The increase in demand for food has resulted in increased demand for tools that help streamline plant breeding process in order to create new varieties of crops. Identifying the underlying genetic mechanism of favourable characteristics is essential in order to make the best breeding decisions. In this project we have developed a modified autoencoder model which allows for lateral phenotype injection into the latent layer, in order to identify causal SNPs for phenotypes of interest in wheat. SNP and phenotype data for 500 samples of Lantmännen SW Seed provided by Lantmännen was used to train the network. Artificial phenotype created using a single SNP was used during training instead of real phenotype, since the relationship between the phenotype and SNP is already known. The modified training model with lateral phenotype injection showed significant increase in genotype concordance of the artificial phenotype when compared to the control model without phenotype injection. Causal SNP was successfully identified by using concordance terrain graph, where the difference in concordance of individual SNPs  between the modified modified model and control model was plotted against the genomic position of each SNP. The model requires further testing to elucidate its behaviour for phenotypes linked to multiple SNPs.

Time series anomaly detection has been a longstanding area of research with applications across various domains. In recent years, there has been a surge of interest in applying deep learning models to this problem domain. This thesis presents a critical examination of the efficacy of deep learning models in comparison to classical approaches for time series anomaly detection. Contrary to the widespread belief in the superiority of deep learning models, our research findings suggest that their performance may be misleading and the progress illusory. Through rigorous experimentation and evaluation, we reveal that classical models outperform deep learning counterparts in various scenarios, challenging the prevailing assumptions. In addition to model performance, our study delves into the intricacies of evaluation metrics commonly employed in time series anomaly detection. We uncover how it inadvertently inflates the performance scores of models, potentially leading to misleading conclusions. By identifying and addressing these issues, our research contributes to providing valuable insights for researchers, practitioners, and decision-makers in the field of time series anomaly detection, encouraging a critical reevaluation of the role of deep learning models and the metrics used to assess their performance. / Tidsperiods avvikelsedetektering har varit ett långvarigt forskningsområde med tillämpningar inom olika områden. Under de senaste åren har det uppstått ett ökat intresse för att tillämpa djupinlärningsmodeller på detta problemområde. Denna avhandling presenterar en kritisk granskning av djupinlärningsmodellers effektivitet jämfört med klassiska metoder för tidsperiods avvikelsedetektering. I motsats till den allmänna övertygelsen om överlägsenheten hos djupinlärningsmodeller tyder våra forskningsresultat på att deras prestanda kan vara vilseledande och framsteg illusoriskt. Genom rigorös experimentell utvärdering avslöjar vi att klassiska modeller överträffar djupinlärningsalternativ i olika scenarier och därmed utmanar de rådande antagandena. Utöver modellprestanda går vår studie in på detaljerna kring utvärderings-metoder som oftast används inom tidsperiods avvikelsedetektering. Vi avslöjar hur dessa oavsiktligt överdriver modellernas prestandapoäng och kan därmed leda till vilseledande slutsatser. Genom att identifiera och åtgärda dessa problem bidrar vår forskning till att erbjuda värdefulla insikter för forskare, praktiker och beslutsfattare inom området tidsperiods avvikelsedetektering, och uppmanar till en kritisk omvärdering av djupinlärningsmodellers roll och de metoder som används för att bedöma deras prestanda.