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  • 1.
    Bae, Juhee
    et al.
    University of Skövde, School of Informatics. University of Skövde, The Informatics Research Centre.
    Karlsson, Alexander
    University of Skövde, School of Informatics. University of Skövde, The Informatics Research Centre.
    Mellin, Jonas
    University of Skövde, The Informatics Research Centre. University of Skövde, School of Informatics.
    Ståhl, Niclas
    University of Skövde, School of Informatics. University of Skövde, The Informatics Research Centre.
    Torra, Vicenç
    University of Skövde, School of Informatics. University of Skövde, The Informatics Research Centre.
    Complex Data Analysis2019In: Data science in Practice / [ed] Alan Said, Vicenç Torra, Springer, 2019, p. 157-169Chapter in book (Refereed)
    Abstract [en]

    Data science applications often need to deal with data that does not fit into the standard entity-attribute-value model. In this chapter we discuss three of these other types of data. We discuss texts, images and graphs. The importance of social media is one of the reason for the interest on graphs as they are a way to represent social networks and, in general, any type of interaction between people. In this chapter we present examples of tools that can be used to extract information and, thus, analyze these three types of data. In particular, we discuss topic modeling using a hierarchical statistical model as a way to extract relevant topics from texts, image analysis using convolutional neural networks, and measures and visual methods to summarize information from graphs.

  • 2.
    Duarte, Denio
    et al.
    Universidade Federal da Fronteira Sul Chapecó Brazil.
    Ståhl, Niclas
    University of Skövde, School of Informatics. University of Skövde, The Informatics Research Centre.
    Machine Learning: A Concise Overview2019In: Data science in Practice / [ed] Alan Said, Vicenç Torra, Springer, 2019, p. 27-58Chapter in book (Refereed)
    Abstract [en]

    Machine learning is a sub-field of computer science that aims to make computers learn. It is a simple view of this field, but since the first computer was built, we have wondered whether or not they can learn as we do.

  • 3.
    Ståhl, Niclas
    University of Skövde, School of Informatics. University of Skövde, The Informatics Research Centre.
    Challenges and opportunities of analysing complex data using deep learning2017Report (Other academic)
  • 4.
    Ståhl, Niclas
    et al.
    University of Skövde, School of Informatics. University of Skövde, The Informatics Research Centre.
    Falkman, Göran
    University of Skövde, School of Informatics. University of Skövde, The Informatics Research Centre.
    Karlsson, Alexander
    University of Skövde, School of Informatics. University of Skövde, The Informatics Research Centre.
    Mathiason, Gunnar
    University of Skövde, School of Informatics. University of Skövde, The Informatics Research Centre.
    Boström, Jonas
    Department of Medicinal Chemistry, CVMD iMED, AstraZeneca, Mölndal, Sweden.
    Deep Convolutional Neural Networks for the Prediction of Molecular Properties: Challenges and Opportunities Connected to the Data2018In: Journal of Integrative Bioinformatics, E-ISSN 1613-4516, Vol. 16, no 1Article in journal (Refereed)
    Abstract [en]

    We present a flexible deep convolutional neural network method for the analysis of arbitrary sized graph structures representing molecules. This method, which makes use of the Lipinski RDKit module, an open-source cheminformatics software, enables the incorporation of any global molecular (such as molecular charge and molecular weight) and local (such as atom hybridization and bond orders) information. In this paper, we show that this method significantly outperforms another recently proposed method based on deep convolutional neural networks on several datasets that are studied. Several best practices for training deep convolutional neural networks on chemical datasets are also highlighted within the article, such as how to select the information to be included in the model, how to prevent overfitting and how unbalanced classes in the data can be handled.

  • 5.
    Ståhl, Niclas
    et al.
    University of Skövde, School of Informatics. University of Skövde, The Informatics Research Centre.
    Falkman, Göran
    University of Skövde, School of Informatics. University of Skövde, The Informatics Research Centre.
    Karlsson, Alexander
    University of Skövde, School of Informatics. University of Skövde, The Informatics Research Centre.
    Mathiason, Gunnar
    University of Skövde, School of Informatics. University of Skövde, The Informatics Research Centre.
    Boström, Jonas
    Medicinal Chemistry, Early Cardiovascular, Renal and Metabolism, R&D BioPharmaceuticals , AstraZeneca , Mölndal , Sweden.
    Deep Reinforcement Learning for Multiparameter Optimization in de novo Drug Design2019In: Journal of Chemical Information and Modeling, ISSN 1549-9596, E-ISSN 1549-960X, Vol. 59, no 7, p. 3166-3176Article in journal (Refereed)
    Abstract [en]

    In medicinal chemistry programs it is key to design and make compounds that are efficacious and safe. This is a long, complex, and difficult multiparameter optimization process, often including several properties with orthogonal trends. New methods for the automated design of compounds against profiles of multiple properties are thus of great value. Here we present a fragment-based reinforcement learning approach based on an actor-critic model, for the generation of novel molecules with optimal properties. The actor and the critic are both modeled with bidirectional long short-term memory (LSTM) networks. The AI method learns how to generate new compounds with desired properties by starting from an initial set of lead molecules and then improving these by replacing some of their fragments. A balanced binary tree based on the similarity of fragments is used in the generative process to bias the output toward structurally similar molecules. The method is demonstrated by a case study showing that 93% of the generated molecules are chemically valid and more than a third satisfy the targeted objectives, while there were none in the initial set.

  • 6.
    Ståhl, Niclas
    et al.
    University of Skövde, School of Informatics. University of Skövde, The Informatics Research Centre.
    Falkman, Göran
    University of Skövde, School of Informatics. University of Skövde, The Informatics Research Centre.
    Karlsson, Alexander
    University of Skövde, School of Informatics. University of Skövde, The Informatics Research Centre.
    Mathiason, Gunnar
    University of Skövde, School of Informatics. University of Skövde, The Informatics Research Centre.
    Boström, Jonas
    Department of Medicinal Chemistry, CVMD iMED, AstraZeneca, Sweden.
    Improving the use of deep convolutional neural networks for the prediction of molecular properties2019In: Practical Applications of Computational Biology and Bioinformatics, 12th International Conference / [ed] Florentino Fdez-Riverola, Mohd Saberi Mohamad, Miguel Rocha, Juan F. De Paz, Pascual González, Cham: Springer, 2019, Vol. 803, p. 71-79Conference paper (Refereed)
    Abstract [en]

    We present a flexible deep convolutional neural network method for the analyse of arbitrary sized graph structures representing molecules. The method makes use of RDKit, an open-source cheminformatics software, allowing the incorporation of any global molecular (such as molecular charge) and local (such as atom type) information. We evaluate the method on the Side Effect Resource (SIDER) v4.1 dataset and show that it significantly outperforms another recently proposed method based on deep convolutional neural networks. We also reflect on how different types of information and input data affect the predictive power of our model. This reflection highlights several open problems that should be solved to further improve the use of deep learning within cheminformatics.

  • 7.
    Ståhl, Niclas
    et al.
    University of Skövde, School of Informatics. University of Skövde, The Informatics Research Centre.
    Falkman, Göran
    University of Skövde, School of Informatics. University of Skövde, The Informatics Research Centre.
    Mathiason, Gunnar
    University of Skövde, School of Informatics. University of Skövde, The Informatics Research Centre.
    Karlsson, Alexander
    University of Skövde, School of Informatics. University of Skövde, The Informatics Research Centre.
    A self-organizing ensemble of deep neural networks for the classification of data from complex processes2018In: INFORMATION PROCESSING AND MANAGEMENT OF UNCERTAINTY IN KNOWLEDGE-BASED SYSTEMS: APPLICATIONS, IPMU 2018, PT III / [ed] Medina, J., Ojeda-Aciego, M., Verdegay, J.L., Perfilieva, I., Bouchon-Meunier, B., Yager, R.R., 2018, Vol. 855, p. 248-259Conference paper (Refereed)
    Abstract [en]

    We present a new self-organizing algorithm for classification of a data that combines and extends the strengths of several common machine learning algorithms, such as algorithms in self-organizing neural networks, ensemble methods and deep neural networks. The increased expression power is combined with the explanation power of self-organizing networks. Our algorithm outperforms both deep neural networks and ensembles of deep neural networks. For our evaluation case, we use production monitoring data from a complex steel manufacturing process, where data is both high-dimensional and has many nonlinear interdependencies. In addition to the improved prediction score, the algorithm offers a new deep-learning based approach for how computational resources can be focused in data exploration, since the algorithm points out areas of the input space that are more challenging to learn.

  • 8.
    Ståhl, Niclas
    et al.
    University of Skövde, School of Informatics. University of Skövde, The Informatics Research Centre.
    Mathiason, Gunnar
    University of Skövde, School of Informatics. University of Skövde, The Informatics Research Centre.
    Falkman, Göran
    University of Skövde, School of Informatics. University of Skövde, The Informatics Research Centre.
    Karlsson, Alexander
    University of Skövde, School of Informatics. University of Skövde, The Informatics Research Centre.
    Using recurrent neural networks with attention for detecting problematic slab shapes in steel rolling2019In: Applied Mathematical Modelling, ISSN 0307-904X, E-ISSN 1872-8480, Vol. 70, p. 365-377Article in journal (Refereed)
    Abstract [en]

    The competitiveness in the manufacturing industry raises demands for using recent data analysis algorithms for manufacturing process development. Data-driven analysis enables extraction of novel knowledge from already existing sensors and data, which is necessary for advanced manufacturing process refinement involving aged machinery. Improved data analysis enables factories to stay competitive against newer factories, but without any hefty investment. In large manufacturing operations, the dependencies between data are highly complex and therefore very difficult to analyse manually. This paper applies a deep learning approach, using a recurrent neural network with long short term memory cells together with an attention mechanism to model the dependencies between the measured product shape, as measured before the most critical manufacturing operation, and the final product quality. Our approach predicts the ratio of flawed products already before the critical operation with an AUC-ROC score of 0.85, i.e., we can detect more than 80 % of all flawed products while having less than 25 % false positive predictions (false alarms). In contrast to previous deep learning approaches, our method shows how the recurrent neural network reasons about the input shape, using the attention mechanism to point out which parts of the product shape that have the highest influence on the predictions. Such information is crucial for both process developers, in order to understand and improve the process, and for process operators who can use the information to learn how to better trust the predictions and control the process.

1 - 8 of 8
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