Malikussaid

Malikussaid, Imad Gohar

Automated industrial inspection requires both precise defect localization and structured maintenance report generation; in current practice these tasks are handled separately, with linguistic interpretation left to human experts. This paper describes a decoupled, edge-deployable pipeline for wind turbine blade inspection built from three components that each handle a distinct sub-task. The Eyes a YOLO26-x-obb oriented bounding-box detector localizes defects at dataset-native resolution. The Bridge a deterministic, parameter-free encoding module maps each detected bounding box to grid-referenced spatial tokens embedded in a structured prompt. The Brain a 4-bit quantized Qwen-2.5-1.5B model adapted with Quantized Low-Rank Adaptation (QLoRA) on 947 synthetically generated maintenance reports generates a structured JSON report from that prompt. Retrieval-Augmented Fine-Tuning (RAFT) further grounds each recommendation in indexed maintenance procedures. Five ablation experiments, scored by BLEU-4, ROUGE-L, Hallucination Rate (HR), and an LLM-as-a-Judge rubric, compare the pipeline against a monolithic vision-language model (VLM) baseline and against partial configurations in which one component is removed. The complete system achieves BLEU-4 0.41, HR=4%, and Expert Score = 8.6/10 compared with 0.07, 65%, and 3.3/10 for the zero-shot VLM baseline. The QLoRA-adapted 1.5B model generates higher-quality reports than a 671B-parameter generalist API model given identical detection evidence, at 47 tokens per second on a single T4-class GPU. The results show that purpose-built decoupled architecture with a small domain-specific training corpus outperforms a generalist end-to-end model on this structured generation task.

Malikussaid, Septian Caesar Floresko, Ade Romadhony et al.

Lipophilicity (logP) prediction remains central to drug discovery, yet linear regression models for this task frequently violate statistical assumptions in ways that invalidate their reported performance metrics. We analyzed 426,850 bioactive molecules from a rigorously curated intersection of PubChem, ChEMBL, and eMolecules databases, revealing severe heteroskedasticity in linear models predicting computed logP values (XLOGP3): residual variance increases 4.2-fold in lipophilic regions (logP greater than 5) compared to balanced regions (logP 2 to 4). Classical remediation strategies (Weighted Least Squares and Box-Cox transformation) failed to resolve this violation (Breusch-Pagan p-value less than 0.0001 for all variants). Tree-based ensemble methods (Random Forest R-squared of 0.764, XGBoost R-squared of 0.765) proved inherently robust to heteroskedasticity while delivering superior predictive performance. SHAP analysis resolved a critical multicollinearity paradox: despite a weak bivariate correlation of 0.146, molecular weight emerged as the single most important predictor (mean absolute SHAP value of 0.573), with its effect suppressed in simple correlations by confounding with topological polar surface area (TPSA). These findings demonstrate that standard linear models face fundamental challenges for computed lipophilicity prediction and provide a principled framework for interpreting ensemble models in QSAR applications.

Malikussaid, Hilal Hudan Nuha, Isman Kurniawan

Large Language Models demonstrate substantial promise for advancing scientific discovery, yet their deployment in disciplines demanding factual precision and specialized domain constraints presents significant challenges. Within molecular design for pharmaceutical development, these models can propose innovative molecular modifications but frequently generate chemically infeasible structures. We introduce VALID-Mol, a comprehensive framework that integrates chemical validation with LLM-driven molecular design, achieving an improvement in valid chemical structure generation from 3% to 83%. Our methodology synthesizes systematic prompt optimization, automated chemical verification, and domain-adapted fine-tuning to ensure dependable generation of synthesizable molecules with enhanced properties. Our contribution extends beyond implementation details to provide a transferable methodology for scientifically-constrained LLM applications with measurable reliability enhancements. Computational analyses indicate our framework generates promising synthesis candidates with up to 17-fold predicted improvements in target binding affinity while preserving synthetic feasibility.

Malikussaid, Hilal Hudan Nuha, Isman Kurniawan

Large Language Models frequently generate outputs that appear scientifically reasonable yet violate fundamental principles--a phenomenon we characterize as the "plausibility-validity gap." This challenge proves especially acute in chemistry, where superficial correctness masks deeper errors in molecular structure, reaction mechanisms, and synthetic pathways. We present a systematic approach combining a reasoning-centric model architecture (Magistral Small) with Low-Rank Adaptation fine-tuning on a dual-domain dataset covering molecular properties and chemical transformations. Evaluation reveals substantial improvements: the fine-tuned system achieves 96.3% format adherence, 97.4% chemical validity, and 74.4% synthesis feasibility. Comparative analysis shows our approach outperforms specialized translation models like MolT5 (97.4% vs 77.2% validity) while achieving performance comparable to complex tool-augmented systems like ChemCrow (9.0/10 vs 9.24/10 expert rating) through a more transparent, efficient methodology. Results demonstrate a learning hierarchy where syntactic correctness develops before chemical understanding, which precedes synthetic planning capability. This work establishes a reproducible framework for transforming generalist language models into dependable scientific tools while identifying critical areas including stereochemical precision, knowledge currency, and computational accessibility as key challenges for future advancement.

Malikussaid, Septian Caesar Floresko, Sutiyo

The integration of large-scale chemical databases represents a critical bottleneck in modern cheminformatics research, particularly for machine learning applications requiring high-quality, multi-source validated datasets. This paper presents a case study of integrating three major public chemical repositories: PubChem (176 million compounds), ChEMBL, and eMolecules, to construct a curated dataset for molecular property prediction. We investigate whether byte-offset indexing can practically overcome brute-force scalability limits while preserving data integrity at hundred-million scale. Our results document the progression from an intractable brute-force search algorithm with projected 100-day runtime to a byte-offset indexing architecture achieving 3.2-hour completion-a 740-fold performance improvement through algorithmic complexity reduction from O(NxM) to O(N+M). Systematic validation of 176 million database entries revealed hash collisions in InChIKey molecular identifiers, necessitating pipeline reconstruction using collision-free full InChI strings. We present performance benchmarks, quantify trade-offs between storage overhead and scientific rigor, and compare our approach with alternative large-scale integration strategies. The resulting system successfully extracted 435,413 validated compounds and demonstrates generalizable principles for large-scale scientific data integration where uniqueness constraints exceed hash-based identifier capabilities.

Malikussaid, Sutiyo

The convergence of Information Technology and Operational Technology has exposed Industrial Control Systems to adaptive, intelligent adversaries that render static defenses obsolete. This paper introduces the Adversarial Resilience Co-evolution (ARC) framework, addressing the "Trinity of Trust" comprising model fidelity, data integrity, and analytical resilience. ARC establishes a co-evolutionary arms race within a Fortified Secure Digital Twin (F-SCDT), where a Deep Reinforcement Learning "Red Agent" autonomously discovers attack paths while an ensemble-based "Blue Agent" is continuously hardened against these threats. Experimental validation on the Tennessee Eastman Process (TEP) and Secure Water Treatment (SWaT) testbeds demonstrates superior performance in detecting novel attacks, with F1-scores improving from 0.65 to 0.89 and detection latency reduced from over 1200 seconds to 210 seconds. A comprehensive ablation study reveals that the co-evolutionary process itself contributes a 27% performance improvement. By integrating Explainable AI and proposing a Federated ARC architecture, this work presents a necessary paradigm shift toward dynamic, self-improving security for critical infrastructure.