Integration of multiple data types is beneficial for prediction of geological characteristics. From the perspective that geochemistry characterizes the composition of a rock mass, hyperspectral data characterizes alteration mineralogy, and image feature extraction characterizes texture, most geological classifications would be well-informed by the combination of these three features. The process of meaningfully integrating distinctly sourced datasets and producing scale-relevant predictions for geological classifications involves several steps. We demonstrate a workflow to comprehensively structure and integrate these three feature families, refine training data, predict alteration classes, and mitigate noise derived from scale mismatch in output predictions. The dataset, compiled from the Josemaria porphyry copper deposit in Argentina, is comprised of more than 14,000 intervals of approximately 2 m, taken from 36 drillholes, where geochemistry was merged with hyperspectral mineralogy represented as tabular pixel abundances, and textural metrics extracted from core imagery, structured into the geochemical interval. Feature engineering and principal component analysis provided insights into the behavior of the ore system during intermediate steps, as well as providing uncorrelated feature inputs for a random forest predictor. Training data were refined by producing an initial prediction, thresholding the predictions to >70% dominant class probability and using those (high probability) samples to produce a final model encoding better constrained separation between alteration assemblages. Prediction using the final model returned an accuracy of 82.5 %, as a function of model discrepancy combined with logging ambiguity and a scale mismatch between generalized logged intervals and much more granular (2 m) feature inputs. Noise reduction and generalization to desired resolution of output was achieved by applying the multiscale multivariate continuous wavelet transform tessellation method to class membership probabilities. Ultimately a large database of logged drill-core was homogenized using empirical methodologies. The described workflow is adaptable to distinct scenarios with some modification and is apt for integrating multiple input feature types and using them to systematically define geological classifications in drill-hole data.