Prompt-to-Paper: Agentic AI System for Bioinformatics

arXiv:2607.05456v1 Announce Type: new
Abstract: While recent advances in large language models have enabled end-to-end automated manuscript generation, existing systems suffer from three critical deficiencies: (i) generated claims are not deterministically grounded in verifiable literature, (ii) experimental results are frequently fabricated rather than executed, and (iii) there exists no standardized, multi-dimensional framework to assess whether AI-generated manuscripts meet the quality and rigor required for real-world publication. We present Prompt-to-Paper, a multi-agent framework that directly addresses this evaluation gap through three integrated innovations. First, a deterministic retrieval-augmented generation pipeline with section-aware relevance scoring and snowball citation expansion grounds every claim in a verifiable corpus of 60–100 papers. Second, an autonomous coding agent executes real computational biology experiments replacing synthetic outputs with genuine numerical results. Third, an eight-dimensional automated quality scorer, benchmarked with approximate reference statistics from published papers and augmented with explicit hallucination penalties, provides standardized, reproducible quality assessments. The quality-driven improvement loop uses a context-rich reviser that routes each iteration to one of three researcher actions and fires a deep research cycle every ten iterations to re-run experiments and re-manuscript from stronger outputs. We validate the system on five bioinformatics case studies; all five cases compiled submission-formatted PDFs with zero out-of-range citations. The improvement loop raises manuscript quality by an average of +17.96 points on a 0–100 scale (maximum +26.04. As partial external checks, a human reviewer scored the five manuscripts at an average of 7.0 out of 10. Complete manuscripts are produced at approximately 0.31 USD per paper.
Continue ReadingPrompt-to-Paper: Agentic AI System for Bioinformatics

From Graphs to Gradients: Physics-Inspired Structural Attribution for Cyber-Physical IoT Systems and Beyond

arXiv:2607.05563v1 Announce Type: new
Abstract: Interpretable explanation methods in Artificial Intelligence aim to uncover the underlying causes and their effects, enabling a deeper understanding of why a system behaves in a certain way under different inputs. Unlike traditional explainability methods, which mainly highlight correlations between input and output variables, causal explanation focuses on interventional questions. By doing so, it provides more robust insights, helping users understand automated decisions, especially in high-risk domains. Recovering an explicit directed causal structure, however, is often impractical in large-scale, hybrid cyber-physical systems with feedback loops and partial observability. This paper introduces a novel framework inspired by statistical mechanics that instead models variable dependencies through an undirected, energy-based representation of cyber-physical IoT systems. Our approach enables rigorous dependency-aware attribution by analysing how variations in the energy landscape reflect the influence of individual components, without recovering a directed causal graph. It also supports reasoning about perturbation effects across hybrid interactions, providing reliable explanations of abnormal behaviours. We empirically examined our framework through simulations on an industrial IoT testbed with hybrid continuous and discrete variables, demonstrating higher attribution accuracy, improved robustness and better scalability than state-of-the-art graph-based approaches. While the attributions are not intended to fully recover the system’s generative dynamics, they provide valuable, dependency-aware explanations supporting both human interpretation and downstream predictive and diagnostic tasks. Although demonstrated in industrial IoT security, our framework also applies to other high-dimensional cyber-physical and socio-technical systems requiring principled, structural explanations.
Continue ReadingFrom Graphs to Gradients: Physics-Inspired Structural Attribution for Cyber-Physical IoT Systems and Beyond

CSTutorBench: Benchmarking Small Language Models as Tutors for Block-Based Programming

arXiv:2607.05571v1 Announce Type: new
Abstract: Large language models are increasingly explored as AI tutors, yet deploying them in K-12 settings raises concerns around privacy, cost, and reliance on proprietary models. Small language models (SLMs) offer a promising alternative, but selecting the right model for a specific educational context remains difficult, particularly when the target domain, such as block-based programming, is largely absent from model training data. We introduce CSTutorBench, a benchmark for evaluating language models as CS tutors in VEX VR, a block-based robotics environment. The benchmark comprises 17 scenario-based questions scored against a pedagogical rubric grounded in established tutoring and feedback research, with a human-in-the-loop LLM-as-judge pipeline for evaluation. Preliminary findings across 11 models (4B-120B parameters) reveal that models perform well on surface-level criteria such as vocabulary and tone but struggle with deeper pedagogical behaviors, particularly avoiding answer leakage and engaging with student debugging histories. In our sample, model family and instruction-tuning approach appear to be better predictors of tutoring quality than parameter count alone, though the small number of models limits the strength of this conclusion. A targeted prompt revision grounded in recent educational prompt engineering research improved scores for 10 of 11 models. These results underscore the value of context-specific, pedagogically grounded benchmarks for SLM selection in educational deployment.
Continue ReadingCSTutorBench: Benchmarking Small Language Models as Tutors for Block-Based Programming