From owner-chemistry@ccl.net Wed Nov  5 12:24:00 2025
From: "Andrea Mauri andrea.mauri-,-alvascience.com" <owner-chemistry|server.ccl.net>
To: CCL
Subject: CCL: Release of alvaModel 3.0.0
Message-Id: <-55422-251105104708-17698-Z//UrwvJVlBRyivDiIaWLw|server.ccl.net>
X-Original-From: "Andrea  Mauri" <andrea.mauri\a/alvascience.com>
Date: Wed, 5 Nov 2025 10:47:03 -0500


Sent to CCL by: "Andrea  Mauri" [andrea.mauri[#]alvascience.com]
Dear colleagues,

We are pleased to announce the release of alvaModel version 3.0.0, a major 
update to our software for building, validating, and analyzing QSAR/QSPR 
models.

This release introduces several important features aimed at expanding modeling 
capabilities, improving interpretability, and streamlining the model 
development workflow.

New Modeling Capabilities

Regression and Classification Models
- Decision Tree (Regression and Classification)
- Random Forest (Regression and Classification)
- Consensus Classification Model (weighted on reliability)

Customizable Model Parameters
Users can now define sets of custom parameters for:
- K-Nearest Neighbors (KNN)
- Support Vector Machine (SVM)
- Consensus (Classification)
- Decision Tree
- Random Forest

Applicability Domain
- New method: Bounding Box

Similarity Measures
- Dice and Cosine distances are now supported

Enhanced Evaluation Metrics

New Classification Scores
- AUROC (Area Under the Receiver Operating Characteristic Curve)
- F1 Score
- Matthews Correlation Coefficient (MCC)
- Cohens Kappa

Improved Visualization and User Interface

Model Comparison Features
- New interface for comparing multiple models
- Display of 95% confidence intervals for scores
- Automatic highlighting of best/worst scores
New comparison charts:
- Simultaneous Confidence Interval Plot
- Radar Plot

Classification Model View Enhancements
- New Reliability column
- Color-coded indicators for:
- Correct predictions
- Reliability
- Applicability Domain (A.D.)
- Colored Confusion Matrix with molecule filtering capability

Workflow and Usability Improvements
- Prediction of external datasets without the need for alvaRunner
- New Open Recent Project menu
- Batch model saving in automatic model generation
- Improved dataset management:
- Move or copy molecules between datasets
- Rename external variable columns
- Contextual popup menus for dataset and model tables

Charts and Visualization Enhancements
- Unified chart toolbar for easy selection of chart types and settings
- For regression models: R and RMSE are now displayed in plot legends
- For classification models: ROC Curve and PrecisionRecall Curve available


For an overview of the new features, you can watch the introduction video:
https://youtu.be/5TVcpxTdQAY

More information is available on the alvaModel product page:
https://www.alvascience.com/alvamodel

Best regards,
Andrea Mauri