Antiprotozoal peptide prediction using machine learning with effective feature selection techniques
Bibliographic record
Abstract
Background: Protozoal pathogens pose a considerable threat, leading to notable mortality rates and the ongoing challenge of developing resistance to drugs. This situation underscores the urgent need for alternative therapeutic approaches. Antimicrobial peptides stand out as promising candidates for drug development. However, there is a lack of published research focusing on predicting antimicrobial peptides specifically targeting protozoal pathogens. In this study, we introduce a successful machine learning-based framework designed to predict potential antiprotozoal peptides effective against protozoal pathogens. Objective: The primary objective of this study is to classify and predict antiprotozoal peptides using diverse negative datasets. Methods: A comprehensive literature review was conducted to gather experimentally validated antiprotozoal peptides, forming the positive dataset for our study. To construct a robust machine learning classifier, multiple negative datasets were incorporated, including (i) non-antimicrobial, (ii) antiviral, (iii) antibacterial, (iv) antifungal, and (v) antimicrobial peptides excluding those targeting protozoal pathogens. Various compositional features of the peptides were extracted using the pfeature algorithm. Two feature selection methods, SVC-L1 and mRMR, were employed to identify highly relevant features crucial for distinguishing between the positive and negative datasets. Additionally, five popular classifiers i.e. Decision Tree, Random Forest, Support Vector Machine, Logistic Regression, and XGBoost were used to build efficient decision models. Results: XGBoost was the most effective in classifying antiprotozoal peptides from each negative dataset based on the features selected by the mRMR feature selection method. The proposed machine learning framework efficiently differentiate the antiprotozoal peptides from (i) non-antimicrobial (ii) antiviral (iii) antibacterial (iv) antifungal and (v) antimicrobial with accuracy of 97.27 %, 93.64 %, 86.36 %, 90.91 %, and 89.09 % respectively on the validation dataset. Conclusion: The models are incorporated in a user-friendly web server (www.soodlab.com/appred) to predict the antiprotozoal activity of given peptides.
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.
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 | 0.003 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.002 |
| Bibliometrics | 0.004 | 0.002 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.001 |
| Open science | 0.001 | 0.000 |
| 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".