Timed hazard networks: Incorporating temporal difference for oncogenetic analysis.
Oncogenetic graphical models are crucial for understanding cancer progression by analyzing the accumulation of genetic events. These models are used to identify statistical dependencies and temporal order of genetic events, which helps design targeted therapies. However, existing algorithms do not a...
| Main Author: | |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2023-01-01
|
| Series: | PLoS ONE |
| Online Access: | https://doi.org/10.1371/journal.pone.0283004 |
| _version_ | 1827963529575006208 |
|---|---|
| author | Jian Chen |
| author_facet | Jian Chen |
| author_sort | Jian Chen |
| collection | DOAJ |
| description | Oncogenetic graphical models are crucial for understanding cancer progression by analyzing the accumulation of genetic events. These models are used to identify statistical dependencies and temporal order of genetic events, which helps design targeted therapies. However, existing algorithms do not account for temporal differences between samples in oncogenetic analysis. This paper introduces Timed Hazard Networks (TimedHN), a new statistical model that uses temporal differences to improve accuracy and reliability. TimedHN models the accumulation process as a continuous-time Markov chain and includes an efficient gradient computation algorithm for optimization. Our simulation experiments demonstrate that TimedHN outperforms current state-of-the-art graph reconstruction methods. We also compare TimedHN with existing methods on a luminal breast cancer dataset, highlighting its potential utility. The Matlab implementation and data are available at https://github.com/puar-playground/TimedHN. |
| first_indexed | 2024-04-09T17:00:43Z |
| format | Article |
| id | doaj.art-82c45e90f2454f69a50197dd5c1d9ee6 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-04-09T17:00:43Z |
| publishDate | 2023-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-82c45e90f2454f69a50197dd5c1d9ee62023-04-21T05:32:53ZengPublic Library of Science (PLoS)PLoS ONE1932-62032023-01-01183e028300410.1371/journal.pone.0283004Timed hazard networks: Incorporating temporal difference for oncogenetic analysis.Jian ChenOncogenetic graphical models are crucial for understanding cancer progression by analyzing the accumulation of genetic events. These models are used to identify statistical dependencies and temporal order of genetic events, which helps design targeted therapies. However, existing algorithms do not account for temporal differences between samples in oncogenetic analysis. This paper introduces Timed Hazard Networks (TimedHN), a new statistical model that uses temporal differences to improve accuracy and reliability. TimedHN models the accumulation process as a continuous-time Markov chain and includes an efficient gradient computation algorithm for optimization. Our simulation experiments demonstrate that TimedHN outperforms current state-of-the-art graph reconstruction methods. We also compare TimedHN with existing methods on a luminal breast cancer dataset, highlighting its potential utility. The Matlab implementation and data are available at https://github.com/puar-playground/TimedHN.https://doi.org/10.1371/journal.pone.0283004 |
| spellingShingle | Jian Chen Timed hazard networks: Incorporating temporal difference for oncogenetic analysis. PLoS ONE |
| title | Timed hazard networks: Incorporating temporal difference for oncogenetic analysis. |
| title_full | Timed hazard networks: Incorporating temporal difference for oncogenetic analysis. |
| title_fullStr | Timed hazard networks: Incorporating temporal difference for oncogenetic analysis. |
| title_full_unstemmed | Timed hazard networks: Incorporating temporal difference for oncogenetic analysis. |
| title_short | Timed hazard networks: Incorporating temporal difference for oncogenetic analysis. |
| title_sort | timed hazard networks incorporating temporal difference for oncogenetic analysis |
| url | https://doi.org/10.1371/journal.pone.0283004 |
| work_keys_str_mv | AT jianchen timedhazardnetworksincorporatingtemporaldifferenceforoncogeneticanalysis |