An incremental approach to genetic algorithms based classification

Incremental learning has been widely addressed in the machine learning literature to cope with learning tasks where the learning environment is ever changing or training samples become available over time. However, most research work explores incremental learning with statistical algorithms or neural networks, rather than evolutionary algorithms. The work in this paper employs genetic algorithms (GAs) as basic learning algorithms for incremental learning within one or more classifier agents in a multi-agent environment. Four new approaches with different initialization schemes are proposed. They keep the old solutions and use an “integration” operation to integrate them with new elements to accommodate new attributes, while biased mutation and crossover operations are adopted to further evolve a reinforced solution. The simulation results on benchmark classification data sets show that the proposed approaches can deal with the arrival of new input attributes and integrate them with the original input space. It is also shown that the proposed approaches can be successfully used for incremental learning and improve classification rates as compared to the retraining GA. Possible applications for continuous incremental training and feature selection are also discussed

Incremental multiple objective genetic algorithms

This paper presents a new genetic algorithm approach to multi-objective optimization problemsIncremental Multiple Objective Genetic Algorithms (IMOGA). Different from conventional MOGA methods, it takes each objective into consideration incrementally. The whole evolution is divided into as many phases as the number of objectives, and one more objective is considered in each phase. Each phase is composed of two stages: first, an independent population is evolved to optimize one specific objective; second, the better-performing individuals from the evolved single-objective population and the multi-objective population evolved in the last phase are joined together by the operation of integration. The resulting population then becomes an initial multi-objective population, to which a multi-objective evolution based on the incremented objective set is applied. The experiment results show that, in most problems, the performance of IMOGA is better than that of three other MOGAs, NSGA-II, SPEA and PAES. IMOGA can find more solutions during the same time span, and the quality of solutions is better

Foundations and modelling of dynamic networks using Dynamic Graph Neural Networks: A survey

Dynamic networks are used in a wide range of fields, including social network analysis, recommender systems, and epidemiology. Representing complex networks as structures changing over time allow network models to leverage not only structural but also temporal patterns. However, as dynamic network literature stems from diverse fields and makes use of inconsistent terminology, it is challenging to navigate. Meanwhile, graph neural networks (GNNs) have gained a lot of attention in recent years for their ability to perform well on a range of network science tasks, such as link prediction and node classification. Despite the popularity of graph neural networks and the proven benefits of dynamic network models, there has been little focus on graph neural networks for dynamic networks. To address the challenges resulting from the fact that this research crosses diverse fields as well as to survey dynamic graph neural networks, this work is split into two main parts. First, to address the ambiguity of the dynamic network terminology we establish a foundation of dynamic networks with consistent, detailed terminology and notation. Second, we present a comprehensive survey of dynamic graph neural network models using the proposed terminologyComment: 28 pages, 9 figures, 8 table

Categorical Ontology of Complex Systems, Meta-Systems and Theory of Levels: The Emergence of Life, Human Consciousness and Society

Single cell interactomics in simpler organisms, as well as somatic cell interactomics in multicellular organisms, involve biomolecular interactions in complex signalling pathways that were recently represented in modular terms by quantum automata with ‘reversible behavior’ representing normal cell cycling and division. Other implications of such quantum automata, modular modeling of signaling pathways and cell differentiation during development are in the fields of neural plasticity and brain development leading to quantum-weave dynamic patterns and specific molecular processes underlying extensive memory, learning, anticipation mechanisms and the emergence of human consciousness during the early brain development in children. Cell interactomics is here represented for the first time as a mixture of ‘classical’ states that determine molecular dynamics subject to Boltzmann statistics and ‘steady-state’, metabolic (multi-stable) manifolds, together with ‘configuration’ spaces of metastable quantum states emerging from complex quantum dynamics of interacting networks of biomolecules, such as proteins and nucleic acids that are now collectively defined as quantum interactomics. On the other hand, the time dependent evolution over several generations of cancer cells --that are generally known to undergo frequent and extensive genetic mutations and, indeed, suffer genomic transformations at the chromosome level (such as extensive chromosomal aberrations found in many colon cancers)-- cannot be correctly represented in the ‘standard’ terms of quantum automaton modules, as the normal somatic cells can. This significant difference at the cancer cell genomic level is therefore reflected in major changes in cancer cell interactomics often from one cancer cell ‘cycle’ to the next, and thus it requires substantial changes in the modeling strategies, mathematical tools and experimental designs aimed at understanding cancer mechanisms. Novel solutions to this important problem in carcinogenesis are proposed and experimental validation procedures are suggested. From a medical research and clinical standpoint, this approach has important consequences for addressing and preventing the development of cancer resistance to medical therapy in ongoing clinical trials involving stage III cancer patients, as well as improving the designs of future clinical trials for cancer treatments.\ud \ud \ud KEYWORDS: Emergence of Life and Human Consciousness;\ud Proteomics; Artificial Intelligence; Complex Systems Dynamics; Quantum Automata models and Quantum Interactomics; quantum-weave dynamic patterns underlying human consciousness; specific molecular processes underlying extensive memory, learning, anticipation mechanisms and human consciousness; emergence of human consciousness during the early brain development in children; Cancer cell ‘cycling’; interacting networks of proteins and nucleic acids; genetic mutations and chromosomal aberrations in cancers, such as colon cancer; development of cancer resistance to therapy; ongoing clinical trials involving stage III cancer patients’ possible improvements of the designs for future clinical trials and cancer treatments. \ud \u

Protein-Ligand Binding Affinity Directed Multi-Objective Drug Design Based on Fragment Representation Methods

Drug discovery is a challenging process with a vast molecular space to be explored and numerous pharmacological properties to be appropriately considered. Among various drug design protocols, fragment-based drug design is an effective way of constraining the search space and better utilizing biologically active compounds. Motivated by fragment-based drug search for a given protein target and the emergence of artificial intelligence (AI) approaches in this field, this work advances the field of in silico drug design by (1) integrating a graph fragmentation-based deep generative model with a deep evolutionary learning process for large-scale multi-objective molecular optimization, and (2) applying protein-ligand binding affinity scores together with other desired physicochemical properties as objectives. Our experiments show that the proposed method can generate novel molecules with improved property values and binding affinities

Transcriptional regulatory network analysis during epithelial-mesenchymal transformation of retinal pigment epithelium

PURPOSE: Phenotypic transformation of retinal pigment epithelial (RPE) cells contributes to the onset and progression of ocular proliferative disorders such as proliferative vitreoretinopathy (PVR). The formation of epiretinal membranes in PVR may involve an epithelial-mesenchymal transformation (EMT) of RPE cells as part of an aberrant wound healing response. While the underlying mechanism remains unclear, this likely involves changes in RPE cell gene expression under the control of specific transcription factors (TFs). Thus, the purpose of the present study was to identify TFs that may play a role in this process. METHODS: Regulatory regions of genes that are differentially regulated during phenotypic transformation of ARPE-19 cells, a human RPE cell line, were subjected to computational analysis using the promoter analysis and interaction network toolset (PAINT). The PAINT analysis was used to identify transcription response elements (TREs) statistically overrepresented in the promoter and first intron regions of two reciprocally regulated RPE gene clusters, across four species including the human genome. These TREs were then used to construct transcriptional regulatory network models of the two RPE gene clusters. The validity of these models was then tested using RT-PCR to detect differential expression of the corresponding TF mRNAs during RPE differentiation in both undifferentiated and differentiated ARPE-19 and primary chicken RPE cell cultures. RESULTS: The computational analysis resulted in the successful identification of specific transcription response elements (TREs) and their cognate TFs that are candidates for serving as nodes in a transcriptional regulatory network regulating EMT in RPE cells. The models predicted TFs whose differential expression during RPE EMT was successfully verified by reverse transcriptase polymerase chain reaction (RT-PCR) analysis, including Oct-1, hepatocyte nuclear factor 1 (HNF-1), similar to mothers against decapentaplegic 3 (SMAD3), transcription factor E (TFE), core binding factor, erythroid transcription factor-1 (GATA-1), interferon regulatory factor-1 (IRF), natural killer homeobox 3A (NKX3A), Sterol regulatory element binding protein-1 (SREBP-1), and lymphocyte enhancer factor-1 (LEF-1). CONCLUSIONS: These studies successfully applied computational modeling and biochemical verification to identify biologically relevant transcription factors that are likely to regulate RPE cell phenotype and pathological changes in RPE in response to diseases or trauma. These TFs may provide potential therapeutic targets for the prevention and treatment of ocular proliferative disorders such as PVR

Design of a Machine Learning-based Approach for Fragment Retrieval on Models

[ES] El aprendizaje automático (ML por sus siglas en inglés) es conocido como la rama de la inteligencia artificial que reúne algoritmos estadísticos, probabilísticos y de optimización, que aprenden empíricamente. ML puede aprovechar el conocimiento y la experiencia que se han generado durante años en las empresas para realizar automáticamente diferentes procesos. Por lo tanto, ML se ha aplicado a diversas áreas de investigación, que estudian desde la medicina hasta la ingeniería del software. De hecho, en el campo de la ingeniería del software, el mantenimiento y la evolución de un sistema abarca hasta un 80% de la vida útil del sistema. Las empresas, que se han dedicado al desarrollo de sistemas software durante muchos años, han acumulado grandes cantidades de conocimiento y experiencia. Por lo tanto, ML resulta una solución atractiva para reducir sus costos de mantenimiento aprovechando los recursos acumulados. Específicamente, la Recuperación de Enlaces de Trazabilidad, la Localización de Errores y la Ubicación de Características se encuentran entre las tareas más comunes y relevantes para realizar el mantenimiento de productos software. Para abordar estas tareas, los investigadores han propuesto diferentes enfoques. Sin embargo, la mayoría de las investigaciones se centran en métodos tradicionales, como la indexación semántica latente, que no explota los recursos recopilados. Además, la mayoría de las investigaciones se enfocan en el código, descuidando otros artefactos de software como son los modelos. En esta tesis, presentamos un enfoque basado en ML para la recuperación de fragmentos en modelos (FRAME). El objetivo de este enfoque es recuperar el fragmento del modelo que realiza mejor una consulta específica. Esto permite a los ingenieros recuperar el fragmento que necesita ser trazado, reparado o ubicado para el mantenimiento del software. Específicamente, FRAME combina la computación evolutiva y las técnicas ML. En FRAME, un algoritmo evolutivo es guiado por ML para extraer de manera eficaz distintos fragmentos de un modelo. Estos fragmentos son posteriormente evaluados mediante técnicas ML. Para aprender a evaluarlos, las técnicas ML aprovechan el conocimiento (fragmentos recuperados de modelos) y la experiencia que las empresas han generado durante años. Basándose en lo aprendido, las técnicas ML determinan qué fragmento del modelo realiza mejor una consulta. Sin embargo, la mayoría de las técnicas ML no pueden entender los fragmentos de los modelos. Por lo tanto, antes de aplicar las técnicas ML, el enfoque propuesto codifica los fragmentos a través de una codificación ontológica y evolutiva. En resumen, FRAME está diseñado para extraer fragmentos de un modelo, codificarlos y evaluar cuál realiza mejor una consulta específica. El enfoque ha sido evaluado a partir de un caso real proporcionado por nuestro socio industrial (CAF, un proveedor internacional de soluciones ferroviarias). Además, sus resultados han sido comparados con los resultados de los enfoques más comunes y recientes. Los resultados muestran que FRAME obtuvo los mejores resultados para la mayoría de los indicadores de rendimiento, proporcionando un valor medio de precisión igual a 59.91%, un valor medio de exhaustividad igual a 78.95%, una valor-F medio igual a 62.50% y un MCC (Coeficiente de Correlación Matthews) medio igual a 0.64. Aprovechando los fragmentos recuperados de los modelos, FRAME es menos sensible al conocimiento tácito y al desajuste de vocabulario que los enfoques basados en información semántica. Sin embargo, FRAME está limitado por la disponibilidad de fragmentos recuperados para llevar a cabo el aprendizaje automático. Esta tesis presenta una discusión más amplia de estos aspectos así como el análisis estadístico de los resultados, que evalúa la magnitud de la mejora en comparación con los otros enfoques.[CAT] L'aprenentatge automàtic (ML per les seues sigles en anglés) és conegut com la branca de la intel·ligència artificial que reuneix algorismes estadístics, probabilístics i d'optimització, que aprenen empíricament. ML pot aprofitar el coneixement i l'experiència que s'han generat durant anys en les empreses per a realitzar automàticament diferents processos. Per tant, ML s'ha aplicat a diverses àrees d'investigació, que estudien des de la medicina fins a l'enginyeria del programari. De fet, en el camp de l'enginyeria del programari, el manteniment i l'evolució d'un sistema abasta fins a un 80% de la vida útil del sistema. Les empreses, que s'han dedicat al desenvolupament de sistemes programari durant molts anys, han acumulat grans quantitats de coneixement i experiència. Per tant, ML resulta una solució atractiva per a reduir els seus costos de manteniment aprofitant els recursos acumulats. Específicament, la Recuperació d'Enllaços de Traçabilitat, la Localització d'Errors i la Ubicació de Característiques es troben entre les tasques més comunes i rellevants per a realitzar el manteniment de productes programari. Per a abordar aquestes tasques, els investigadors han proposat diferents enfocaments. No obstant això, la majoria de les investigacions se centren en mètodes tradicionals, com la indexació semàntica latent, que no explota els recursos recopilats. A més, la majoria de les investigacions s'enfoquen en el codi, descurant altres artefactes de programari com són els models. En aquesta tesi, presentem un enfocament basat en ML per a la recuperació de fragments en models (FRAME). L'objectiu d'aquest enfocament és recuperar el fragment del model que realitza millor una consulta específica. Això permet als enginyers recuperar el fragment que necessita ser traçat, reparat o situat per al manteniment del programari. Específicament, FRAME combina la computació evolutiva i les tècniques ML. En FRAME, un algorisme evolutiu és guiat per ML per a extraure de manera eficaç diferents fragments d'un model. Aquests fragments són posteriorment avaluats mitjançant tècniques ML. Per a aprendre a avaluar-los, les tècniques ML aprofiten el coneixement (fragments recuperats de models) i l'experiència que les empreses han generat durant anys. Basant-se en l'aprés, les tècniques ML determinen quin fragment del model realitza millor una consulta. No obstant això, la majoria de les tècniques ML no poden entendre els fragments dels models. Per tant, abans d'aplicar les tècniques ML, l'enfocament proposat codifica els fragments a través d'una codificació ontològica i evolutiva. En resum, FRAME està dissenyat per a extraure fragments d'un model, codificar-los i avaluar quin realitza millor una consulta específica. L'enfocament ha sigut avaluat a partir d'un cas real proporcionat pel nostre soci industrial (CAF, un proveïdor internacional de solucions ferroviàries). A més, els seus resultats han sigut comparats amb els resultats dels enfocaments més comuns i recents. Els resultats mostren que FRAME va obtindre els millors resultats per a la majoria dels indicadors de rendiment, proporcionant un valor mitjà de precisió igual a 59.91%, un valor mitjà d'exhaustivitat igual a 78.95%, una valor-F mig igual a 62.50% i un MCC (Coeficient de Correlació Matthews) mig igual a 0.64. Aprofitant els fragments recuperats dels models, FRAME és menys sensible al coneixement tàcit i al desajustament de vocabulari que els enfocaments basats en informació semàntica. No obstant això, FRAME està limitat per la disponibilitat de fragments recuperats per a dur a terme l'aprenentatge automàtic. Aquesta tesi presenta una discussió més àmplia d'aquests aspectes així com l'anàlisi estadística dels resultats, que avalua la magnitud de la millora en comparació amb els altres enfocaments.[EN] Machine Learning (ML) is known as the branch of artificial intelligence that gathers statistical, probabilistic, and optimization algorithms, which learn empirically. ML can exploit the knowledge and the experience that have been generated for years to automatically perform different processes. Therefore, ML has been applied to a wide range of research areas, from medicine to software engineering. In fact, in software engineering field, up to an 80% of a system's lifetime is spent on the maintenance and evolution of the system. The companies, that have been developing these software systems for a long time, have gathered a huge amount of knowledge and experience. Therefore, ML is an attractive solution to reduce their maintenance costs exploiting the gathered resources. Specifically, Traceability Link Recovery, Bug Localization, and Feature Location are amongst the most common and relevant tasks when maintaining software products. To tackle these tasks, researchers have proposed a number of approaches. However, most research focus on traditional methods, such as Latent Semantic Indexing, which does not exploit the gathered resources. Moreover, most research targets code, neglecting other software artifacts such as models. In this dissertation, we present an ML-based approach for fragment retrieval on models (FRAME). The goal of this approach is to retrieve the model fragment which better realizes a specific query in a model. This allows engineers to retrieve the model fragment, which must be traced, fixed, or located for software maintenance. Specifically, the FRAME approach combines evolutionary computation and ML techniques. In the FRAME approach, an evolutionary algorithm is guided by ML to effectively extract model fragments from a model. These model fragments are then assessed through ML techniques. To learn how to assess them, ML techniques takes advantage of the companies' knowledge (retrieved model fragments) and experience. Then, based on what was learned, ML techniques determine which model fragment better realizes a query. However, model fragments are not understandable for most ML techniques. Therefore, the proposed approach encodes the model fragments through an ontological evolutionary encoding. In short, the FRAME approach is designed to extract model fragments, encode them, and assess which one better realizes a specific query. The approach has been evaluated in our industrial partner (CAF, an international provider of railway solutions) and compared to the most common and recent approaches. The results show that the FRAME approach achieved the best results for most performance indicators, providing a mean precision value of 59.91%, a recall value of 78.95%, a combined F-measure of 62.50%, and a MCC (Matthews correlation coefficient) value of 0.64. Leveraging retrieved model fragments, the FRAME approach is less sensitive to tacit knowledge and vocabulary mismatch than the approaches based on semantic information. However, the approach is limited by the availability of the retrieved model fragments to perform the learning. These aspects are further discussed, after the statistical analysis of the results, which assesses the magnitude of the improvement in comparison to the other approaches.Marcén Terraza, AC. (2020). Design of a Machine Learning-based Approach for Fragment Retrieval on Models [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/158617TESI

An Approach to Pattern Recognition by Evolutionary Computation

Evolutionary Computation has been inspired by the natural phenomena of evolution. It provides a quite general heuristic, exploiting few basic concepts: reproduction of individuals, variation phenomena that affect the likelihood of survival of individuals, inheritance of parents features by offspring. EC has been widely used in the last years to effectively solve hard, non linear and very complex problems. Among the others, EC–based algorithms have also been used to tackle classification problems. Classification is a process according to which an object is attributed to one of a finite set of classes or, in other words, it is recognized as belonging to a set of equal or similar entities, identified by a label. Most likely, the main aspect of classification concerns the generation of prototypes to be used to recognize unknown patterns. The role of prototypes is that of representing patterns belonging to the different classes defined within a given problem. For most of the problems of practical interest, the generation of such prototypes is a very hard problem, since a prototype must be able to represent patterns belonging to the same class, which may be significantly dissimilar each other. They must also be able to discriminate patterns belonging to classes different from the one that they represent. Moreover, a prototype should contain the minimum amount of information required to satisfy the requirements just mentioned. The research presented in this thesis, has led to the definition of an EC–based framework to be used for prototype generation. The defined framework does not provide for the use of any particular kind of prototypes. In fact, it can generate any kind of prototype once an encoding scheme for the used prototypes has been defined. The generality of the framework can be exploited to develop many applications. The framework has been employed to implement two specific applications for prototype generation. The developed applications have been tested on several data sets and the results compared with those obtained by other approaches previously presented in the literature