Integrating Sparse Learning-Based Feature Detectors into Simultaneous Localization and Mapping-A Benchmark Study.

Simultaneous localization and mapping (SLAM) is one of the cornerstones of autonomous navigation systems in robotics and the automotive industry. Visual SLAM (V-SLAM), which relies on image features, such as keypoints and descriptors to estimate the pose transformation between consecutive frames, is a highly efficient and effective approach for gathering environmental information. With the rise of representation learning, feature detectors based on deep neural networks (DNNs) have emerged as an alternative to handcrafted solutions. This work examines the integration of sparse learned features into a state-of-the-art SLAM framework and benchmarks handcrafted and learning-based approaches by comparing the two methods through in-depth experiments. Specifically, we replace the ORB detector and BRIEF descriptor of the ORBSLAM3 pipeline with those provided by Superpoint, a DNN model that jointly computes keypoints and descriptors. Experiments on three publicly available datasets from different application domains were conducted to evaluate the pose estimation performance and resource usage of both solutions.

Data-Driven Fault Diagnosis Techniques: Non-Linear Directional Residual vs. Machine-Learning-Based Methods.

Linear dependence of variables is a commonly used assumption in most diagnostic systems for which many robust methodologies have been developed over the years. In case the system nonlinearities are relevant, fault diagnosis methods, relying on the assumption of linearity, might potentially provide unsatisfactory results in terms of false alarms and missed detections. In recent years, many authors have proposed machine learning (ML) techniques to improve fault diagnosis performance to mitigate this problem. Although very powerful, these techniques require faulty data samples that are representative of any fault scenario. Additionally, ML techniques suffer from issues related to overfitting and unpredictable performance in regions which are not fully explored in the training phase. This paper proposes a non-linear additive model to characterize the non-linear redundancy relationships among the system signals. Using the multivariate adaptive regression splines (MARS) algorithm, these relationships are identified directly from the data. Next, the non-linear redundancy relationships are linearized to derive a local time-dependent fault signature matrix. The faulty sensor can then be isolated by measuring the angular distance between the column vectors of the fault signature matrix and the primary residual vector. A quantitative analysis of fault isolation and fault estimation performance is performed by exploiting real data from multiple flights of a semi-autonomous aircraft, thus allowing a detailed quantitative comparison with state-of-the-art machine-learning-based fault diagnosis algorithms.

Application of conditional robust calibration to ordinary differential equations models in computational systems biology: a comparison of two sampling strategies.

Mathematical modelling is a widely used technique for describing the temporal behaviour of biological systems. One of the most challenging topics in computational systems biology is the calibration of non-linear models; i.e. the estimation of their unknown parameters. The state-of-the-art methods in this field are the frequentist and Bayesian approaches. For both of them, the performance and accuracy of results greatly depend on the sampling technique employed. Here, the authors test a novel Bayesian procedure for parameter estimation, called conditional robust calibration (CRC), comparing two different sampling techniques: uniform and logarithmic Latin hypercube sampling. CRC is an iterative algorithm based on parameter space sampling and on the estimation of parameter density functions. They apply CRC with both sampling strategies to the three ordinary differential equations (ODEs) models of increasing complexity. They obtain a more precise and reliable solution through logarithmically spaced samples.

CRA toolbox: software package for conditional robustness analysis of cancer systems biology models in MATLAB.

BACKGROUND: In cancer research, robustness of a complex biochemical network is one of the most relevant properties to investigate for the development of novel targeted therapies. In cancer systems biology, biological networks are typically modeled through Ordinary Differential Equation (ODE) models. Hence, robustness analysis consists in quantifying how much the temporal behavior of a specific node is influenced by the perturbation of model parameters. The Conditional Robustness Algorithm (CRA) is a valuable methodology to perform robustness analysis on a selected output variable, representative of the proliferation activity of cancer disease. RESULTS: Here we introduce our new freely downloadable software, the CRA Toolbox. The CRA Toolbox is an Object-Oriented MATLAB package which implements the features of CRA for ODE models. It offers the users the ability to import a mathematical model in Systems Biology Markup Language (SBML), to perturb the model parameter space and to choose the reference node for the robustness analysis. The CRA Toolbox allows the users to visualize and save all the generated results through a user-friendly Graphical User Interface (GUI). The CRA Toolbox has a modular and flexible architecture since it is designed according to some engineering design patterns. This tool has been successfully applied in three nonlinear ODE models: the Prostate-specific Pten-/- mouse model, the Pulse Generator Network and the EGFR-IGF1R pathway. CONCLUSIONS: The CRA Toolbox for MATLAB is an open-source tool implementing the CRA to perform conditional robustness analysis. With its unique set of functions, the CRA Toolbox is a remarkable software for the topological study of biological networks. The source and example code and the corresponding documentation are freely available at the web site: http://gitlab.ict4life.com/SysBiOThe/CRA-Matlab .

Conditional robustness analysis for fragility discovery and target identification in biochemical networks and in cancer systems biology.

BACKGROUND: The study of cancer therapy is a key issue in the field of oncology research and the development of target therapies is one of the main problems currently under investigation. This is particularly relevant in different types of tumor where traditional chemotherapy approaches often fail, such as lung cancer. RESULTS: We started from the general definition of robustness introduced by Kitano and applied it to the analysis of dynamical biochemical networks, proposing a new algorithm based on moment independent analysis of input/output uncertainty. The framework utilizes novel computational methods which enable evaluating the model fragility with respect to quantitative performance measures and parameters such as reaction rate constants and initial conditions. The algorithm generates a small subset of parameters that can be used to act on complex networks and to obtain the desired behaviors. We have applied the proposed framework to the EGFR-IGF1R signal transduction network, a crucial pathway in lung cancer, as an example of Cancer Systems Biology application in drug discovery. Furthermore, we have tested our framework on a pulse generator network as an example of Synthetic Biology application, thus proving the suitability of our methodology to the characterization of the input/output synthetic circuits. CONCLUSIONS: The achieved results are of immediate practical application in computational biology, and while we demonstrate their use in two specific examples, they can in fact be used to study a wider class of biological systems.

An approach for optimally extending mathematical models of signaling networks using omics data.

Mathematical modeling is a key process in Systems Biology and the use of computational tools such as Cytoscape for omics data processing, need to be integrated in the modeling activity. In this paper we propose a new methodology for modeling signaling networks by combining ordinary differential equation models and a gene recommender system, GeneMANIA. We started from existing models, that are stored in the BioModels database, and we generated a query to use as input for the GeneMANIA algorithm. The output of the recommender system was then led back to the kinetic reactions that were finally added to the starting model. We applied the proposed methodology to EGFR-IGF1R signal transduction network, which plays an important role in translational oncology and cancer therapy of non small cell lung cancer.

Computational model of EGFR and IGF1R pathways in lung cancer: a Systems Biology approach for Translational Oncology.

In this paper we propose a Systems Biology approach to understand the molecular biology of the Epidermal Growth Factor Receptor (EGFR, also known as ErbB1/HER1) and type 1 Insulin-like Growth Factor (IGF1R) pathways in non-small cell lung cancer (NSCLC). This approach, combined with Translational Oncology methodologies, is used to address the experimental evidence of a close relationship among EGFR and IGF1R protein expression, by immunohistochemistry (IHC) and gene amplification, by in situ hybridization (FISH) and the corresponding ability to develop a more aggressive behavior. We develop a detailed in silico model, based on ordinary differential equations, of the pathways and study the dynamic implications of receptor alterations on the time behavior of the MAPK cascade down to ERK, which in turn governs proliferation and cell migration. In addition, an extensive sensitivity analysis of the proposed model is carried out and a simplified model is proposed which allows us to infer a similar relationship among EGFR and IGF1R activities and disease outcome.

A Kalman filtering approach to estimation of maximum ventricle elastance.

In this paper a method for estimating maximum ventricular elastance through an extended Kalman filter is proposed, based on measurement of ventricular volume and aortic pressure. The Kalman filter is particularly well suited to this task, since it produces an optimal estimate (in the sense that the error is statistically minimized) given noise corrupted data. The EKF model is derived from an electrical-analog model of the left ventricle and systemic load. An observability study was a priori conducted on the model, restricted to the ejection phase, to validate the estimation procedure. The method has been evaluated with simulated data and produced good results (the estimate error was 7.14%).

An architecture for rapid prototyping of control schemes for artificial ventricles.

This paper presents an experimental system aimed at rapid prototyping of feedback control schemes for ventricular assist devices, and artificial ventricles in general. The system comprises a classical mock circulatory system, an actuated bellow-based ventricle chamber, and a software architecture for control schemes implementation and experimental data acquisition, visualization and storing. Several experiments have been carried out, showing good performance of ventricular pressure tracking control schemes.