API Reference

Complete reference for all public classes and functions in MaldiAMRKit, organized by module.

Core Data Structures

maldiamrkit.MaldiSpectrum	A single MALDI-TOF spectrum.
maldiamrkit.MaldiSet	A collection of MALDI-TOF spectra with metadata.

Filters

maldiamrkit.filters.SpectrumFilter	Base filter with operator overloading.
maldiamrkit.filters.SpeciesFilter	Filter by species name(s).
maldiamrkit.filters.DrugFilter	Filter by antibiotic resistance status.
maldiamrkit.filters.QualityFilter	Filter by quality metrics stored in metadata columns.
maldiamrkit.filters.MetadataFilter	Filter by arbitrary metadata column condition.

Preprocessing

maldiamrkit.preprocessing.PreprocessingPipeline	Composable pipeline of preprocessing steps for MALDI-TOF spectra.
maldiamrkit.preprocessing.preprocess	Apply preprocessing pipeline to a raw MALDI-TOF spectrum.
maldiamrkit.preprocessing.bin_spectrum	Bin spectrum intensities into m/z intervals.
maldiamrkit.preprocessing.get_bin_metadata	Generate bin metadata from edges.
maldiamrkit.preprocessing.BinningMethod	Supported binning methods.
maldiamrkit.preprocessing.estimate_snr	Estimate signal-to-noise ratio of a spectrum.
maldiamrkit.preprocessing.SpectrumQuality	Comprehensive quality assessment for MALDI-TOF spectra.
maldiamrkit.preprocessing.SpectrumQualityReport	Quality metrics report for a single MALDI-TOF spectrum.
maldiamrkit.preprocessing.SignalMethod	Method for estimating the signal level in SNR computation.
maldiamrkit.preprocessing.merge_replicates	Merge replicate spectra into a single consensus spectrum.
maldiamrkit.preprocessing.detect_outlier_replicates	Identify outlier replicates using correlation with the median spectrum.
maldiamrkit.preprocessing.MergingMethod	Supported replicate merging methods.

Transformers

maldiamrkit.preprocessing.ClipNegatives	Clip negative intensity values to zero.
maldiamrkit.preprocessing.SqrtTransform	Variance-stabilizing square root transformation.
maldiamrkit.preprocessing.LogTransform	Log1p intensity transformation (alternative to sqrt).
maldiamrkit.preprocessing.SavitzkyGolaySmooth	Savitzky-Golay smoothing filter.
maldiamrkit.preprocessing.MovingAverageSmooth	Moving-average smoothing filter.
maldiamrkit.preprocessing.SNIPBaseline	SNIP (Statistics-sensitive Non-linear Iterative Peak-clipping) baseline correction.
maldiamrkit.preprocessing.TopHatBaseline	Morphological top-hat baseline subtraction.
maldiamrkit.preprocessing.ConvexHullBaseline	Parameter-free baseline from the lower convex hull of the spectrum.
maldiamrkit.preprocessing.MedianBaseline	Rolling-median baseline subtraction.
maldiamrkit.preprocessing.MzTrimmer	Trim spectrum to a specified m/z range.
maldiamrkit.preprocessing.TICNormalizer	Total Ion Current normalization (intensities sum to 1).
maldiamrkit.preprocessing.MedianNormalizer	Normalize intensities by median value.
maldiamrkit.preprocessing.PQNNormalizer	Probabilistic Quotient Normalization.
maldiamrkit.preprocessing.MzMultiTrimmer	Keep only specific m/z ranges from the spectrum.

Alignment

maldiamrkit.alignment.Warping	Align MALDI-TOF spectra to a reference using different strategies.
maldiamrkit.alignment.RawWarping	Align MALDI-TOF spectra using raw (full resolution) data.
maldiamrkit.alignment.create_raw_input	Create input DataFrame for RawWarping from a directory of spectrum files.
maldiamrkit.alignment.AlignmentStrategy	Base class for alignment strategies.
maldiamrkit.alignment.AlignmentMethod	Supported alignment/warping methods.

Peak Detection

maldiamrkit.detection.MaldiPeakDetector	Peak detector for MALDI-TOF spectra with local maxima and topological methods.
maldiamrkit.detection.PeakMethod	Supported peak detection methods.

Evaluation

Metrics

maldiamrkit.evaluation.very_major_error_rate	Very Major Error rate: resistant isolates classified as susceptible.
maldiamrkit.evaluation.major_error_rate	Major Error rate: susceptible isolates classified as resistant.
maldiamrkit.evaluation.sensitivity_score	Sensitivity (recall) for the resistant class.
maldiamrkit.evaluation.specificity_score	Specificity (true negative rate) for the susceptible class.
maldiamrkit.evaluation.categorical_agreement	Categorical agreement (accuracy) as reported in AST studies.

Reports

maldiamrkit.evaluation.amr_classification_report	Full AMR classification report.
maldiamrkit.evaluation.mic_regression_report	Compute MIC regression metrics on log2-MIC predictions.
maldiamrkit.evaluation.amr_multilabel_report	AMR classification report for multiple antibiotics.
maldiamrkit.evaluation.vme_me_curve	VME and ME rates at varying decision thresholds.

Scorers

maldiamrkit.evaluation.vme_scorer
maldiamrkit.evaluation.me_scorer

Splitting

maldiamrkit.evaluation.stratified_species_drug_split	Stratified train/test split preserving species-drug label distributions.
maldiamrkit.evaluation.case_based_split	Train/test split keeping all samples from the same patient together.
maldiamrkit.evaluation.SpeciesDrugStratifiedKFold	K-fold cross-validation with species-drug stratification.
maldiamrkit.evaluation.CaseGroupedKFold	K-fold cross-validation keeping patient cases together and stratified by y.

Susceptibility

MIC encoding, clinical breakpoint tables, and R/I/S label encoding.

maldiamrkit.susceptibility.MICEncoder	Encode MIC strings into log2 numeric values and optional S/I/R labels.
maldiamrkit.susceptibility.BreakpointTable	Clinical breakpoint table for MIC interpretation.
maldiamrkit.susceptibility.BreakpointResult	Result of applying a clinical breakpoint to a single MIC value.
maldiamrkit.susceptibility.LabelEncoder	Encode R/I/S resistance labels to binary (0/1).
maldiamrkit.susceptibility.IntermediateHandling	Strategy for handling intermediate (I) resistance labels.

Similarity

maldiamrkit.similarity.spectral_distance	Compute distance between two spectra.
maldiamrkit.similarity.SpectralMetric	Supported spectral distance/similarity metrics.
maldiamrkit.similarity.pairwise_distances	Compute an n x n symmetric distance matrix.
maldiamrkit.similarity.cluster_spectra	Cluster spectra from a precomputed distance matrix.
maldiamrkit.similarity.hierarchical_clustering	Agglomerative hierarchical clustering on a precomputed distance matrix.
maldiamrkit.similarity.hdbscan_clustering	HDBSCAN clustering on a precomputed distance matrix.
maldiamrkit.similarity.kmedoids_clustering	K-medoids clustering using the PAM algorithm.
maldiamrkit.similarity.silhouette_scores	Silhouette score for a clustering on a precomputed distance matrix.
maldiamrkit.similarity.cluster_metadata_concordance	Evaluate clustering agreement with known metadata labels.
maldiamrkit.similarity.ClusteringMethod	Supported clustering algorithms for cluster_spectra().
maldiamrkit.similarity.KMedoidsInit	Initialization strategy for kmedoids_clustering().
maldiamrkit.similarity.plot_distance_heatmap	Plot a pairwise distance matrix as a heatmap.
maldiamrkit.similarity.plot_dendrogram	Plot a dendrogram from a hierarchical clustering linkage matrix.

Differential Analysis

Analysis

maldiamrkit.differential.DifferentialAnalysis	Identify discriminative m/z peaks between resistant and susceptible groups.
maldiamrkit.differential.StatisticalTest	Supported statistical tests for run().
maldiamrkit.differential.CorrectionMethod	Supported multiple-testing corrections for run().

Plots

maldiamrkit.differential.plot_volcano	Volcano plot of log2 fold change vs. -log10 adjusted p-value.
maldiamrkit.differential.plot_manhattan	Manhattan plot along the m/z axis.
maldiamrkit.differential.plot_drug_comparison	Visualise a multi-drug differential-peak comparison matrix.
maldiamrkit.differential.DrugComparisonKind	Rendering kind for plot_drug_comparison().

Drift Monitoring

Monitor

maldiamrkit.drift.DriftMonitor

Monitor spectral drift over time using baseline-anchored metrics.

Plots

maldiamrkit.drift.plot_reference_drift	Line plot of reference-similarity distance over time.
maldiamrkit.drift.plot_pca_drift	PCA centroid trajectory colored by time.
maldiamrkit.drift.plot_peak_stability	Line plot of peak-selection Jaccard stability over time.
maldiamrkit.drift.plot_effect_size_drift	Multi-line plot of per-peak Cohen's d over time.

Visualization

maldiamrkit.visualization.plot_spectrum	Plot a single MALDI-TOF spectrum with real m/z axis.
maldiamrkit.visualization.plot_pseudogel	Display a pseudogel heatmap of the spectra.
maldiamrkit.visualization.plot_peaks	Plot detected peaks overlaid on original spectra.
maldiamrkit.visualization.plot_alignment	Plot comparison of original vs aligned spectra against reference.
maldiamrkit.visualization.plot_pca	Scatter plot of a PCA embedding colored by metadata.
maldiamrkit.visualization.plot_tsne	Scatter plot of a t-SNE embedding colored by metadata.
maldiamrkit.visualization.plot_umap	Scatter plot of a UMAP embedding colored by metadata.

Dataset Building & Loading

Builder

maldiamrkit.data.DatasetBuilder	Build a standardised dataset from any supported input layout.
maldiamrkit.data.ProcessingHandler	Define an additional processing output folder.
maldiamrkit.data.BuildReport	Summary of a dataset build.

Input Layouts

maldiamrkit.data.InputLayout	Abstract adapter for discovering spectra and metadata.
maldiamrkit.data.FlatLayout	Flat directory of pre-exported text spectrum files + metadata CSV.
maldiamrkit.data.BrukerTreeLayout	Hierarchical directory tree containing raw Bruker binary data.

Loader

maldiamrkit.data.DatasetLoader

Load a dataset into a MaldiSet.

Dataset Layouts

maldiamrkit.data.DatasetLayout	Abstract adapter for navigating and loading from a dataset.
maldiamrkit.data.DRIAMSLayout	Navigate a DRIAMS-like dataset structure.
maldiamrkit.data.MARISMaLayout	Navigate a dataset of raw Bruker spectra organised in a tree.

Duplicate Handling

maldiamrkit.data.DuplicateStrategy

Strategy for handling duplicate spectrum identifiers.

I/O

maldiamrkit.io.read_spectrum	Read a raw spectrum file into a DataFrame.
maldiamrkit.io.parse_mic_column	Parse a column of MIC strings into numeric values and qualifiers.