[{"data":1,"prerenderedAt":-1},["ShallowReactive",2],{"doc-detail-121585-en":3,"doc-seo-121585-105":30,"detail-sidebar-cat-0-en-105":91},{"code":4,"msg":5,"data":6},0,"success",{"doc_id":7,"user_id":8,"nickname":9,"user_avatar":10,"doc_module":4,"category_id":11,"category_name":12,"doc_title":13,"doc_description":14,"doc_content":15,"file_id":16,"file_url":17,"file_type":18,"file_size":19,"view_count":20,"is_deleted":4,"is_public":20,"is_downloadable":20,"audit_status":20,"page_count":21,"language":22,"language_code":23,"site_id":24,"html_lang":23,"table_of_contents":25,"faqs":26,"seo_title":27,"seo_description":14,"update_tm":28,"read_time":29},121585,13056703020460,"Valentina","https://ap-avatar.wpscdn.com/avatar/be000253dac470eee5d?_k=1778207105932848923",8,"Research & Report","Optimization and Machine Learning Approaches for Tumor Phylogeny Reconstruction","Focuses on optimization and machine learning methods for reconstructing tumor phylogeny, emphasizing robust evidence-based inference rather than ad-hoc demonstrations. The work is conducted through a research-intensive thesis process supervised by experienced academic mentors, highlighting careful objective definition, critical thinking toward scientific practice, and cautious interpretation of conclusions. It also reflects extensive cross-disciplinary collaboration between biomedicine and computing groups, supported by feedback, guidance, and research culture during multi-year efforts.","Optimization and Machine Learning Approaches for Tumor Phylogeny Reconstruction  \nby  \nMaitena Tellaetxe Abete  \nSupervised by Borja Calvo and Charles Lawrie  \n2025  \n(c) 2025 Maitena Tellaetxe Abete  \nA mi padre, siempre.  \nTen siempre a I´taca en tu mente.  \nLlegar all´ı es tu destino.  \nMas no apresures nunca el viaje. Mejor que dure muchos a˜nosy atracar, viejo ya, en la isla,  \nenriquecido de cuanto ganaste en el camino sin aguantar a que I´taca te enriquezca.  \nI´taca te brind´o tan hermoso viaje. Sin ella no habr´ıas emprendido el camino.  \nPero ya no tiene nada que darte.  \nAunque la halles pobre, I´taca no te ha enga˜nado. As´ı, sabio como te has vuelto, con tanta experiencia, entender´as ya qu´e significan las I´tacas.  \nKonstantinos Kavafis  \nAcknowledgements  \nDespu´es de m´as de siete a˜nos de trabajo, es inevitable que me extienda alagradecer a todas aquellas personas que han contribuido a esta tesis. Este proyecto ha supuesto un esfuerzo colectivo de quienes mencionar´e a continuaci´on, y seguramente de alguna otra que me olvide, y a pesar del desaf´ıo que ha supuesto la tesis, me dispongo a escribir estas palabras llena degratitud y con cierto grado de nostalgia.  \nEn primer lugar, quiero dar las gracias a mis directores, Borja y Charles. Su conocimiento y experiencia han sido indispensables para guiarme en este largo camino. He tenido suerte, ya que, adem´as de ser grandes acad´emicos, son personas con un profundo valor humano que siempre han sabido entender lo que me ha sucedido m´as all´a de mi vida acad´emica. Su apoyo incondicional y el espacio que me brindaron en los momentos m´as dif´ıciles han sido fundamentales en este trayecto.  \nCharles had complete trust in me from day one. He assigned me responsibilities right from the start while also granting me the freedom to conduct interesting research. I have always felt highly valued by him. At the same time, he has provided me with perspective and helped me understand the inner workings of the academic world.  \nBorja ha guiado cada uno de mis pasos y me ha dedicado much´ısimo (de verdad, much´ısimo) tiempo pese a tener una apretada agenda. Me ha escuchado pacientemente, me ha dado serenidad cuando m´as lo necesitaba y ha cre´ıdo en m´ı y en mi trabajo cuando yo no lo hac´ıa. Borja me ha ense˜nado, con suejemplo, lo que significa ser un buen investigador. M´as all´a de lo puramentemetodol´ogico, que ha sido mucho, como podr´a imaginar cualquiera que lo conozca, me ha ense˜nado a desarrollar una mirada cr´ıtica hacia la ciencia. Me ha ense˜nado a definir los objetivos de una investigaci´on y a reflexionar sobre los m´etodos m´as adecuados sin dejarse llevar por modas. Ha enfatizadola importancia de la robustez de los resultados y me ha ense˜nado a tratar las conclusiones que podemos extraer de los mismos con criterio y cautela.  \nX  \nHe aprendido a a hablar de evidencia y no de demostraciones, a huir de las recetas y de los 0.05 ... Y, en ´ultima instancia, Borja me ha animado a combatir pr´acticas establecidas poco rigurosas y a reflexionar sobre qu´e significa verdaderamente hacer ciencia. Aunque esta tesis llegue a su fin, espero poder seguir disfrutando de largas charlas en su despacho en las que ´el intenta arreglar este mundo de hoy en d´ıa mientras yo lo catalogo de idealista y optimista.  \nDurante este periodo he tenido la suerte de nutrirme de personas con trayectorias muy diversas que han contribuido a ampliar mis conocimientos tanto de biomedicina como de computaci´on, y es que en este camino me hanacompa˜nado tanto los miembros del grupo de Oncolog´ıa Molecular de Biodonostia como los del Intelligent Systems Group de la Facultad de Inform´aticade la UPV/EHU. Gracias en especial a estos ´ultimos, quienes me hicieron sentir parte del grupo pese a ser una “forastera”. Con ellos me queda claro que“Acreditaci´on” es pura ficci´on. Merecen tambi´en una menci´on especial mis compa˜neras de pecera en Biodonostia, Mar´ıa y Lorea, a quien atosigaba a pregun","cbCaig4kD8RBkez2","https://ap.wps.com/l/cbCaig4kD8RBkez2","pdf",21273666,1,196,"English","en",105,"# Acknowledgements\n## Research supervision and guidance\n## Cross-disciplinary collaboration\n## Visiting research experience","[{\"question\":\"What is the document’s main research focus?\",\"answer\":\"The document focuses on optimization and machine learning approaches for tumor phylogeny reconstruction.\"},{\"question\":\"How does the thesis emphasize scientific rigor?\",\"answer\":\"It emphasizes evidence-based thinking, robustness of results, and careful interpretation of conclusions rather than relying on rigid recipes.\"},{\"question\":\"Which fields and research groups are involved in the work?\",\"answer\":\"The acknowledgements highlight contributions and collaboration spanning biomedicine and computing, including molecular oncology and intelligent 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