Engineering, Mathematics and Physical Sciences Intranet
MTHM015 - AI and Data Science Methods for Life and Health Sciences (2023)
MODULE TITLE | AI and Data Science Methods for Life and Health Sciences | CREDIT VALUE | 15 |
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MODULE CODE | MTHM015 | MODULE CONVENER | Prof Kirsty Wan (Coordinator) |
DURATION: TERM | 1 | 2 | 3 |
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DURATION: WEEKS | 11 |
Number of Students Taking Module (anticipated) | 20 |
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DESCRIPTION - summary of the module content
Analysing data and quantitatively comparing mathematical models to data are crucial when using mathematics to improve our understanding of complex biological systems. Data from biology experiments and clinical recordings are diverse and often present challenges for analysis and modelling, such as high dimensionality and non-stationarity. This module will introduce you to some common kinds of data observed in biological and clinical applications such as images, time series and high dimensional sequencing data. You will be introduced to advanced methods that deal with these data, but can also be applicable in other fields, for example in climate systems and finance.
AIMS - intentions of the module
We will introduce data and methods that arise in the above application areas but are also applicable in other fields. The content will be centred on real-world applications: for example, the analysis of motility in single cell organisms, analysis of clinical time series in neurology and neuroendocrinology as well as analysis of next generation sequencing (NGS) data. The study of these examples will require theory in:
image analysis: feature extraction/identification, object tracking, deep learning; time series analysis: clustering, linear and nonlinear time series analysis methods, calibration of models from dynamic data; NGS data: enrichment analysis and dimension reduction (e.g. PCA, UMAP, t-SNE). The presentation of theory will be given in the context of practical, hands-on analysis of real-world data.
INTENDED LEARNING OUTCOMES (ILOs) (see assessment section below for how ILOs will be assessed)
On successful completion of this module you should be able to:
Module Specific Skills and Knowledge
1. Apply common tools for image and time series analysis
2. Apply common algorithms for object detection
2. Apply common algorithms for object detection
3. Develop a working knowledge of supervised and unsupervised learning
4. Study common tools for dimension reduction
5. Learn how to link mechanistic models and data.
Discipline Specific Skills and Knowledge
6. Develop practical skills in handling different kinds of data
7. Develop practical skills to link models and data
7. Develop practical skills to link models and data
Personal and Key Transferable / Employment Skills and Knowledge
9. Develop practical skills in handling diverse data
10. Build the ability to identify which techniques are suitable for which problems
10. Build the ability to identify which techniques are suitable for which problems
11. Communicate ideas effectively by interpreting real data
SYLLABUS PLAN - summary of the structure and academic content of the module
(i) Image analysis
- Introduction to the problem of detecting and tracking objects in images (application to microswimmers and medical MRI)
- Deep learning for object detection
(ii) Time series analysis
- Spectral decomposition using Fourier transform and wavelets
- Deep autoencoders for time series clustering
- Linear and nonlinear models for complex physiological systems’ dynamics
(iii) RNA-seq data analysis
- Enrichment analysis
- Dimension reduction (UMAP, PCA, t-SNE)
(iv) Model calibration
- Global optimisation heuristics (particle swarm, genetic algorithms)
- Probabilistic and Bayesian methods.
LEARNING AND TEACHING
LEARNING ACTIVITIES AND TEACHING METHODS (given in hours of study time)
Scheduled Learning & Teaching Activities | 50.00 | Guided Independent Study | 100.00 | Placement / Study Abroad | 0.00 |
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DETAILS OF LEARNING ACTIVITIES AND TEACHING METHODS
Category | Hours of study time | Description |
Scheduled learning and teaching activities | 20 | In lectures, problems and data are introduced; background theory is described |
Scheduled learning and teaching activities | 30 |
Students use the knowledge from the lecture to perform a hands-on data analysis task with real data
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Guided Independent Study | 100 |
Independent reading and problem solving
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ASSESSMENT
FORMATIVE ASSESSMENT - for feedback and development purposes; does not count towards module grade
Form of Assessment | Size of Assessment (e.g. duration/length) | ILOs Assessed | Feedback Method |
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Questions in practical sessions | 10 x 3 hours | All | The lecturer will provide feedback on solutions. |
SUMMATIVE ASSESSMENT (% of credit)
Coursework | 100 | Written Exams | 0 | Practical Exams | 0 |
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DETAILS OF SUMMATIVE ASSESSMENT
Form of Assessment | % of Credit | Size of Assessment (e.g. duration/length) | ILOs Assessed | Feedback Method |
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Coursework 1 | 50 | 4 weeks to complete | All | Marked script |
Coursework 2 | 50 | 4 weeks to complete | All | Marked script |
DETAILS OF RE-ASSESSMENT (where required by referral or deferral)
Original Form of Assessment | Form of Re-assessment | ILOs Re-assessed | Time Scale for Re-assessment |
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Coursework 1 | Coursework piece (50%) | All | During the August Ref/Def period |
Coursework 2 | Coursework piece (50%) | All | During the August Ref/Def period |
RE-ASSESSMENT NOTES
Reassessment will be by coursework in the failed or deferred element only. For deferred candidates, the module mark will be uncapped. For referred candidates, the module mark will be capped at 40%.
RESOURCES
INDICATIVE LEARNING RESOURCES - The following list is offered as an indication of the type & level of
information that you are expected to consult. Further guidance will be provided by the Module Convener
information that you are expected to consult. Further guidance will be provided by the Module Convener
Reading list for this module:
Type | Author | Title | Edition | Publisher | Year | ISBN | Search |
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Reference | Cohen, M.X. | Analyzing Neural Time Series Data: Theory and Practice | [Library] | ||||
Reference | Eberhart, R. Shui, Y. and Kennedy, J. | Swarm Intelligence | [Library] | ||||
Reference | Lee, J.A. , Verleysen, M. and Schölkopf, B. | Nonlinear Dimensionality Reduction | [Library] |
CREDIT VALUE | 15 | ECTS VALUE | 7.5 |
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PRE-REQUISITE MODULES | None |
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CO-REQUISITE MODULES | None |
NQF LEVEL (FHEQ) | 7 | AVAILABLE AS DISTANCE LEARNING | No |
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ORIGIN DATE | Tuesday 17 January 2023 | LAST REVISION DATE | Tuesday 17 January 2023 |
KEY WORDS SEARCH | Data analytics, Biomedical data, Health data, Model calibration, AI, Time series analysis, Modelling, Image analysis |
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