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This dissertation is concerned with three problems within the field of optimization for agent--based systems. Firstly, the inverse optimal control problem is investigated for the single-agent system. Given a dynamic process, the goal is to recover the quadratic cost function from the observation of optimal control sequences. Such estimation could then help us develop a better understanding of the physical system and reproduce a similar optimal controller in other applications. Next, problems of optimization over networked systems are considered. A novel differential game approach is proposed for the optimal intrinsic formation control of multi-agent systems. As for the credit scoring problem, an optimal filtering framework is utilized to recursively improve the scoring accuracy based on dynamic network information. In paper A, the problem of finite horizon inverse optimal control problem is investigated, where the linear quadratic (LQ) cost function is required to be estimated from the optimal feedback controller. Although the infinite-horizon inverse LQ problem is well-studied with numerous results, the finite-horizon case is still an open problem. To the best of our knowledge, we propose the first complete result of the necessary and sufficient condition for the existence of corresponding LQ cost functions. Under feasible cases, the analytic expression of the whole solution space is derived and the equivalence of weighting matrices is discussed. For infeasible problems, an infinite dimensional convex problem is formulated to obtain a best-fit approximate solution with minimal control residual, where the optimality condition is solved under a static quadratic programming framework to facilitate the computation. In paper B, the optimal formation control problem of a multi-agent system is studied. The foraging behavior of N agents is modeled as a finite-horizon non-cooperative differential game under local information, and its Nash equilibrium is studied. The collaborative swarming behaviour derived from non-cooperative individual actions also sheds new light on understanding such phenomenon in the nature. The proposed framework has a tutorial meaning since a systematic approach for formation control is proposed, where the desired formation can be obtained by only intrinsically adjusting individual costs and network topology. In contrast to most of the existing methodologies based on regulating formation errors to the pre-defined pattern, the proposed method does not need to involve any information of the desired pattern beforehand. We refer to this type of formation control as intrinsic formation control. Patterns of regular polygons, antipodal formations and Platonic solids can be achieved as Nash equilibria of the game while inter-agent collisions are naturally avoided. Paper C considers the credit scoring problem by incorporating dynamic network information, where the advantages of such incorporation are investigated in two scenarios. Firstly, when the scoring publishment is merely individual--dependent, an optimal Bayesian filter is designed for risk prediction, where network observations are utilized to provide a reference for the bank on future financial decisions. Furthermore, a recursive Bayes estimator is proposed to improve the accuracy of score publishment by incorporating the dynamic network topology as well. It is shown that under the proposed evolution framework, the designed estimator has a higher precision than all the efficient estimators, and the mean square errors are strictly smaller than the Cramér-Rao lower bound for clients within a certain range of scores. / I denna avhandling behandlas tre problem inom optimering för agentbaserade system. Inledningsvis undersöks problemet rörande invers optimal styrning för ett system med en agent. Målet är att, givet en dynamisk process, återskapa den kvadratiska kostnadsfunktionen från observationer av sekvenser av optimal styrning. En sådan uppskattning kan ge ökad förståelse av det underliggande fysikaliska systemet, samt vara behjälplig vid konstruktion av en liknande optimal regulator för andra tillämpningar. Vidare betraktas problem rörande optimering över nätverkssystem. Ett nytt angreppssätt, baserat på differentialspel, föreslås för optimal intrinsisk formationsstyrning av system med fler agenter. För kreditutvärderingsproblemet utnyttjas ett filtreringsramverk för att rekursivt förbättra kreditvärderingens noggrannhet baserat på dynamisk nätverksinformation. I artikel A undersöks problemet med invers optimal styrning med ändlig tidshorisont, där den linjärkvadratiska (LQ) kostnadsfunktionen måste uppskattas från den optimala återkopplingsregulatorn. Trots att det inversa LQ-problemet med oändlig tidshorisont är välstuderat och med flertalet resultat, är fallet med ändlig tidshorisont fortfarande ett öppet problem. Så vitt vi vet presenterar vi det första kompletta resultatet med både tillräckliga och nödvändiga villkor för existens av en motsvarande LQ-kostnadsfunktion. I fallet med lösbara problem härleds ett analytiskt uttryck för hela lösningsrummet och frågan om ekvivalens med viktmatriser behandlas. För de olösbara problemen formuleras ett oändligtdimensionellt konvext optimeringsproblem för att hitta den bästa approximativa lösningen med den minsta styrresidualen. För att underlätta beräkningarna löses optimalitetsvillkoren i ett ramverk för statisk kvadratisk programmering. I artikel B studeras problemet rörande optimal formationsstyrning av ett multiagentsystem. Agenternas svärmbeteende modelleras som ett icke-kooperativt differentialspel med ändlig tidshorisont och enbart lokal information. Vi studerar detta spels Nashjämvikt. Att, ur icke-kooperativa individuella handlingar, härleda ett kollaborativt svärmbeteende kastar nytt ljus på vår förståelse av sådana, i naturen förekommande, fenomen. Det föreslagna ramverket är vägledande i den meningen att det är ett systematiskt tillvägagångssätt för formationsstyrning, där den önskade formeringen kan erhållas genom att endast inbördes justera individuella kostnader samt nätverkstopologin. I motstat till de flesta befintliga metoder, vilka baseras på att reglera felet i formeringen relativt det fördefinierade mönstret, så behöver den föreslagna metoden inte på förhand ta hänsyn till det önskade mönstret. Vi kallar denna typ av formationsstyrning för intrinsisk formationsstyrning. Mönster så som regelbundna polygoner, antipodala formeringar och Platonska kroppar kan uppnås som Nashjämvikter i spelet, samtidigt som kollisioner mellan agenter undviks på ett naturligt sätt. Artikel C behandlar kreditutvärderingsproblemet genom att lägga till dynamisk nätverksinformation. Fördelarna med en sådan integrering undersöks i två scenarier. Då kreditvärdigheten enbart är individberoende utformas ett optimalt Bayesiskt filter för riskvärdering, där observationer från nätverket används för att tillhandahålla en referens för banken på framtida finansiella beslut. Vidare föreslås en rekursiv Bayesisk estimator (stickprovsvariabel) för att förbättra noggrannheten på den skattade kreditvärdigheten genom att integrera även den dynamiska nätverkstopologin. Inom den föreslagna ramverket för tidsutveckling kan vi visa att, för kunder inom ett visst intervall av värderingar, har den utformade estimatorn högre precision än alla effektiva estimatorer och medelkvadrafelet är strikt mindre än den nedre gränsen från Cramér-Raos olikhet. / <p>QC 20190603</p>

Yes / Introduction: Evolution of a patient-reported symptom-based risk stratification system to redesign the suspected head and neck cancer (HNC) referral pathway (EVEREST-HN) will use a broad and open approach to the nomenclature and symptomatology. It aims to capture and utilise the patient reported symptoms in a modern way to identify patients’ clinical problems more effectively and risk stratify the patient. Method: The review followed the PRISMA checklist for scoping reviews. A search strategy was carried out using Medline, Embase and Web of Science between January 1st 2012 and October 31st 2023. All titles, abstracts and full paper were screened for eligibility, papers were assessed for inclusion using predetermined criteria. Data was extracted pertaining to the aims, type of study, cancer type, numbers of patients included and symptoms, presenting complaints or signs and symptoms. Results: There were 9,331 publications identified in the searches, following title screening 350 abstracts were reviewed for inclusion and 120 were considered for eligibility for the review. 48 publications met the eligibility criteria and were included in the final review. Data from almost 11,000 HNC patients was included. Twenty-one of the publications were from the UK, most were retrospective examination of patient records. Data was extracted and charted according to the anatomical area of the head and neck where the symptoms are subjectively and objectively found, and presented according to lay terms for symptoms, clinical terms for symptoms and the language of objective clinical findings. Discussion: Symptoms of HNC are common presenting complaints, interpreting these along with clinical history, examination and risk factors will inform a clinician’s decision to refer as suspected cancer. UK Head and Neck specialists believe a different way of triaging the referrals is needed to assess the clinical risk of an undiagnosed HNC. EVEREST-HN aims to achieve this using the patient history of their symptoms. This review has highlighted issues in terms of what is considered a symptom, a presenting complaint and a clinical finding or sign. / National Institute for Health and Care Research Programme Grant for Applied Research NIHR 202862.

published_or_final_version / Education / Master / Master of Education

Molecular docking has been extensively applied in virtual screening of small molecule libraries for lead identification and optimization. A necessary prerequisite for successful differentiation between active and non-active ligands is the accurate prediction of their binding affinities in the complex by use of docking scoring functions. However, many studies have shown rather poor correlations between docking scores and experimental binding affinities. Our work aimed to improve this correlation by implementing a multipose binding concept in the docking scoring scheme. Multipose binding, i.e., the property of certain protein-ligand complexes to exhibit different ligand binding modes, has been shown to occur in nature for a variety of molecules. We conducted a high-throughput docking study and implemented multipose binding in the scoring procedure by considering multiple docking solutions in binding affinity prediction. In general, improvement of the agreement between docking scores and experimental data was observed, and this was most pronounced in complexes with large and flexible ligands and high binding affinities. Further developments of the selection criteria for docking solutions for each individual complex are still necessary for a general utilization of the multipose binding concept for accurate binding affinity prediction by molecular docking.

I takt med att digitala medier har utvecklats under de senaste åren har köpresan för-ändrats till att kunder idag i ett mycket senare skede släpper in leverantörer i dialogen. Marketing Automation adresserar den problembilden och har växt fram som en brygga mellan sälj- och marknadsprocessen. Systemet ger möjlighet att effektivt och automatiserat utveckla leads (potentiell kund). Syftet med denna studie är att undersöka hur Marketing Automation påverkar sälj- och marknadsprocesserna. Vilka förutsättningar krävs för en implementation? Ökar lönsamheten? Vi har därför valt att i det teoretiska ramverket beskriva Marketing Automation och bland annat undersöka om ett införande av Marketing Automation medför att sälj- och marknadsorganisationerna slås samman till en organisatorisk enhet. I studien har vi dessutom kartlagt och beskrivit den moderna köpresan och det som ibland kallas intäktsorganisationen. Vi har funnit att Marketing Automation är relativt outforskat i en svensk kontext. För att utröna om teorin, som i stor utsträckning bygger på internationell litteratur och internationella undersökningar, går att överföra till en svensk kontext har vi valt att genomföra en kvalitativ studie i form av en fallstudie av leverantörer av produkter och tjänster inom området samt företag, med den gemensamma nämnaren att de re-presenterar ett kunskapsintensivt erbjudande och har implementerat lösningar för Marketing Automation. I vår analys finns en samsyn mellan leverantörer och kunder i förutsättningar för ett införande, men vi kan även se hur resultaten divergerar och pekar på implikationer, inte minst avseende måluppfyllnad och samverkan mellan sälj- och marknadsorgani-sationerna. Vår slutsats visar bland annat att Marketing Automation kan leda till uppfyllnad av mjuka värden i företaget men har inte bevisats leda till ökad lönsamhet per automatik. Vi ser lönsamhet och Return on Investment (ROI) som ett område som bör utforskas vidare. / Parallel to the evolution of digital media in recent years, the buyer’s journey has changed. B2B-customers today let suppliers in at the end of the process rather than from the beginning. Marketing Automation addresses that problem and has emerged as a bridge between the sales and marketing processes as it support efficient and au-tomated lead development. The purpose of this study is to examine how marketing automation affects the sales and marketing processes. What conditions are needed for an implementation? Will it increase profitability? We have therefore chosen to describe Marketing Automation, and in particular con-sider whether the introduction of marketing automation means that sales and market-ing organizations merges into one organizational unit? In the study, we have identi-fied and described the modern buyer’s journey and what sometimes is called the rev-enue department. We have found that Marketing Automation is relatively unexplored in a Swedish con-text. To explore if the theory, which is largely based on international literature and research, can be transferred to a Swedish context, we have chosen to conduct a quali-tative study and case study of suppliers of products and services in the area as well as companies, representing a knowledge based offering, which has implemented solu-tions for marketing automation. In our analysis, there is a general consensus between suppliers and customers of the conditions for implementation, but we can also see how the results diverge, not least regarding aspects such as increase of revenue, ROI and collaboration between sales and marketing organizations. Our conclusion shows that marketing automation can lead to fulfillment of the core values of the company but has not been proven to lead to increased profitability au-tomatically. We see profitability and ROI as potential areas of further exploration.

Le docking moléculaire est une méthode permettant de prédire l'orientation d'une molécule donnée relativement à une autre lorsque celles-ci forment un complexe. Le premier algorithme de docking moléculaire a vu jour en 1990 afin de trouver de nouveaux candidats face à la protéase du VIH-1. Depuis, l'utilisation de protocoles de docking est devenue une pratique standard dans le domaine de la conception de nouveaux médicaments. Typiquement, un protocole de docking comporte plusieurs phases. Il requiert l'échantillonnage exhaustif du site d'interaction où les éléments impliqués sont considérées rigides. Des algorithmes de clustering sont utilisés afin de regrouper les candidats à l'appariement similaires. Des méthodes d'affinage sont appliquées pour prendre en compte la flexibilité au sein complexe moléculaire et afin d'éliminer de possibles artefacts de docking. Enfin, des algorithmes d'évaluation sont utilisés pour sélectionner les meilleurs candidats pour le docking. Cette thèse présente de nouveaux algorithmes de protocoles de docking qui facilitent la prédiction des structures de complexes protéinaires, une des cibles les plus importantes parmi les cibles visées par les méthodes de conception de médicaments. Une première contribution concerne l‘algorithme Docktrina qui permet de prédire les conformations de trimères protéinaires triangulaires. Celui-ci prend en entrée des prédictions de contacts paire-à-paire à partir d'hypothèse de corps rigides. Ensuite toutes les combinaisons possibles de paires de monomères sont évalués à l'aide d'un test de distance RMSD efficace. Cette méthode à la fois rapide et efficace améliore l'état de l'art sur les protéines trimères. Deuxièmement, nous présentons RigidRMSD une librairie C++ qui évalue en temps constant les distances RMSD entre conformations moléculaires correspondant à des transformations rigides. Cette librairie est en pratique utile lors du clustering de positions de docking, conduisant à des temps de calcul améliorés d'un facteur dix, comparé aux temps de calcul des algorithmes standards. Une troisième contribution concerne KSENIA, une fonction d'évaluation à base de connaissance pour l'étude des interactions protéine-protéine. Le problème de la reconstruction de fonction d'évaluation est alors formulé et résolu comme un problème d'optimisation convexe. Quatrièmement, CARBON, un nouvel algorithme pour l'affinage des candidats au docking basés sur des modèles corps-rigides est proposé. Le problème d'optimisation de corps-rigides est vu comme le calcul de trajectoires quasi-statiques de corps rigides influencés par la fonction énergie. CARBON fonctionne aussi bien avec un champ de force classique qu'avec une fonction d'évaluation à base de connaissance. CARBON est aussi utile pour l'affinage de complexes moléculaires qui comportent des clashes stériques modérés à importants. Finalement, une nouvelle méthode permet d'estimer les capacités de prédiction des fonctions d'évaluation. Celle-ci permet d‘évaluer de façon rigoureuse la performance de la fonction d'évaluation concernée sur des benchmarks de complexes moléculaires. La méthode manipule la distribution des scores attribués et non pas directement les scores de conformations particulières, ce qui la rend avantageuse au regard des critères standard basés sur le score le plus élevé. Les méthodes décrites au sein de la thèse sont testées et validées sur différents benchmarks protéines-protéines. Les algorithmes implémentés ont été utilisés avec succès pour la compétition CAPRI concernant la prédiction de complexes protéine-protéine. La méthodologie développée peut facilement être adaptée pour de la reconnaissance d'autres types d'interactions moléculaires impliquant par exemple des ligands, de l'ARN… Les implémentations en C++ des différents algorithmes présentés seront mises à disposition comme SAMSON Elements de la plateforme logicielle SAMSON sur http://www.samson-connect.net ou sur http://nano-d.inrialpes.fr/software. / Molecular docking is a method that predicts orientation of one molecule with respect to another one when forming a complex. The first computational method of molecular docking was applied to find new candidates against HIV-1 protease in 1990. Since then, using of docking pipelines has become a standard practice in drug discovery. Typically, a docking protocol comprises different phases. The exhaustive sampling of the binding site upon rigid-body approximation of the docking subunits is required. Clustering algorithms are used to group similar binding candidates. Refinement methods are applied to take into account flexibility of the molecular complex and to eliminate possible docking artefacts. Finally, scoring algorithms are employed to select the best binding candidates. The current thesis presents novel algorithms of docking protocols that facilitate structure prediction of protein complexes, which belong to one of the most important target classes in the structure-based drug design. First, DockTrina - a new algorithm to predict conformations of triangular protein trimers (i.e. trimers with pair-wise contacts between all three pairs of proteins) is presented. The method takes as input pair-wise contact predictions from a rigid-body docking program. It then scans and scores all possible combinations of pairs of monomers using a very fast root mean square deviation (RMSD) test. Being fast and efficient, DockTrina outperforms state-of-the-art computational methods dedicated to predict structure of protein oligomers on the collected benchmark of protein trimers. Second, RigidRMSD - a C++ library that in constant time computes RMSDs between molecular poses corresponding to rigid-body transformations is presented. The library is practically useful for clustering docking poses, resulting in ten times speed up compared to standard RMSD-based clustering algorithms. Third, KSENIA - a novel knowledge-based scoring function for protein-protein interactions is developed. The problem of scoring function reconstruction is formulated and solved as a convex optimization problem. As a result, KSENIA is a smooth function and, thus, is suitable for the gradient-base refinement of molecular structures. Remarkably, it is shown that native interfaces of protein complexes provide sufficient information to reconstruct a well-discriminative scoring function. Fourth, CARBON - a new algorithm for the rigid-body refinement of docking candidates is proposed. The rigid-body optimization problem is viewed as the calculation of quasi-static trajectories of rigid bodies influenced by the energy function. To circumvent the typical problem of incorrect stepsizes for rotation and translation movements of molecular complexes, the concept of controlled advancement is introduced. CARBON works well both in combination with a classical force-field and a knowledge-based scoring function. CARBON is also suitable for refinement of molecular complexes with moderate and large steric clashes between its subunits. Finally, a novel method to evaluate prediction capability of scoring functions is introduced. It allows to rigorously assess the performance of the scoring function of interest on benchmarks of molecular complexes. The method manipulates with the score distributions rather than with scores of particular conformations, which makes it advantageous compared to the standard hit-rate criteria. The methods described in the thesis are tested and validated on various protein-protein benchmarks. The implemented algorithms are successfully used in the CAPRI contest for structure prediction of protein-protein complexes. The developed methodology can be easily adapted to the recognition of other types of molecular interactions, involving ligands, polysaccharides, RNAs, etc. The C++ versions of the presented algorithms will be made available as SAMSON Elements for the SAMSON software platform at http://www.samson-connect.net or at http://nano-d.inrialpes.fr/software.

Le docking moléculaire est une méthode permettant de prédire l'orientation d'une molécule donnée relativement à une autre lorsque celles-ci forment un complexe. Le premier algorithme de docking moléculaire a vu jour en 1990 afin de trouver de nouveaux candidats face à la protéase du VIH-1. Depuis, l'utilisation de protocoles de docking est devenue une pratique standard dans le domaine de la conception de nouveaux médicaments. Typiquement, un protocole de docking comporte plusieurs phases. Il requiert l'échantillonnage exhaustif du site d'interaction où les éléments impliqués sont considérées rigides. Des algorithmes de clustering sont utilisés afin de regrouper les candidats à l'appariement similaires. Des méthodes d'affinage sont appliquées pour prendre en compte la flexibilité au sein complexe moléculaire et afin d'éliminer de possibles artefacts de docking. Enfin, des algorithmes d'évaluation sont utilisés pour sélectionner les meilleurs candidats pour le docking. Cette thèse présente de nouveaux algorithmes de protocoles de docking qui facilitent la prédiction des structures de complexes protéinaires, une des cibles les plus importantes parmi les cibles visées par les méthodes de conception de médicaments. Une première contribution concerne l‘algorithme Docktrina qui permet de prédire les conformations de trimères protéinaires triangulaires. Celui-ci prend en entrée des prédictions de contacts paire-à-paire à partir d'hypothèse de corps rigides. Ensuite toutes les combinaisons possibles de paires de monomères sont évalués à l'aide d'un test de distance RMSD efficace. Cette méthode à la fois rapide et efficace améliore l'état de l'art sur les protéines trimères. Deuxièmement, nous présentons RigidRMSD une librairie C++ qui évalue en temps constant les distances RMSD entre conformations moléculaires correspondant à des transformations rigides. Cette librairie est en pratique utile lors du clustering de positions de docking, conduisant à des temps de calcul améliorés d'un facteur dix, comparé aux temps de calcul des algorithmes standards. Une troisième contribution concerne KSENIA, une fonction d'évaluation à base de connaissance pour l'étude des interactions protéine-protéine. Le problème de la reconstruction de fonction d'évaluation est alors formulé et résolu comme un problème d'optimisation convexe. Quatrièmement, CARBON, un nouvel algorithme pour l'affinage des candidats au docking basés sur des modèles corps-rigides est proposé. Le problème d'optimisation de corps-rigides est vu comme le calcul de trajectoires quasi-statiques de corps rigides influencés par la fonction énergie. CARBON fonctionne aussi bien avec un champ de force classique qu'avec une fonction d'évaluation à base de connaissance. CARBON est aussi utile pour l'affinage de complexes moléculaires qui comportent des clashes stériques modérés à importants. Finalement, une nouvelle méthode permet d'estimer les capacités de prédiction des fonctions d'évaluation. Celle-ci permet d‘évaluer de façon rigoureuse la performance de la fonction d'évaluation concernée sur des benchmarks de complexes moléculaires. La méthode manipule la distribution des scores attribués et non pas directement les scores de conformations particulières, ce qui la rend avantageuse au regard des critères standard basés sur le score le plus élevé. Les méthodes décrites au sein de la thèse sont testées et validées sur différents benchmarks protéines-protéines. Les algorithmes implémentés ont été utilisés avec succès pour la compétition CAPRI concernant la prédiction de complexes protéine-protéine. La méthodologie développée peut facilement être adaptée pour de la reconnaissance d'autres types d'interactions moléculaires impliquant par exemple des ligands, de l'ARN… Les implémentations en C++ des différents algorithmes présentés seront mises à disposition comme SAMSON Elements de la plateforme logicielle SAMSON sur http://www.samson-connect.net ou sur http://nano-d.inrialpes.fr/software. / Molecular docking is a method that predicts orientation of one molecule with respect to another one when forming a complex. The first computational method of molecular docking was applied to find new candidates against HIV-1 protease in 1990. Since then, using of docking pipelines has become a standard practice in drug discovery. Typically, a docking protocol comprises different phases. The exhaustive sampling of the binding site upon rigid-body approximation of the docking subunits is required. Clustering algorithms are used to group similar binding candidates. Refinement methods are applied to take into account flexibility of the molecular complex and to eliminate possible docking artefacts. Finally, scoring algorithms are employed to select the best binding candidates. The current thesis presents novel algorithms of docking protocols that facilitate structure prediction of protein complexes, which belong to one of the most important target classes in the structure-based drug design. First, DockTrina - a new algorithm to predict conformations of triangular protein trimers (i.e. trimers with pair-wise contacts between all three pairs of proteins) is presented. The method takes as input pair-wise contact predictions from a rigid-body docking program. It then scans and scores all possible combinations of pairs of monomers using a very fast root mean square deviation (RMSD) test. Being fast and efficient, DockTrina outperforms state-of-the-art computational methods dedicated to predict structure of protein oligomers on the collected benchmark of protein trimers. Second, RigidRMSD - a C++ library that in constant time computes RMSDs between molecular poses corresponding to rigid-body transformations is presented. The library is practically useful for clustering docking poses, resulting in ten times speed up compared to standard RMSD-based clustering algorithms. Third, KSENIA - a novel knowledge-based scoring function for protein-protein interactions is developed. The problem of scoring function reconstruction is formulated and solved as a convex optimization problem. As a result, KSENIA is a smooth function and, thus, is suitable for the gradient-base refinement of molecular structures. Remarkably, it is shown that native interfaces of protein complexes provide sufficient information to reconstruct a well-discriminative scoring function. Fourth, CARBON - a new algorithm for the rigid-body refinement of docking candidates is proposed. The rigid-body optimization problem is viewed as the calculation of quasi-static trajectories of rigid bodies influenced by the energy function. To circumvent the typical problem of incorrect stepsizes for rotation and translation movements of molecular complexes, the concept of controlled advancement is introduced. CARBON works well both in combination with a classical force-field and a knowledge-based scoring function. CARBON is also suitable for refinement of molecular complexes with moderate and large steric clashes between its subunits. Finally, a novel method to evaluate prediction capability of scoring functions is introduced. It allows to rigorously assess the performance of the scoring function of interest on benchmarks of molecular complexes. The method manipulates with the score distributions rather than with scores of particular conformations, which makes it advantageous compared to the standard hit-rate criteria. The methods described in the thesis are tested and validated on various protein-protein benchmarks. The implemented algorithms are successfully used in the CAPRI contest for structure prediction of protein-protein complexes. The developed methodology can be easily adapted to the recognition of other types of molecular interactions, involving ligands, polysaccharides, RNAs, etc. The C++ versions of the presented algorithms will be made available as SAMSON Elements for the SAMSON software platform at http://www.samson-connect.net or at http://nano-d.inrialpes.fr/software.

Made available in DSpace on 2016-06-02T20:06:06Z (GMT). No. of bitstreams: 1 4300.pdf: 2695135 bytes, checksum: c7742258a75f77aa35ccb54abc3439fe (MD5) Previous issue date: 2012-03-16 / Financiadora de Estudos e Projetos / In credit scoring problems, the interest is to associate to an element who request some kind of credit, a probability of default. However, traditional models uses samples biased because the data obtained from the tenderers has only clients who won a approval of a request for previous credit. In order to reduce the bias sample of these models, we use strategies to extract information about individuals rejected to be able to infer a response, good or bad payer. This is what we call the reject inference. With the use of these strategies, we also use the bagging technique (bootstrap aggregating), which consist in generate models based in some bootstrap samples of the training data in order to get a new predictor, when these models is combined. In this work we will discuss about some of the combination methods in the literature, especially the method of combination by logistic regression, although little used but with interesting results.We'll also discuss some strategies relating to reject inference. Analyses are given through a simulation study, in data sets generated and real data sets of public domain. / Em problemas de credit scoring, o interesse é associar a um elemento solicitante de algum tipo de crédito, uma probabilidade de inadimplência. No entanto, os modelos tradicionais utilizam amostras viesadas, pois constam apenas de dados obtidos dos proponentes que conseguiram a aprovação de uma solicitação de crédito anterior. Com o intuito de reduzir o vício amostral desses modelos, utilizamos estratégias para extrair informações acerca dos indivíduos rejeitados para que nele seja inferida uma resposta do tipo bom/- mau pagador. Isto é o que chamamos de inferência dos rejeitados. Juntamente com o uso dessas estratégias utilizamos a técnica bagging (bootstrap aggregating ), que é baseada na construção de diversos modelos a partir de réplicas bootstrap dos dados de treinamento, de modo que, quando combinados, gera um novo preditor. Nesse trabalho discutiremos sobre alguns dos métodos de combinação presentes na literatura, em especial o método de combinação via regressão logística, que é ainda pouco utilizado, mas com resultados interessantes. Discutiremos também as principais estratégias referentes à inferência dos rejeitados. As análises se dão por meio de um estudo simulação, em conjuntos de dados gerados e em conjuntos de dados reais de domínio público.

Made available in DSpace on 2016-06-02T20:06:06Z (GMT). No. of bitstreams: 1 4338.pdf: 1335557 bytes, checksum: 8e0bef5711ff8c398be194e335deecec (MD5) Previous issue date: 2012-02-28 / Universidade Federal de Sao Carlos / Classification consists in the discovery of rules of prediction to assist with planning and decision-making, being a continuously indispensable tool and a highly discussed subject in literature. As a special case in classification, we have the process of credit risk rating, within which there is interest in identifying good and bad paying customers through binary classification methods. Therefore, in many application backgrounds, as in financial, several techniques can be utilized, such as discriminating analysis, probit analysis, logistic regression and neural nets. However, the Probabilistic Nets technique, also known as Bayesian Networks, have showed itself as a practical convenient classification method with successful applications in several areas. In this paper, we aim to display the appliance of Probabilistic Nets in the classification scenario, specifically, the technique named K-dependence Bayesian Networks also known as KDB nets, as well as compared its performance with conventional techniques applied within context of the Credit Scoring and Medical diagnosis. Applications of the technique based in real and artificial datasets and its performance assisted by the bagging procedure will be displayed as results. / A classificação consiste na descoberta de regras de previsão para auxílio no planejamento e tomada de decisões, sendo uma ferramenta indispensável e um tema bastante discutido na literatura. Como caso especial de classificação, temos o processo de avaliação de risco de crédito, no qual temos o interesse de identificar clientes bons e maus pagadores através de métodos de classificação binária. Assim, em diversos enredos de aplicação, como nas financeiras, diversas técnicas podem ser utilizadas, tais como análise discriminante, análise probito, regressão logística e redes neurais. Porém, a técnica de Redes Probabilísticas, também conhecida como Redes Bayesianas, tem se mostrado um método prático de classificação e com aplicações bem sucedidas em diversos campos. Neste trabalho, visamos exibir a aplicação das Redes Probabilísticas no contexto de classificação, em específico, a técnica denominada Redes Probabilísticas com K-dependência, também conhecidas como redes KDB, bem como comparar seu desempenho com as técnicas convencionais aplicadas no contexto de Credit Scoring e Diagnose Médica. Exibiremos como resultado aplicações da técnica baseadas em conjuntos de dados reais e artificiais e seu desempenho auxiliado pelo procedimento de bagging.