STATE-SPACE MODEL WITH TIME DELAYS FOR GENE REGULATORY NETWORKS
Bibliographic record
Abstract
A gene regulatory network can be considered a dynamic cellular system which describes the behavior (development) of a living cell and depends completely on the current internal state plus any external inputs, if these exist. Although many details inside a cell are not precisely known, gene expression data on a genome scale provide useful insights into such a cellular system. With gene expression data, a wide variety of models, such as Boolean networks and differential/difference equations, have been proposed to model gene regulatory networks. In these previously proposed models, genes are viewed as the internal state variables of a cellular system. This viewpoint has suffered from the underestimation of the model parameters. In addition, these models ignore an important problem with a gene regulatory network — time delay. Instead, this paper proposes a state-space model with time delays for gene regulatory networks. The proposed model views genes as the observation variables, whose expression values depend on the current internal state variables and any external inputs. Bayesian information criterion (BIC) and probabilistic principal component analysis (PPCA) are used to estimate the number of internal state variables and their expression profiles from gene expression data. By constructing dynamic equations with time delays for the internal state variables and the relationships between the internal state variables and the observation variables (gene expression profiles), state-space models with time delays for gene regulatory networks are constructed. The parameters of the proposed model can be unambiguously identified from time-course gene expression data with a lower computational cost. The proposed model is applied to two time-course gene expression datasets, and two gene regulatory~networks are inferred, respectively. The analysis shows that the inferred gene regulatory networks have several features of the real gene regulatory networks, such as the stability, the robustness, and the periodicity. Further, compared to state-space models without time delays, the proposed model with time delays has better prediction accuracy.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.004 |
| Meta-epidemiology (narrow) | 0.001 | 0.001 |
| Meta-epidemiology (broad) | 0.002 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.001 | 0.001 |
| Scholarly communication | 0.002 | 0.002 |
| Open science | 0.002 | 0.001 |
| Research integrity | 0.002 | 0.003 |
| Insufficient payload (model declined to judge) | 0.003 | 0.001 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".