arXiv subjects

Aicha Boutorh

Publications and source records attributed to Aicha Boutorh.

5 recordsLinked to original sources

arXiv2026

DuaDeep-SeqAffinity: Dual-Branch Deep Learning for Tri-Stream Sequence-Based Antibody--Antigen Affinity Prediction

DuaDeep-SeqAffinity is a sequence-only deep learning framework that predicts antibody--antigen binding affinity directly from primary amino acid sequences, avoiding the cost and scarcity of resolved three-dimensional structures. The antigen and the antibody heavy and light chains are processed as three independent streams, each embedded with a frozen ESM-2 protein language model and passed through parallel Transformer and convolutional neural network (CNN) branches before late fusion, a decoupled design intended to preserve local complementarity-determining region (CDR) signal that monolithic encoders can dilute. On a sequence-disjoint split of the AbRank benchmark, the model achieves a Pearson correlation of 0.683, an R^2 of 0.460, and a pairwise ranking AUC of 0.895, significantly outperforming single-branch ablations (paired t-test, p < 0.05). Attention-map and gradient-based saliency analyses further show that the model preferentially attends to CDR loops and candidate epitope residues, supporting its use as a scalable, structure-free tool for high-throughput antibody screening.

cs.LG↗

arXiv2026

TriSP: Tri-Signal Structured Pruning for Large Language Models

Large language models (LLMs) achieve strong performance across diverse tasks but their deployment is constrained by the memory and compute cost of their parameters. Structured pruning addresses this by removing entire structures such as attention heads and Multi-Layer Perceptron (MLP) neurons to produce smaller dense models that run efficiently on standard hardware. However, existing methods rely on either gradient-based importance estimation, which is memory-prohibitive, or activation-based statistical proxies, which do not directly measure the effect of removal on the loss. Furthermore, the interaction between the importance criterion and the post-pruning recovery strategy has not been systematically studied. We propose TriSP (Tri-Signal Structured Pruning), an importance metric that combines weight magnitude scaled by activation norm with first-order gradient sensitivity via a geometric mean, producing a channel-level score that captures both structural and loss-sensitivity signals. Combined with adaptive per-layer budget allocation and low-rank adaptation (LoRA) recovery, TriSP achieves the lowest perplexity and highest zero-shot accuracy across all tested configurations, reaching 6.80 WikiText-2 perplexity at 20% pruning on LLaMA-7B. Inference throughput improves by 82% at 50% pruning, while still maintaining competitive performance.

cs.AI↗

arXiv2026

SelKV: Selective KV Cache Merging with Per-Token Merge-or-Drop and Attention Compensation

Large Language Models (LLMs) generate text autoregressively, relying on a key-value (KV) cache whose memory footprint grows linearly with context length, creating a major bottleneck. Recent compression methods mitigate this cost via token merging; however, these approaches often rely on indiscriminate aggregation, which degrades representations and introduces attention sag, a mismatch where merged tokens receive the same softmax mass as individual tokens despite encoding multiple inputs. We propose a training-free, dual-component framework for KV cache compression that addresses these limitations. First, a soft cosine gate adaptively modulates merging decisions based on value-vector similarity, suppressing or discarding dissimilar tokens to preserve semantic fidelity. Second, we introduce an attention-ratio compensation mechanism that applies a decoding-time logit bias derived from prefill attention statistics, correcting the softmax imbalance induced by merging. Evaluated on LongBench (16 English datasets) while retaining only 25% of the KV cache, our framework achieves strong compressed performance against representative one-shot baselines. It is especially robust on the evaluated grouped-query attention (GQA) models, maintaining nearlossless generation quality. Furthermore, the method outperforms the full-cache baseline on complex multi-document QA tasks and delivers a 3.3x decoding speedup at 100k tokens.

cs.AI↗

arXiv2026

VAMP-Net: An Interpretable Multi-Path Network of Genomic Permutation-Invariant Set Attention and Quality-Aware 1D-CNN for MTB Drug Resistance

Genomic prediction of drug resistance in Mycobacterium tuberculosis is often hindered by complex epistatic interactions and variable sequencing quality. We present the Interpretable Variant-Aware Multi-Path Network (VAMP-Net), a novel architecture addressing these challenges through a dual-pathway approach. Path-1 utilizes a Set Attention Transformer to model permutation-invariant variant sets and capture epistatic dependencies, while Path-2 employs a 1D-CNN to analyze VCF quality metrics for adaptive confidence scoring. Evaluated on four critical anti-TB drugs, VAMP-Net significantly outperforms baseline CNN and MLP models, achieving accuracies > 95% and AUCs around 0.97 for Rifampicin and Rifabutin. Feature attribution analysis via Integrated Gradients successfully recovered canonical targets (rpoB, embB, katG) and discovered high-impact novel loci. Functional enrichment confirmed these novel variants constitute non-random metabolic modules (p=0.00239) centered on cell-wall remodeling. Furthermore, systematic ablation of the Quality-Aware pathway demonstrates that the model performs a learned "integrated audit," prioritizing the Fraction of Supporting Reads and relative confidence over raw depth to mitigate technical noise. This dual-layer interpretability, bridging genomic pathogenicity with technical reliability, establishes a new paradigm for robust, auditable, and clinically actionable resistance prediction, positioning VAMP-Net as an important tool for both diagnostic classification and mechanistic discovery in clinical genomics.

cs.LG↗

arXiv2026

AgrI Challenge: A Data-Centric AI Competition for Cross-Team Validation in Agricultural Vision

Machine learning models in agricultural vision often achieve high accuracy on curated datasets but fail to generalize under real field conditions due to distribution shifts between training and deployment environments. Moreover, most machine learning competitions focus primarily on model design while treating datasets as fixed resources, leaving the role of data collection practices in model generalization largely unexplored. We introduce the AgrI Challenge, a data-centric competition framework in which multiple teams independently collect field datasets, producing a heterogeneous multi-source benchmark that reflects realistic variability in acquisition conditions. To systematically evaluate cross-domain generalization across independently collected datasets, we propose Cross-Team Validation (CTV), an evaluation paradigm that treats each team's dataset as a distinct domain. CTV includes two complementary protocols: Train-on-One-Team-Only (TOTO), which measures single-source generalization, and Leave-One-Team-Out (LOTO), which evaluates collaborative multi-source training. Experiments reveal substantial generalization gaps under single-source training: models achieve near-perfect validation accuracy yet exhibit validation-test gaps of up to 16.20% (DenseNet121) and 11.37% (Swin Transformer) when evaluated on datasets collected by other teams. In contrast, collaborative multi-source training dramatically improves robustness, reducing the gap to 2.82% and 1.78%, respectively. The challenge also produced a publicly available dataset of 50,673 field images of six tree species collected by twelve independent teams, providing a diverse benchmark for studying domain shift and data-centric learning in agricultural vision.

cs.CV↗