Region of interest selection for GC×GC–MS data using a pseudo fisher ratio moving window with connected components segmentation
Why this work is in the frame
A frame that forgets how it found something cannot be audited. These are the routes that admitted this work.
Bibliographic record
Abstract
Comprehensive two-dimensional gas chromatography mass spectrometry (GC×GC-MS) data present several challenges for analysis largely because chemical factors drift along the chromatographic modes across different chromatographic runs, and there is frequently a lack of reliable molecular ion measurements with which to align data across multiple samples. Tensor decomposition techniques such as Parallel Factor Analysis (PARAFAC2/PARAFAC2×N) allow analysts to deconvolve closely eluting signals for quantitative and qualitative purposes. These techniques make relatively few assumptions about chromatographic peak shapes or the relative abundance of noise and allow for highly accurate representations of the underlying chemical phenomena using well-characterized and scrutinized principles of chemometrics. However, expert intervention and supervision is required to select appropriate Regions of Interest (ROI) and numbers of chemical components present in each ROI. We previously reported an automated ROI selection algorithm for GC-MS data in Giebelhaus et al. where we observed the ratio of the first and second eigenvalues within a moving window across the entire chromatogram. Here, we present an extension of this work to automatically detect ROIs in GC×GC-MS chromatograms, while making no assumptions about peak shape. First, we calculate the probabilities of each acquisition being in a ROI, then apply connected components segmentation to discretize the regions of interest. For sparse chromatograms we found the algorithm detected spurious peaks. To address this, we implemented an iterative ROI selection process where we autoscaled the moving window to the standard deviation of the noise from the previous iteration. Using three user-defined parameters, we generated informative ROIs on a wide range of GC×GC-TOFMS chromatograms.
Fetched live from OpenAlex and de-inverted. Abstracts are not stored in this database: the inverted indexes are 8.6 GB of the frame’s 9.3 GB of text, and the host has 13 GB free.
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 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 it