Statistical relational learning of semantic models and grammar rules for 3D building reconstruction from 3D point clouds

Formal grammars are well suited for the estimation of models with an a-priori unknown number of parameters such as buildings and have proven their worth for 3D modeling and reconstruction of cities. However, the generation and design of corresponding grammar rules is a laborious task and relies on expert knowledge. This thesis presents novel approaches for the reduction of this effort using advanced machine learning methods resulting in automatically learned sophisticated grammar rules. Indeed, the learning of a wide range of sophisticated rules, that reflect the variety and complexity, is a challenging task. This is especially the case if a simultaneous machine learning of building structures and the underlying aggregation hierarchies as well as the building parameters and the constraints among them for a semantic interpretation is expected. Thus, in this thesis, an incremental approach is followed. It separates the structure learning from the parameter distribution learning of building parts. Moreover, the so far procedural approaches with formal grammars are mostly rather convenient for the generation of virtual city models than for the reconstruction of existing buildings. To this end, Inductive Logic Programming (ILP) techniques are transferred and applied for the first time in the field of 3D building modeling. This enables the automatic learning of declarative logic programs, which are equivalent to attribute grammars and separate the representation of buildings and their parts from the reconstruction task. A stepwise bottom-up learning, starting from the smallest atomic features of a building part together with the semantic, topological and geometric constraints, is a key to a successful learning of a whole building part. Only few examples are sufficient to learn from precise as well as noisy observations. The learning from uncertain data is realized using probability density functions, decision trees and uncertain projective geometry. This enables the handling and modeling of uncertain topology and geometric reasoning taking noise into consideration. The uncertainty of models itself is also considered. Therefore, a novel method is developed for the learning of Weighted Attribute Context-Free Grammar (WACFG). On the one hand, the structure learning of façades – context-free part of the Grammar – is performed based on annotated derivation trees using specific Support Vector Machines (SVMs). The latter are able to derive probabilistic models from structured data and to predict a most likely tree regarding to given observations. On the other hand, to the best of my knowledge, Statistical Relational Learning (SRL), especially Markov Logic Networks (MLNs), are applied for the first time in order to learn building part (shape and location) parameters as well as the constraints among these parts. The use of SRL enables to take profit from the elegant logical relational description and to benefit from the efficiency of statistical inference methods. In order to model latent prior knowledge and exploit the architectural regularities of buildings, a novel method is developed for the automatic identification of translational as well as axial symmetries. For symmetry identification a supervised machine learning approach is followed based on an SVM classifier. Building upon the classification results, algorithms are designed for the representation of symmetries using context-free grammars from authoritative building footprints. In all steps the machine learning is performed based on real- world data such as 3D point clouds and building footprints. The handling with uncertainty and occlusions is assured. The presented methods have been successfully applied on real data. The belonging classification and reconstruction results are shown.Statistisches relationales Lernen von semantischen Modellen und Grammatikregeln für 3D Gebäuderekonstruktion aus 3D Punktwolken Formale Grammatiken eignen sich sehr gut zur Schätzung von Modellen mit a-priori unbekannter Anzahl von Parametern und haben sich daher als guter Ansatz zur Rekonstruktion von Städten mittels 3D Stadtmodellen bewährt. Der Entwurf und die Erstellung der dazugehörigen Grammatikregeln benötigt jedoch Expertenwissen und ist mit großem Aufwand verbunden. Im Rahmen dieser Arbeit wurden Verfahren entwickelt, die diesen Aufwand unter Zuhilfenahme von leistungsfähigen Techniken des maschinellen Lernens reduzieren und automatisches Lernen von Regeln ermöglichen. Das Lernen umfangreicher Grammatiken, die die Vielfalt und Komplexität der Gebäude und ihrer Bestandteile widerspiegeln, stellt eine herausfordernde Aufgabe dar. Dies ist insbesondere der Fall, wenn zur semantischen Interpretation sowohl das Lernen der Strukturen und Aggregationshierarchien als auch von Parametern der zu lernenden Objekte gleichzeitig statt finden soll. Aus diesem Grund wird hier ein inkrementeller Ansatz verfolgt, der das Lernen der Strukturen vom Lernen der Parameterverteilungen und Constraints zielführend voneinander trennt. Existierende prozedurale Ansätze mit formalen Grammatiken sind eher zur Generierung von synthetischen Stadtmodellen geeignet, aber nur bedingt zur Rekonstruktion existierender Gebäude nutzbar. Hierfür werden in dieser Schrift Techniken der Induktiven Logischen Programmierung (ILP) zum ersten Mal auf den Bereich der 3D Gebäudemodellierung übertragen. Dies führt zum Lernen deklarativer logischer Programme, die hinsichtlich ihrer Ausdrucksstärke mit attributierten Grammatiken gleichzusetzen sind und die Repräsentation der Gebäude von der Rekonstruktionsaufgabe trennen. Das Lernen von zuerst disaggregierten atomaren Bestandteilen sowie der semantischen, topologischen und geometrischen Beziehungen erwies sich als Schlüssel zum Lernen der Gesamtheit eines Gebäudeteils. Das Lernen erfolgte auf Basis einiger weniger sowohl präziser als auch verrauschter Beispielmodelle. Um das Letztere zu ermöglichen, wurde auf Wahrscheinlichkeitsdichteverteilungen, Entscheidungsbäumen und unsichere projektive Geometrie zurückgegriffen. Dies erlaubte den Umgang mit und die Modellierung von unsicheren topologischen Relationen sowie unscharfer Geometrie. Um die Unsicherheit der Modelle selbst abbilden zu können, wurde ein Verfahren zum Lernen Gewichteter Attributierter Kontextfreier Grammatiken (Weighted Attributed Context-Free Grammars, WACFG) entwickelt. Zum einen erfolgte das Lernen der Struktur von Fassaden –kontextfreier Anteil der Grammatik – aus annotierten Herleitungsbäumen mittels spezifischer Support Vektor Maschinen (SVMs), die in der Lage sind, probabilistische Modelle aus strukturierten Daten abzuleiten und zu prädizieren. Zum anderen wurden nach meinem besten Wissen Methoden des statistischen relationalen Lernens (SRL), insbesondere Markov Logic Networks (MLNs), erstmalig zum Lernen von Parametern von Gebäuden sowie von bestehenden Relationen und Constraints zwischen ihren Bestandteilen eingesetzt. Das Nutzen von SRL erlaubt es, die eleganten relationalen Beschreibungen der Logik mit effizienten Methoden der statistischen Inferenz zu verbinden. Um latentes Vorwissen zu modellieren und architekturelle Regelmäßigkeiten auszunutzen, ist ein Verfahren zur automatischen Erkennung von Translations- und Spiegelsymmetrien und deren Repräsentation mittels kontextfreier Grammatiken entwickelt worden. Hierfür wurde mittels überwachtem Lernen ein SVM-Klassifikator entwickelt und implementiert. Basierend darauf wurden Algorithmen zur Induktion von Grammatikregeln aus Grundrissdaten entworfen

Machine Learning Enabled Functional Discovery in Yeast Systems Biology

Saccharomyces cerevisiae is a well-studied organism, yet roughly 20 percent of its proteins remain poorly characterized. Recent studies also seem to indicate that the pace of functional discovery is slow. Previous work has implied that the most probable path forward is via not only regular automation but fully autonomous systems that can automatically guide and perform high-throughput experimentation. This thesis explores various concepts to accelerate and perform functional discovery of gene and protein functions in Saccharomyces cerevisiae. It does so by combining ideas from artificial intelligence, such as active learning, with highthroughput analytical techniques like mass-spectrometry. The work performed as the basis for this thesis also served to aid in the further characterization of different aspects of yeast systems biology. Specifically, it delved into the diauxic shift and its regulators through the lens of untargeted metabolomics, as well as the regulatory patterns behind genome-wide intracellular proteomic abundances.We find that it is essential not only to develop tools and techniques for facilitating high-throughput experimentation, but also to ensure their optimal utilization of already existing knowledge. It is also of paramount importance to ensure a holistic and encompassing view of systems biology by more fully integrating and using different levels of cellular organization and analytical techniques

Evolutionary Computation and QSAR Research

[Abstract] The successful high throughput screening of molecule libraries for a specific biological property is one of the main improvements in drug discovery. The virtual molecular filtering and screening relies greatly on quantitative structure-activity relationship (QSAR) analysis, a mathematical model that correlates the activity of a molecule with molecular descriptors. QSAR models have the potential to reduce the costly failure of drug candidates in advanced (clinical) stages by filtering combinatorial libraries, eliminating candidates with a predicted toxic effect and poor pharmacokinetic profiles, and reducing the number of experiments. To obtain a predictive and reliable QSAR model, scientists use methods from various fields such as molecular modeling, pattern recognition, machine learning or artificial intelligence. QSAR modeling relies on three main steps: molecular structure codification into molecular descriptors, selection of relevant variables in the context of the analyzed activity, and search of the optimal mathematical model that correlates the molecular descriptors with a specific activity. Since a variety of techniques from statistics and artificial intelligence can aid variable selection and model building steps, this review focuses on the evolutionary computation methods supporting these tasks. Thus, this review explains the basic of the genetic algorithms and genetic programming as evolutionary computation approaches, the selection methods for high-dimensional data in QSAR, the methods to build QSAR models, the current evolutionary feature selection methods and applications in QSAR and the future trend on the joint or multi-task feature selection methods.Instituto de Salud Carlos III, PIO52048Instituto de Salud Carlos III, RD07/0067/0005Ministerio de Industria, Comercio y Turismo; TSI-020110-2009-53)Galicia. Consellería de Economía e Industria; 10SIN105004P

Graph Neural Networks and its applications

This project will explore some of the most prominent Graph Neural Network variants and apply them to two tasks: approximation of the community detection Girvan-Newman algorithm and compiled code snippet classification

East-West Paths to Unconventional Computing

Unconventional computing is about breaking boundaries in thinking, acting and computing. Typical topics of this non-typical field include, but are not limited to physics of computation, non-classical logics, new complexity measures, novel hardware, mechanical, chemical and quantum computing. Unconventional computing encourages a new style of thinking while practical applications are obtained from uncovering and exploiting principles and mechanisms of information processing in and functional properties of, physical, chemical and living systems; in particular, efficient algorithms are developed, (almost) optimal architectures are designed and working prototypes of future computing devices are manufactured. This article includes idiosyncratic accounts of ‘unconventional computing’ scientists reflecting on their personal experiences, what attracted them to the field, their inspirations and discoveries.info:eu-repo/semantics/publishedVersio

A relational learning approach to Structure-Activity Relationships in drug design toxicity studies.

It has been recognized that the development of new therapeutic drugs is a complex and expensive process. A large number of factors affect the activity in vivo of putative candidate molecules and the propensity for causing adverse and toxic effects is recognized as one of the major hurdles behind the current "target-rich, lead-poor" scenario. Structure-Activity Relationship (SAR) studies, using relational Machine Learning (ML) algorithms, have already been shown to be very useful in the complex process of rational drug design. Despite the ML successes, human expertise is still of the utmost importance in the drug development process. An iterative process and tight integration between the models developed by ML algorithms and the know-how of medicinal chemistry experts would be a very useful symbiotic approach. In this paper we describe a software tool that achieves that goal--iLogCHEM. The tool allows the use of Relational Learners in the task of identifying molecules or molecular fragments with potential to produce toxic effects, and thus help in stream-lining drug design in silico. It also allows the expert to guide the search for useful molecules without the need to know the details of the algorithms used. The models produced by the algorithms may be visualized using a graphical interface, that is of common use amongst researchers in structural biology and medicinal chemistry. The graphical interface enables the expert to provide feedback to the learning system. The developed tool has also facilities to handle the similarity bias typical of large chemical databases. For that purpose the user can filter out similar compounds when assembling a data set. Additionally, we propose ways of providing background knowledge for Relational Learners using the results of Graph Mining algorithms. Copyright 2011 The Author(s). Published by Journal of Integrative Bioinformatics