Sakira Hassan

Syeda Sakira Hassan, Rahul Mangayil, Tommi Aho et al.

In this paper, we utilize a machine learning approach to identify the significant pathways for c-di-GMP signaling proteins. The dataset involves gene counts from 12 pathways and 5 essential c-di-GMP binding domains for 1024 bacterial genomes. Two novel approaches, Least absolute shrinkage and selection operator (Lasso) and Random forests, have been applied for analyzing and modeling the dataset. Both approaches show that bacterial chemotaxis is the most essential pathway for c-di-GMP encoding domains. Though popular for feature selection, the strong regularization of Lasso method fails to associate any pathway to MshE domain. Results from the analysis may help to understand and emphasize the supporting pathways involved in bacterial cellulose production. These findings demonstrate the need for a chassis to restrict the behavior or functionality by deactivating the selective pathways in cellulose production.

Sakira Hassan, Simo Särkkä, Ángel F. García-Fernández

This paper presents algorithms for parallelization of inference in hidden Markov models (HMMs). In particular, we propose parallel backward-forward type of filtering and smoothing algorithm as well as parallel Viterbi-type maximum-a-posteriori (MAP) algorithm. We define associative elements and operators to pose these inference problems as parallel-prefix-sum computations in sum-product and max-product algorithms and parallelize them using parallel-scan algorithms. The advantage of the proposed algorithms is that they are computationally efficient in HMM inference problems with long time horizons. We empirically compare the performance of the proposed methods to classical methods on a highly parallel graphical processing unit (GPU).

Syeda Sakira Hassan, Heikki Huttunen, Jari Niemi et al.

We propose a novel classifier accuracy metric: the Bayesian Area Under the Receiver Operating Characteristic Curve (CBAUC). The method estimates the area under the ROC curve and is related to the recently proposed Bayesian Error Estimator. The metric can assess the quality of a classifier using only the training dataset without the need for computationally expensive cross-validation. We derive a closed-form solution of the proposed accuracy metric for any linear binary classifier under the Gaussianity assumption, and study the accuracy of the proposed estimator using simulated and real-world data. These experiments confirm that the closed-form CBAUC is both faster and more accurate than conventional AUC estimators.