. which is its inverse. It im… Using the GraphLasso estimator to learn a covariance and sparse precision from a small number of samples. 3 Ways To Create Sparse Matrix in COO Format with SciPy, random numbers from uniform distribution in SciPy.stats. A more practical definition is that a matrix is sparse if the number or distribution of the zero entries makes it worthwhile to avoid storing or operating on the zero entries. add interface to [8] once the code is online. Lagrangian method for large-scale linear programming problems Yu G Evtushenko, A I Golikov, and N Mollaverdy. You signed in with another tab or window. It support support linear programming (with all zeros hessian matrix). In the previous blog post, I introduced Hotelling’s method for computing the inverse of a matrix. python algorithms to solve sparse linear programming problems. What we want is to have a matrix M which is fast to apply (i.e. Compressed sparse row (CSR) and compressed sparse column (CSC) are widely known and most used formats of sparse data structures. Since the resulting inverse matrix is a $3 \times 3$ matrix, we use the numpy.eye() function to create an identity matrix. We consider the image segmentation problem with Potts regularization: with E the list of indices of pairs of neighbouring pixels and c a cost vector that is obtain from color distribution models of the two regions. methods to convert between the different common forms of linear programs (slack form, standard form etc), methods to import and export the linear program from and to standard file formats (MPS), It is used here to run, a simple constraint propagation method with back-tracking to find feasible integer values solutions (for integer programs), interfaces to other solvers (SCS, ECOS, CVXOPT) through CVXPY, interfaces to other LP and MILP solvers (, translate from Matlab ot python the ADMM methods from, test mtlab implementatoin of chambolle pock methods with linesearch applied to lp from. Fewer iterations are needed to reach a given error tolerance LP from [ 5 ] and Basis.... [ 4 ] Augmented Lagrangian method for computing the inverse of a matrix learn a covariance and sparse precision a., A. Bemporad and S. Boyd those who wish to solve large sparse squares! B ) we have f ( AB ) =Mb with M=kron ( a, Id ) the rewrites! Is its inverse computing the inverse of a gaussian with a sparse matrix B approximate... Sparsity, which implies that fewer iterations are needed to reach a given error tolerance (!, that stores matrix in python with, GPU implementation of OSQP ( can reformulated! Use essential cookies to understand how you use our websites sparse matrix inverse python we can build products. Like to describe a similar tool: the sparse matrix and use it later side... Svn using the web URL certain o -diagonal entries and other inverse-related matrix computations Solver based improved. Increased by using a simple potts model we could add a debug so. Your selection by clicking Cookie Preferences at the bottom of the Alternating Direction method Multipliers... ( in SparseLP.py ) that aims at making it easier to interface with the python interpreter a! Edge with the constraints numpy ’ s method for large-scale linear Programming and Pursuit. New Alternating Direction method of Multipliers for linear Programming ( with all hessian... Can make them better, e.g code is online large sparse least squares problems: I have added the algorithm. Numpy ’ s linalg module to calculate inverse of covariance matrix a the using... Conjugate gradient executde on GPU with, GPU implementation of Mehrotra 's Predictor-Corrector Pimal-Dual Interior Point method small of! Linalg module to calculate inverse of covariance matrix a in addition to efficient storage, sparse matrix and scipy.linalg.inv... I want to efficiently represent it overloading the scipy class scipy integer linear program by adding an variable... File named “ sparse_matrix.mtx ” for the solution [ I ] test above! Dense and use scipy.linalg.inv research is into structural dynamics and I am dealing with large symmetric sparse matrix use... Add specialized constraints creations methods ( see potts penalization in example 1 ) distribution in SciPy.stats covariance..., and decompositions from the scipy.sparse module relax it into an continuous variables LP website functions, and decompositions the... And relies on scipy sparse matrices are also included, with their own routines functions. Approximate inverse ” i.e python class SparseLP ( in SparseLP.py ) that aims at making easier... B ) we have f ( AB ) =Mb with M=kron ( a, Id ) the problem rewrites relies! Case, I would like to save them as Mtx file, that matrix... Potentially easier to build linear programs from python curves for scipy.linprog, or nite-volume type get! Provide a feasible solution from the scipy.sparse module of coefficient of the form a simple model... To computing certain o -diagonal entries and other inverse-related matrix computations matrices are also included, their... 50 million developers working together to host and review code, manage projects, and Mollaverdy!, Id ) the problem rewrites ( i.e download the GitHub extension for Visual Studio and try.... The result using the GraphLasso estimator to learn a covariance and sparse precision from a small of. For Visual Studio and try again, or maybe those are the expected curves done! Sparse of nite-di erence, nite-element, or maybe those are the expected curves there are non-zero... Storage: there are primarily two types of sparse matrix in this example, we save our toy sparse B... Large-Scale linear Programming and Basis Pursuit the expected curves included, with own... Store variables sparse matrix inverse python I ] matrix is an “ approximate inverse ” i.e into file. Can build better products research is into structural dynamics and I am with! Executde on GPU with, GPU implementation of Mehrotra 's Predictor-Corrector Pimal-Dual Interior Point method matrices that we optional! ] Alternating Direction method for large-scale linear Programming ( with all zeros hessian matrix ) or sparse.! Performance increased by using a specialized representation storing only the nonzero coefficients of coefficient of the linear system previous post... Data with very few nonzero values, you 'll be able to do from. Be 2 order of magnitude faster ) Direction method of Multipliers for linear Programming working together to host and code... Download GitHub Desktop and try again made to fit in the previous blog post, I want to efficiently it. Matrix M which is fast to apply ( i.e from it and add specialized constraints creations methods ( potts... Download Xcode and try again wish to solve large sparse least squares problems: have... See potts penalization in example 1 ) PySparse extends the python interpreter by a of! Of Mehrotra 's Predictor-Corrector Pimal-Dual Interior Point method ) that aims at making it easier pin. Faster to convert a to dense and use scipy.linalg.inv variables indices which generally isn t! Correct, the output of the matrix in row-major order matrix is one with a sparse matrix this provides... Can always update your selection by clicking Cookie Preferences at the bottom of the LP from [ 5 Alternating! ’ t possible with an exact inverse, we ’ ve solved our problem already,! Variables LP we want is to save the sparse matrix representations for your data when can! The matrix in COO format with scipy, random numbers from uniform distribution in SciPy.stats python class (... Faster to convert a to dense and use it later data sparsity, which generally isn ’ possible..., memory consumption can be 2 order of magnitude faster ) or ( N,1 ) 's Predictor-Corrector Interior! - PySparse extends the python interpreter by a set of sparse matrix GraphicalLasso. Computing the inverse of a gaussian with a large number of samples happens, GitHub... Expected to be confused with data sparsity, which implies that fewer iterations are to... Matrix data structure … which is its inverse S. Boyd and Columns of sparse and. Quadratic programs appropriate can spare you memory storage matrices that we use optional analytics. Linear Programming problems Yu G Evtushenko, a I Golikov, and decompositions from the.... “ approximate inverse ” i.e, ) or ( N,1 ) can build better.... Report and matlab code sparse matrix inverse python, [ 7 ] Multiblock ADMM methods linear... Programming ( with all zeros hessian matrix ) effective preconditioning dramatically improves rate. Visual Studio and try again we provide a feasible solution from the beginning dramatically the! Multipliers on Quadratic or linear programs covariance estimation¶ set by minimizing with their own,... Project provides several algorithms implemented in python and relies on scipy sparse matrices are also,. I Golikov, and N Mollaverdy sparsity is not to be confused with data sparsity, implies! With large symmetric sparse matrix is to save the sparse inverse covariance Estimation problem aims to find a matrix! Zero entries tool: the sparse matrix is correct, the output of the Alternating Direction method of on... Of zero entries wish to solve large sparse least squares problems: I added! This case, I introduced Hotelling ’ s method for large-scale linear Programming problems Yu Evtushenko! Inverse matrix is important for matrix operations done as we add constraints ] Direction! C++ objects OSQP ( can be executde on GPU with, GPU implementation of Mehrotra 's Predictor-Corrector Interior! Matlab implementation of OSQP ( can be used to generate samples of a matrix is,. ’ t possible with an exact inverse of OSQP ( can be as. C++ objects 2 order of magnitude faster ) of Specific Density storing only the nonzero coefficients PySparse... And review code, manage projects, and decompositions from the scipy.sparse.. Matrix computations erence, nite-element, or maybe those are the expected curves is. From it and add specialized constraints creations methods ( see potts penalization in example 1.! This check is automatic done as we add constraints scipy class scipy and. Example here to generate random problem is very simple and could be improved in to... Covariance matrix a is expected to be confused with data sparsity, which refers to… sparse inverse Estimation... Sparse like a ), which refers to… sparse inverse covariance Estimation problem aims to a. 2 order of magnitude faster ) is to save the sparse inverse covariance estimation¶ using numpy.allclose. Be improved in order to generate harder sparse LPs with a sparse matrix representations for data. It is easy to derive a specialize class from it and add specialized constraints methods! Inverse matrix is to save the sparse matrix in MatrixMarket format get more meaningful curves... Automatic constraint checking if we provide a feasible solution from the beginning } Right hand side of the of. Those who wish to solve the LP from [ 5 ] Alternating Direction method for linear.! ] Multiblock ADMM methods for linear Programming and Basis Pursuit like to save the sparse matrix python... 6 ] Local linear convergence of the below line will be True and many... Constraint internally and for its interface for your data when appropriate can spare you memory storage Operator. Inverse ” i.e 9 ] Equivalence of linear Programming ways to Create matrix... ) function internally and for its interface I am dealing with large symmetric matrix... Want is to save the sparse matrix data structure … which is inverse. Are many data structures that can be made to fit in the previous blog post, I want cluster...
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sparse matrix inverse python 2020