Inferring gene regulatory networks (GRNs) from single-cell RNA-seq (scRNA-seq) data is an important computational question to find regulatory mechanisms involved in fundamental cellular processes. Although many computational methods have been designed to predict GRNs from scRNA-seq data, they usually have high false positive rates and none infer GRNs by directly using the paired datasets of case-versus-control experiments. Here we present a novel deep-learning-based method, named scTIGER, for GRN detection by using the co-differential relationships of gene expression profiles in paired scRNA-seq datasets. scTIGER employs cell-type-based pseudotiming, an attention-based convolutional neural network method and permutation-based significance testing for inferring GRNs among gene modules. As state-of-the-art applications, we first applied scTIGER to scRNA-seq datasets of prostate cancer cells, and successfully identified the dynamic regulatory networks of AR, ERG, PTEN and ATF3 for same-cell type between prostatic cancerous and normal conditions, and two-cell types within the prostatic cancerous environment. We then applied scTIGER to scRNA-seq data from neurons with and without fear memory and detected specific regulatory networks for BDNF, CREB1 and MAPK4. Additionally, scTIGER demonstrates robustness against high levels of dropout noise in scRNA-seq data.
When Simple Statistical Algorithms Outperform Deep Learning: A Case of Keystroke Dynamics [When Simple Statistical Algorithms Outperform Deep Learning: A Case of Keystroke Dynamics]
Keystroke dynamics has gained relevance over the years for its potential in solving practical problems like online fraud and account takeovers. Statistical algorithms such as distance measures have long been a common choice for keystroke authentication due to their simplicity and ease of implementation. However, deep learning has recently started to gain popularity due to their ability to achieve better performance. When should statistical algorithms be preferred over deep learning and vice-versa? To answer this question, we set up experiments to evaluate two state-of-the-art statistical algorithms: Scaled Manhattan and the Instance-based Tail Area Density (ITAD) metric, with a state-of-the-art deep learning model called TypeNet, on three datasets (one small and two large). Our results show that on the small dataset, statistical algorithms significantly outperform the deep learning approach (Equal Error Rate (EER) of 4.3% for Scaled Manhattan / 1.3% for ITAD versus 19.18% for TypeNet ). However, on the two large datasets, the deep learning approach performs better (22.9% & 28.07% for Scaled Manhattan / 12.25% & 20.74% for ITAD versus 0.93% & 6.77% for TypeNet).
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- Award ID(s):
- 2122746
- NSF-PAR ID:
- 10422317
- Date Published:
- Journal Name:
- Proceedings of the 12th International Conference on Pattern Recognition Applications and Methods ICPRAM
- Page Range / eLocation ID:
- 363 to 370
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Conference Paper:
- https://doi.org/10.5220/0011684100003411
