Commenced in January 2007
Frequency: Monthly
Edition: International
Paper Count: 8

Search results for: Lasso

8 Model-Driven and Data-Driven Approaches for Crop Yield Prediction: Analysis and Comparison

Authors: Xiangtuo Chen, Paul-Henry Cournéde

Abstract:

Crop yield prediction is a paramount issue in agriculture. The main idea of this paper is to find out efficient way to predict the yield of corn based meteorological records. The prediction models used in this paper can be classified into model-driven approaches and data-driven approaches, according to the different modeling methodologies. The model-driven approaches are based on crop mechanistic modeling. They describe crop growth in interaction with their environment as dynamical systems. But the calibration process of the dynamic system comes up with much difficulty, because it turns out to be a multidimensional non-convex optimization problem. An original contribution of this paper is to propose a statistical methodology, Multi-Scenarios Parameters Estimation (MSPE), for the parametrization of potentially complex mechanistic models from a new type of datasets (climatic data, final yield in many situations). It is tested with CORNFLO, a crop model for maize growth. On the other hand, the data-driven approach for yield prediction is free of the complex biophysical process. But it has some strict requirements about the dataset. A second contribution of the paper is the comparison of these model-driven methods with classical data-driven methods. For this purpose, we consider two classes of regression methods, methods derived from linear regression (Ridge and Lasso Regression, Principal Components Regression or Partial Least Squares Regression) and machine learning methods (Random Forest, k-Nearest Neighbor, Artificial Neural Network and SVM regression). The dataset consists of 720 records of corn yield at county scale provided by the United States Department of Agriculture (USDA) and the associated climatic data. A 5-folds cross-validation process and two accuracy metrics: root mean square error of prediction(RMSEP), mean absolute error of prediction(MAEP) were used to evaluate the crop prediction capacity. The results show that among the data-driven approaches, Random Forest is the most robust and generally achieves the best prediction error (MAEP 4.27%). It also outperforms our model-driven approach (MAEP 6.11%). However, the method to calibrate the mechanistic model from dataset easy to access offers several side-perspectives. The mechanistic model can potentially help to underline the stresses suffered by the crop or to identify the biological parameters of interest for breeding purposes. For this reason, an interesting perspective is to combine these two types of approaches.

Keywords: Particle Swarm Optimization, Sensitivity Analysis, Crop Model, random forest, crop yield prediction, paramater estimation

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7 Use of NMMO Pretreatment for Biogas Production from Oil Palm Empty Fruit Bunch

Authors: Ria Millati, Fiametta A. Purwandari, Adhitya P. Sanjaya, Muhammad N. Cahyanto, I. Sarvari Horvath, Claes Niklasson, Mohammad J. Taherzadeh

Abstract:

Pretreatment of oil palm empty fruit bunch (OPEFB) with N-Methylmorpholine-N-oxide (NMMO) to enhance biogas production was investigated. The pretreatments were performed at 90 and 120ºC for 1, 3, and 5 h using three different concentrations of NMMO of 73%, 79%, and 85%. The pretreated OPEFB was subsequently anaerobically digested to produce biogas. After pretreatment, there were no significant changes of the main composition of OPEFB and the maximum total solid recovery was 92%. The amorphous phase was increased up to 78% at pretreatment condition using 85% NMMO solution for 3 h at 120oC. In general, higher concentration of NMMO and higher temperature resulted in increased amorphous form and higher biogas production. The best results of biogas production reached enhancement of methane yield of 148% compared to the untreated OPEFB and increased in digestion of 94% compared to starch as reference.

Keywords: Biogas, Pretreatment, oil palm empty fruit bunch, NMMO

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6 Full-genomic Network Inference for Non-model organisms: A Case Study for the Fungal Pathogen Candida albicans

Authors: Jörg Linde, Ekaterina Buyko, Robert Altwasser, Udo Hahn, Reinhard Guthke

Abstract:

Reverse engineering of full-genomic interaction networks based on compendia of expression data has been successfully applied for a number of model organisms. This study adapts these approaches for an important non-model organism: The major human fungal pathogen Candida albicans. During the infection process, the pathogen can adapt to a wide range of environmental niches and reversibly changes its growth form. Given the importance of these processes, it is important to know how they are regulated. This study presents a reverse engineering strategy able to infer fullgenomic interaction networks for C. albicans based on a linear regression, utilizing the sparseness criterion (LASSO). To overcome the limited amount of expression data and small number of known interactions, we utilize different prior-knowledge sources guiding the network inference to a knowledge driven solution. Since, no database of known interactions for C. albicans exists, we use a textmining system which utilizes full-text research papers to identify known regulatory interactions. By comparing with these known regulatory interactions, we find an optimal value for global modelling parameters weighting the influence of the sparseness criterion and the prior-knowledge. Furthermore, we show that soft integration of prior-knowledge additionally improves the performance. Finally, we compare the performance of our approach to state of the art network inference approaches.

Keywords: Modelling, Reverse Engineering, pathogen, network inference, Linear Regression, Candida albicans, LASSO, mutual information, text-mining

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5 Toward a Use of Ontology to Reinforcing Semantic Classification of Message Based On LSA

Authors: S. Lgarch, M. Khalidi Idrissi, S. Bennani

Abstract:

For best collaboration, Asynchronous tools and particularly the discussion forums are the most used thanks to their flexibility in terms of time. To convey only the messages that belong to a theme of interest of the tutor in order to help him during his tutoring work, use of a tool for classification of these messages is indispensable. For this we have proposed a semantics classification tool of messages of a discussion forum that is based on LSA (Latent Semantic Analysis), which includes a thesaurus to organize the vocabulary. Benefits offered by formal ontology can overcome the insufficiencies that a thesaurus generates during its use and encourage us then to use it in our semantic classifier. In this work we propose the use of some functionalities that a OWL ontology proposes. We then explain how functionalities like “ObjectProperty", "SubClassOf" and “Datatype" property make our classification more intelligent by way of integrating new terms. New terms found are generated based on the first terms introduced by tutor and semantic relations described by OWL formalism.

Keywords: Semantic Web, e-Learning, Ontology, OWL, tutoring, semantic relations, thesaurus, Classification of messages, collaborative communication tools, discussion forum, formal description, latente semantic analysis

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4 Novel Hybrid Method for Gene Selection and Cancer Prediction

Authors: Liping Jing, Michael K. Ng, Tieyong Zeng

Abstract:

Microarray data profiles gene expression on a whole genome scale, therefore, it provides a good way to study associations between gene expression and occurrence or progression of cancer. More and more researchers realized that microarray data is helpful to predict cancer sample. However, the high dimension of gene expressions is much larger than the sample size, which makes this task very difficult. Therefore, how to identify the significant genes causing cancer becomes emergency and also a hot and hard research topic. Many feature selection algorithms have been proposed in the past focusing on improving cancer predictive accuracy at the expense of ignoring the correlations between the features. In this work, a novel framework (named by SGS) is presented for stable gene selection and efficient cancer prediction . The proposed framework first performs clustering algorithm to find the gene groups where genes in each group have higher correlation coefficient, and then selects the significant genes in each group with Bayesian Lasso and important gene groups with group Lasso, and finally builds prediction model based on the shrinkage gene space with efficient classification algorithm (such as, SVM, 1NN, Regression and etc.). Experiment results on real world data show that the proposed framework often outperforms the existing feature selection and prediction methods, say SAM, IG and Lasso-type prediction model.

Keywords: Clustering, classification, Gene Selection, LASSO, Cancer Prediction

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3 Word Recognition and Learning based on Associative Memories and Hidden Markov Models

Authors: Zöhre Kara Kayikci, Günther Palm

Abstract:

A word recognition architecture based on a network of neural associative memories and hidden Markov models has been developed. The input stream, composed of subword-units like wordinternal triphones consisting of diphones and triphones, is provided to the network of neural associative memories by hidden Markov models. The word recognition network derives words from this input stream. The architecture has the ability to handle ambiguities on subword-unit level and is also able to add new words to the vocabulary during performance. The architecture is implemented to perform the word recognition task in a language processing system for understanding simple command sentences like “bot show apple".

Keywords: Hidden Markov Models, Hebbian learning, word recognition, neuralassociative memories

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2 Accurate Calculation of Free Frequencies of Beams and Rectangular Plates

Authors: R .Lassoued, M. Guenfoud

Abstract:

An accurate procedure to determine free vibrations of beams and plates is presented. The natural frequencies are exact solutions of governing vibration equations witch load to a nonlinear homogeny system. The bilinear and linear structures considered simulate a bridge. The dynamic behavior of this one is analyzed by using the theory of the orthotropic plate simply supported on two sides and free on the two others. The plate can be excited by a convoy of constant or harmonic loads. The determination of the dynamic response of the structures considered requires knowledge of the free frequencies and the shape modes of vibrations. Our work is in this context. Indeed, we are interested to develop a self-consistent calculation of the Eigen frequencies. The formulation is based on the determination of the solution of the differential equations of vibrations. The boundary conditions corresponding to the shape modes permit to lead to a homogeneous system. Determination of the noncommonplace solutions of this system led to a nonlinear problem in Eigen frequencies. We thus, develop a computer code for the determination of the eigenvalues. It is based on a method of bisection with interpolation whose precision reaches 10 -12. Moreover, to determine the corresponding modes, the calculation algorithm that we develop uses the method of Gauss with a partial optimization of the "pivots" combined with an inverse power procedure. The Eigen frequencies of a plate simply supported along two opposite sides while considering the two other free sides are thus analyzed. The results could be generalized with the case of a beam by regarding it as a plate with low width. We give, in this paper, some examples of treated cases. The comparison with results presented in the literature is completely satisfactory.

Keywords: Beams, rectangular plates, Free frequencies

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1 Morphological Description of Cervical Cell Images for the Pathological Recognition

Authors: N. Lassouaoui, L. Hamami, N. Nouali

Abstract:

The tracking allows to detect the tumor affections of cervical cancer, it is particularly complex and consuming time, because it consists in seeking some abnormal cells among a cluster of normal cells. In this paper, we present our proposed computer system for helping the doctors in tracking the cervical cancer. Knowing that the diagnosis of the malignancy is based in the set of atypical morphological details of all cells, herein, we present an unsupervised genetic algorithm for the separation of cell components since the diagnosis is doing by analysis of the core and the cytoplasm. We give also the various algorithms used for computing the morphological characteristics of cells (Ratio core/cytoplasm, cellular deformity, ...) necessary for the recognition of illness.

Keywords: Recognition, Segmentation, Morphological Analysis, Cervical cell

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