On the properties of the solution path of the constrained and penalized L2-L0 problems

12 pagesTechnical report on the properties of the L0-constrained least-square minimization problem and the L0-penalized least-square minimization problem: domain of optimization, notion of solution path, properties of the "penalized" solution path..

Homotopy based algorithms for ℓ0\ell_0-regularized least-squares

Sparse signal restoration is usually formulated as the minimization of a quadratic cost function $\|y-Ax\|_2^2$, where A is a dictionary and x is an unknown sparse vector. It is well-known that imposing an $\ell_0$ constraint leads to an NP-hard minimization problem. The convex relaxation approach has received considerable attention, where the $\ell_0$-norm is replaced by the $\ell_1$-norm. Among the many efficient $\ell_1$ solvers, the homotopy algorithm minimizes $\|y-Ax\|_2^2+\lambda\|x\|_1$ with respect to x for a continuum of $\lambda$'s. It is inspired by the piecewise regularity of the $\ell_1$-regularization path, also referred to as the homotopy path. In this paper, we address the minimization problem $\|y-Ax\|_2^2+\lambda\|x\|_0$ for a continuum of $\lambda$'s and propose two heuristic search algorithms for $\ell_0$-homotopy. Continuation Single Best Replacement is a forward-backward greedy strategy extending the Single Best Replacement algorithm, previously proposed for $\ell_0$-minimization at a given $\lambda$. The adaptive search of the $\lambda$-values is inspired by $\ell_1$-homotopy. $\ell_0$ Regularization Path Descent is a more complex algorithm exploiting the structural properties of the $\ell_0$-regularization path, which is piecewise constant with respect to $\lambda$. Both algorithms are empirically evaluated for difficult inverse problems involving ill-conditioned dictionaries. Finally, we show that they can be easily coupled with usual methods of model order selection.Comment: 38 page

Integrating fMRI and SNP data for biomarker identification for schizophrenia with a sparse representation based variable selection method

BACKGROUND: In recent years, both single-nucleotide polymorphism (SNP) array and functional magnetic resonance imaging (fMRI) have been widely used for the study of schizophrenia (SCZ). In addition, a few studies have been reported integrating both SNPs data and fMRI data for comprehensive analysis. METHODS: In this study, a novel sparse representation based variable selection (SRVS) method has been proposed and tested on a simulation data set to demonstrate its multi-resolution properties. Then the SRVS method was applied to an integrative analysis of two different SCZ data sets, a Single-nucleotide polymorphism (SNP) data set and a functional resonance imaging (fMRI) data set, including 92 cases and 116 controls. Biomarkers for the disease were identified and validated with a multivariate classification approach followed by a leave one out (LOO) cross-validation. Then we compared the results with that of a previously reported sparse representation based feature selection method. RESULTS: Results showed that biomarkers from our proposed SRVS method gave significantly higher classification accuracy in discriminating SCZ patients from healthy controls than that of the previous reported sparse representation method. Furthermore, using biomarkers from both data sets led to better classification accuracy than using single type of biomarkers, which suggests the advantage of integrative analysis of different types of data. CONCLUSIONS: The proposed SRVS algorithm is effective in identifying significant biomarkers for complicated disease as SCZ. Integrating different types of data (e.g. SNP and fMRI data) may identify complementary biomarkers benefitting the diagnosis accuracy of the disease

Transfer of Bone-Marrow-Derived Mesenchymal Stem Cells Influences Vascular Remodeling and Calcification after Balloon Injury in Hyperlipidemic Rats

Bone-marrow-derived mesenchymal stem cells (BM-MSCs) were found to markedly increase atherosclerotic lesion size. The aim of this paper was to investigate whether BM-MSCs contribute to vascular remodeling and calcification after balloon injury in hyperlipidemic rats. Labeled BM-MSCs were found in the lesion of hyperlipidemic rats after balloon injury. Comparing injury group, transferred BM-MSCs significantly triggered vascular negative remodeling, characterized by the changes of remodeling index (0.628 ± 0.0293 versus 0.544 ± 0.0217), neointimal area (0.078 ± 0.015 mm2 versus 0.098 ± 0.019 mm2), PCNA index (23.91 ± 6.59% versus 43.11 ± 5.31%), and percentage of stenosis (18.20 ± 1.09% versus 30.58 ± 1.21%). Apparent vascular calcification was detected in medial layers at 6 weeks after balloon angioplasty, which may be associated with upregulation of bone morphogenetic protein-2 (BMP-2). Our data indicated that unselected BM-MSCs transfer may induce vascular remodeling and calcification after balloon injury in hyperlipidemic rats

CAME: Contrastive Automated Model Evaluation

The Automated Model Evaluation (AutoEval) framework entertains the possibility of evaluating a trained machine learning model without resorting to a labeled testing set. Despite the promise and some decent results, the existing AutoEval methods heavily rely on computing distribution shifts between the unlabelled testing set and the training set. We believe this reliance on the training set becomes another obstacle in shipping this technology to real-world ML development. In this work, we propose Contrastive Automatic Model Evaluation (CAME), a novel AutoEval framework that is rid of involving training set in the loop. The core idea of CAME bases on a theoretical analysis which bonds the model performance with a contrastive loss. Further, with extensive empirical validation, we manage to set up a predictable relationship between the two, simply by deducing on the unlabeled/unseen testing set. The resulting framework CAME establishes a new SOTA results for AutoEval by surpassing prior work significantly.Comment: ICCV2023 main conferenc

Network pharma cology and GEO chip based elucidation of mechanisms underlying the use of Yi Tieqing for prevention and treatment of postoperative nausea and vomiting

Purpose: To investigate the mechanism(s) involved in the use of Yi Tieqing for the prevention and treatment of postoperative nausea and vomiting (PONV), using network pharmacology and GEO chip. Methods: The chemical constituents and functional targets of five traditional Chinese medicines in Yi Tieqing were obtained by searching TCMSP database. The PONV disease targets were identified through DisGeNET, GeneCards and DrugBank databases, and differential expression genes of the GEO database chip (GSE7762) were mined. From the intersections of the component targets and disease targets, the core targets of drugs and diseases were obtained. The core targets were investigated in R language using GO-biological process and KEGG enrichment analyses, and their biological activities were verified via molecular docking. Finally, the severity and incidence of PONV in control and treatment groups were determined and compared. Results: A total of 254 bioactive components and 301 related potential targets were obtained from the TCMSP database. There were 2092 related targets in PONV, and 6 intersecting targets were obtained from Venn diagram. The results of GO biological process and KEGG enrichment analysis showed that the incidence of PONV was strongly correlated with the negative regulation of response to wounding and nervous system. Clinical results showed that from 24 – 48 h (T2) after operation, the severity and incidence of PONV in the treatment group were significantly lower than those in the control group (p < 0.05). Conclusion: Yi Tieqing alleviates PONV through multi-components, multi-targets, and multi-pathways

Automated Force Volume Image Processing for Biological Samples

Atomic force microscopy (AFM) has now become a powerful technique for investigating on a molecular level, surface forces, nanomechanical properties of deformable particles, biomolecular interactions, kinetics, and dynamic processes. This paper specifically focuses on the analysis of AFM force curves collected on biological systems, in particular, bacteria. The goal is to provide fully automated tools to achieve theoretical interpretation of force curves on the basis of adequate, available physical models. In this respect, we propose two algorithms, one for the processing of approach force curves and another for the quantitative analysis of retraction force curves. In the former, electrostatic interactions prior to contact between AFM probe and bacterium are accounted for and mechanical interactions operating after contact are described in terms of Hertz-Hooke formalism. Retraction force curves are analyzed on the basis of the Freely Jointed Chain model. For both algorithms, the quantitative reconstruction of force curves is based on the robust detection of critical points (jumps, changes of slope or changes of curvature) which mark the transitions between the various relevant interactions taking place between the AFM tip and the studied sample during approach and retraction. Once the key regions of separation distance and indentation are detected, the physical parameters describing the relevant interactions operating in these regions are extracted making use of regression procedure for fitting experiments to theory. The flexibility, accuracy and strength of the algorithms are illustrated with the processing of two force-volume images, which collect a large set of approach and retraction curves measured on a single biological surface. For each force-volume image, several maps are generated, representing the spatial distribution of the searched physical parameters as estimated for each pixel of the force-volume image

Restauration et séparation de signaux polynomiaux par morceaux. Application à la microscopie de force atomique

This thesis handles several inverse problems occurring in sparse signal processing. The main contributions include the conception of algorithms dedicated to the restoration and the separation of sparse signals, and their application to force curve approximation in Atomic Force Microscopy (AFM), where the notion of sparsity is related to the number of discontinuity points in the signal (jumps, change of slope, change of curvature). In the signal processing viewpoint, we propose sub-optimal algorithms dedicated to the sparse signal approximation problem based on the ℓ0 pseudo-norm : the Single Best Replacement algorithm (SBR) is an iterative "forward-backward" algorithm inspired from existing Bernoulli-Gaussian signal restoration algorithms. The Continuation Single Best Replacement algorithm (CSBR) is an extension providing approximations at various sparsity levels. We also address the problem of sparse source separation from delayed mixtures. The proposed algorithm is based on the prior application of CSBR on every mixture followed by a matching procedure which attributes a label for each peak occurring in each mixture. Atomic Force Microscopy (AFM) is a recent technology enabling to measure interaction forces between nano-objects. The force-curve analysis relies on piecewise parametric models. We address the detection of the regions of interest (the pieces) where each model holds and the subsequent estimation of physical parameters (elasticity, adhesion forces, topography, etc.) in each region by least-squares optimization. We finally propose an alternative approach in which a force curve is modeled as a mixture of delayed sparse sources. The research of the source signals and the delays from a force-volume image is done based on a large number of mixtures since there are as many mixtures as the number of image pixels.Cette thèse s'inscrit dans le domaine des problèmes inverses en traitement du signal. Elle est consacrée à la conception d'algorithmes de restauration et de séparation de signaux parcimonieux et à leur application à l'approximation de courbes de forces en microscopie de force atomique (AFM), où la notion de parcimonie est liée au nombre de points de discontinuité dans le signal (sauts, changements de pente, changements de courbure). Du point de vue méthodologique, des algorithmes sous-optimaux sont proposés pour le problème de l'approximation parcimonieuse basée sur la pseudo-norme ℓ0 : l'algorithme Single Best Replacement (SBR) est un algorithme itératif de type « ajout-retrait » inspiré d'algorithmes existants pour la restauration de signaux Bernoulli-Gaussiens. L'algorithme Continuation Single Best Replacement (CSBR) est un algorithme permettant de fournir des approximations à des degrés de parcimonie variables. Nous proposons aussi un algorithme de séparation de sources parcimonieuses à partir de mélanges avec retards, basé sur l'application préalable de l'algorithme CSBR sur chacun des mélanges, puis sur une procédure d'appariement des pics présents dans les différents mélanges. La microscopie de force atomique est une technologie récente permettant de mesurer des forces d'interaction entre nano-objets. L'analyse de courbes de forces repose sur des modèles paramétriques par morceaux. Nous proposons un algorithme permettant de détecter les régions d'intérêt (les morceaux) où chaque modèle s'applique puis d'estimer par moindres carrés les paramètres physiques (élasticité, force d'adhésion, topographie, etc.) dans chaque région. Nous proposons finalement une autre approche qui modélise une courbe de force comme un mélange de signaux sources parcimonieux retardées. La recherche des signaux sources dans une image force-volume s'effectue à partir d'un grand nombre de mélanges car il y autant de mélanges que de pixels dans l'image