arXiv subjects

Khadidja Henni

Publications and source records attributed to Khadidja Henni.

3 recordsLinked to original sources

arXiv2026

Drug-Target Interaction Prediction via Hierarchical Sequential Cross-Attention over Chemical and Protein Language Models

Predicting Drug-Target Interactions~(DTIs) is a central task in computational drug discovery, with direct applications in virtual screening, drug repurposing, and therapeutic candidate prioritization. Although recent deep learning methods have improved DTI prediction, many sequence-based models still process drugs and proteins independently and only combine their representations at a late prediction stage. This limits their ability to explicitly model cross-molecular dependencies between chemical substructures and protein sequence regions. In this paper, we propose a sequence-only DTI prediction architecture that combines two pre-trained language models, ChemBERTa for drug SMILES strings and ESM-2 for protein amino acid sequences, with a hierarchical interaction module. The proposed model first extracts contextual representations using pre-trained encoders, then applies 1D convolutional layers to condense local sequence patterns, followed by a sequential bidirectional cross-attention mechanism inspired by the induced-fit view of molecular recognition. Finally, attention-based pooling constructs fixed-size interaction-aware vectors for binary prediction. Experiments on BIOSNAP, Davis, and BindingDB show that the proposed model achieves the best performance on BIOSNAP, matches the best AUROC on Davis, and remains competitive on BindingDB while using only 25.2 million trainable parameters. Ablation results confirm the contribution of both the CNN and cross-attention modules, and cold-start experiments indicate promising generalization to unseen proteins and drugs.

cs.LG↗

arXiv2026

BERT4DTI : BERT-based Model for Predicting Drug-Protein Interactions

Understanding how drugs interact with protein targets is fundamental to drug discovery, drug repurposing and the early identification of promising therapeutic candidates before costly experimental testing. Sequence-based DTI models face three practical limitations: labelled interactions are scarce and unevenly distributed, large pretrained chemical and protein encoders are expensive to fine-tune end-to-end, and independently encoded sequences do not capture pair-specific dependencies. We present BERT4DTI, which encodes SMILES strings with ChemBERTa and amino-acid sequences with ProtBERT, applies bidirectional mutual attention between token-level representations, and classifies the resulting interaction features using convolutional layers and a multilayer perceptron. To reduce trainable size, ProtBERT is truncated to 18 retained layers and only the last two layers of each encoder are fine-tuned. On BIOSNAP, DAVIS and BindingDB, BERT4DTI is competitive, achieving the best ROC-AUC and PR-AUC on BIOSNAP and the highest sensitivity on all three benchmarks. An ablation on DAVIS shows that mutual attention improves PR-AUC and specificity. With 125M trainable parameters compared with 353M for full BERT fine-tuning, BERT4DTI provides a favourable performance-parameter trade-off for sequence-based DTI screening, while leaving runtime profiling, calibration and leakage-audited validation for future work.

cs.LG↗

arXiv2026

DiffEEG: A Self-Supervised Denoising Diffusion Model for Learning EEG Generic Representations

Deep learning for EEG-based seizure detection faces critical challenges: severe annotation scarcity and extreme class imbalance, where ictal events comprise less than 10\% of clinical recordings. We present DiffEEG, a 9.6M-parameter self-supervised foundation model that addresses both limitations through denoising diffusion pre-training and reinforcement learning (RL)-based fine-tuning. Pre-trained on 1.3M unlabeled segments from the Temple University Hospital Seizure Corpus (TUHSZ), DiffEEG learns generic neural representations via a 1D U-Net with multi-head self-attention. For downstream adaptation, a reinforced decision layer employs policy gradient optimization to directly maximize F1-score, prioritizing sensitivity to rare seizure events over overall accuracy. Under strict patient-wise evaluation (279 patients, Leave-One-Fold-Out), DiffEEG achieves 61\% accuracy and 59\% F1 for 4-class seizure subtyping, and 81\% accuracy with 85\% weighted F1 for binary detection, maintaining clinically viable seizure recall (59\%) despite extreme imbalance (6.7\% prevalence). Segment-level evaluation establishes an upper bound of 97.6\% accuracy, confirming strong architectural capacity. DiffEEG demonstrates that diffusion-based pre-training combined with metric-aware reinforcement learning enables clinically deployable seizure monitoring with minimal labeled data requirements.

cs.LG↗