Morteza Rakhshaninejad

Mira Jürgens, Gaetan De Waele, Morteza Rakhshaninejad et al.

Machine learning methods for identifying molecular structures from tandem mass spectra (MS/MS) have advanced rapidly, yet current approaches still exhibit significant error rates. In high-stakes applications such as clinical metabolomics and environmental screening, incorrect annotations can have serious consequences, making it essential to determine when a prediction can be trusted. We introduce a selective prediction framework for molecular structure retrieval from MS/MS spectra, enabling models to abstain from predictions when uncertainty is too high. We formulate the problem within the risk-coverage tradeoff framework and comprehensively evaluate uncertainty quantification strategies at two levels of granularity: fingerprint-level uncertainty over predicted molecular fingerprint bits, and retrieval-level uncertainty over candidate rankings. We compare scoring functions including first-order confidence measures, aleatoric and epistemic uncertainty estimates from second-order distributions, as well as distance-based measures in the latent space. All experiments are conducted on the MassSpecGym benchmark. Our analysis reveals that while fingerprint-level uncertainty scores are poor proxies for retrieval success, computationally inexpensive first-order confidence measures and retrieval-level aleatoric uncertainty achieve strong risk-coverage tradeoffs across evaluation settings. We demonstrate that by applying distribution-free risk control via generalization bounds, practitioners can specify a tolerable error rate and obtain a subset of annotations satisfying that constraint with high probability.

Navid Yazdanjue, Morteza Rakhshaninejad, Hossein Yazdanjouei et al.

Illegal marketplaces have increasingly shifted to concealed parts of the internet, including the deep and dark web, as well as platforms such as Telegram, Reddit, and Pastebin. These channels enable the anonymous trade of illicit goods including drugs, weapons, and stolen credentials. Detecting and categorizing such content remains challenging due to limited labeled data, the evolving nature of illicit language, and the structural heterogeneity of online sources. This paper presents a hierarchical classification framework that combines fine-tuned language models with a semi-supervised ensemble learning strategy to detect and classify illicit marketplace content across diverse platforms. We extract semantic representations using ModernBERT, a transformer model for long documents, finetuned on domain-specific data from deep and dark web pages, Telegram channels, Subreddits, and Pastebin pastes to capture specialized jargon and ambiguous linguistic patterns. In addition, we incorporate manually engineered features such as document structure, embedded patterns including Bitcoin addresses, emails, and IPs, and metadata, which complement language model embeddings. The classification pipeline operates in two stages. The first stage uses a semi-supervised ensemble of XGBoost, Random Forest, and SVM with entropy-based weighted voting to detect sales-related documents. The second stage further classifies these into drug, weapon, or credential sales. Experiments on three datasets, including our multi-source corpus, DUTA, and CoDA, show that our model outperforms several baselines, including BERT, ModernBERT, DarkBERT, ALBERT, Longformer, and BigBird. The model achieves an accuracy of 0.96489, an F1-score of 0.93467, and a TMCC of 0.95388, demonstrating strong generalization, robustness under limited supervision, and effectiveness in real-world illicit content detection.

Morteza Rakhshaninejad, Mira Jurgens, Nicolas Dewolf et al.

Accurate drug-target interaction (DTI) prediction with machine learning models is essential for drug discovery. Such models should also provide a credible representation of their uncertainty, but applying classical marginal conformal prediction (CP) in DTI prediction often overlooks variability across drug and protein subgroups. In this work, we analyze three cluster-conditioned CP methods for DTI prediction, and compare them with marginal and group-conditioned CP. Clusterings are obtained via nonconformity scores, feature similarity, and nearest neighbors, respectively. Experiments on the KIBA dataset using four data-splitting strategies show that nonconformity-based clustering yields the tightest intervals and most reliable subgroup coverage, especially in random and fully unseen drug-protein splits. Group-conditioned CP works well when one entity is familiar, but residual-driven clustering provides robust uncertainty estimates even in sparse or novel scenarios. These results highlight the potential of cluster-based CP for improving DTI prediction under uncertainty.