Fiche de cours
Bioinformatics Algorithms - ED 24/Série 3
Faculté de gestion: Ecole doctorale (FBM-DOCT)
Responsable(s): Christophe Dessimoz, David Gfeller
Horaires du cours (Apériodique)
Date | Lieu | Remarque | Thématique | Intervenant(s) |
---|---|---|---|---|
27.02.2024 de 09:15 à 12:00 | Salle 336, Amphipôle, Quartier UNIL-Sorge | Introduction. How computers work; fundamentals of algorithm and complexity theory. | Christophe Dessimoz | |
05.03.2024 de 09:15 à 12:00 | Salle 336, Amphipôle, Quartier UNIL-Sorge | Exact sequence matching I: read mapping, indexing | Christophe Dessimoz | |
12.03.2024 de 09:15 à 12:00 | Salle 336, Amphipôle, Quartier UNIL-Sorge | Exact sequence matching II: hashing, edit distances. | Christophe Dessimoz | |
19.03.2024 de 09:15 à 12:00 | Salle 336, Amphipôle, Quartier UNIL-Sorge | Approximate sequence matching: dynamic programming | Christophe Dessimoz | |
26.03.2024 de 09:15 à 12:00 | Salle 336, Amphipôle, Quartier UNIL-Sorge | Alignment significance: permutation test, parameter estimation | Christophe Dessimoz | |
09.04.2024 de 09:15 à 12:00 | Salle 336, Amphipôle, Quartier UNIL-Sorge | Networks I: Introduction to different types of networks. Graph representation and data structure. Graph and tree traversals. | David Gfeller | |
16.04.2024 de 09:15 à 12:00 | Salle 336, Amphipôle, Quartier UNIL-Sorge | Networks II: Clustering. | David Gfeller | |
23.04.2024 de 09:15 à 12:00 | Salle 336, Amphipôle, Quartier UNIL-Sorge | Networks III: Neural networks. | David Gfeller | |
30.04.2024 de 09:15 à 12:00 | Salle 336, Amphipôle, Quartier UNIL-Sorge | Networks IV: Convolutional neural networks. | David Gfeller | |
07.05.2024 de 09:15 à 12:00 | Salle 336, Amphipôle, Quartier UNIL-Sorge | Cross-validation, avoiding overfitting | David Gfeller | |
14.05.2024 de 09:15 à 12:00 | Salle 336, Amphipôle, Quartier UNIL-Sorge | Hidden Markov models. Forward-backward algorithm. | Christophe Dessimoz | |
21.05.2024 de 09:15 à 12:00 | Salle 336, Amphipôle, Quartier UNIL-Sorge | Minimizers and MinHashing | Christophe Dessimoz | |
28.05.2024 de 09:15 à 12:00 | Salle 336, Amphipôle, Quartier UNIL-Sorge | Conclusion. Review key ideas, next steps, feedback | Christophe Dessimoz |
Cours (optionnel)
Annuel
Apériodique
Langue(s) d'enseignement: anglais
Public: Oui
Crédits: 3
Objectif
The course aims at improving the student’s programming skills by gaining a deep understanding of some of the key algorithms in bioinformatics, with a special emphasis on sequence and graph algorithms.
Contenu
Students will learn widely applicable concepts, such as asymptotic time complexity, binary search, suffix trees, dynamic programming, hashing, hidden Markov models, and neuronal networks.
Practicals and home assignments are essential parts of the course. The language of the course is Python, though the concepts covered in the course are applicable to all computer languages.
Evaluation
Mandatory assessment: 20 min oral examination
Final test: date to be confirmed
Bibliographie
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Exigences du cursus d'études
The course assumes familiarity with basic programming concepts (variable and function declaration, arrays, for-loops, conditional statements, etc.). Algorithms are introduced from a practical angle so the mathematical formalism is kept at a minimum.
Conditions d'octroi
Participation active attestée par le responsable. Final test that will take place in summer exam
Conditions d'accès
Inscription auprès de l'Ecole doctorale. Série 3