Machine-learning based approach to examine ecological processes influencing the diversity of riverine dissolved organic matter composition
Bibliographic record
Abstract
Dissolved organic matter (DOM) assemblages in freshwater rivers are formed from mixtures of simple to complex compounds that are highly variable across time and space. These mixtures largely form due to the environmental heterogeneity of river networks and the contribution of diverse allochthonous and autochthonous DOM sources. Most studies are, however, confined to local and regional scales, which precludes an understanding of how these mixtures arise at large, e.g., continental, spatial scales. The processes contributing to these mixtures are also difficult to study because of the complex interactions between various environmental factors and DOM. Here we propose the use of machine learning (ML) approaches to identify ecological processes contributing toward mixtures of DOM at a continental-scale. We related a dataset that characterized the molecular composition of DOM from river water and sediment with Fourier-transform ion cyclotron resonance mass spectrometry to explanatory physicochemical variables such as nutrient concentrations and stable water isotopes (2H and 18O). Using unsupervised ML, distinctive clusters for sediment and water samples were identified, with unique molecular compositions influenced by environmental factors like terrestrial input and microbial activity. Sediment clusters showed a higher proportion of protein-like and unclassified compounds than water clusters, while water clusters exhibited a more diversified chemical composition. We then applied a supervised ML approach, involving a two-stage use of SHapley Additive exPlanations (SHAP) values. In the first stage, SHAP values were obtained and used to identify key physicochemical variables. These parameters were employed to train models using both the default and subsequently tuned hyperparameters of the Histogram-based Gradient Boosting (HGB) algorithm. The supervised ML approach, using HGB and SHAP values, highlighted complex relationships between environmental factors and DOM diversity, in particular the existence of dams upstream, precipitation events, and other watershed characteristics were important in predicting higher chemical diversity in DOM. Our data-driven approach can now be used more generally to reveal the interplay between physical, chemical, and biological factors in determining the diversity of DOM in other ecosystems.
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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 | 0.002 | 0.004 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.002 | 0.001 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.001 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.001 | 0.000 |
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".