AutoSAM: an Agentic Framework for Automating Input File Generation for the SAM Code with Multi-Modal Retrieval-Augmented Generation

In the design and safety analysis of advanced reactor systems, constructing input files for system-level thermal-hydraulics codes such as the System Analysis Module (SAM) remains a labor-intensive task. Analysts must extract and reconcile design data from heterogeneous engineering documents and manually translate it into solver-specific syntax. In this paper, we present AutoSAM, an agentic framework that automates SAM input file generation. The framework combines a large language model agent with retrieval-augmented generation over the solver's user guide and theory manual, together with specialized tools for analyzing PDFs, images, spreadsheets, and text files. AutoSAM ingests unstructured engineering documents, including system diagrams, design reports, and data tables, extracts simulation-relevant parameters into a human-auditable intermediate representation, and synthesizes validated, solver-compatible input decks. Its multimodal retrieval pipeline integrates scientific text extraction, vision-based figure interpretation, semantic embedding, and query answering. We evaluate AutoSAM on four case studies of increasing complexity: a single-pipe steady-state model, a solid-fuel channel with temperature reactivity feedback, the Advanced Burner Test Reactor core, and the Molten Salt Reactor Experiment primary loop. Across all cases, the agent produces runnable SAM models consistent with expected thermal-hydraulic behavior while explicitly identifying missing data and labeling assumed values. The framework achieves 100% utilization of structured inputs, about 88% extraction from PDF text, and 100% completeness in vision-based geometric extraction. These results demonstrate a practical path toward prompt-driven reactor modeling, in which analysts provide system descriptions and supporting documentation while the agent translates them into transparent, and executable, SAM simulations.

Methods for Knowledge Graph Construction from Text Collections: Development and Applications

Virtually every sector of society is experiencing a dramatic growth in the volume of unstructured textual data that is generated and published, from news and social media online interactions, through open access scholarly communications and observational data in the form of digital health records and online drug reviews. The volume and variety of data across all this range of domains has created both unprecedented opportunities and pressing challenges for extracting actionable knowledge for several application scenarios. However, the extraction of rich semantic knowledge demands the deployment of scalable and flexible automatic methods adaptable across text genres and schema specifications. Moreover, the full potential of these data can only be unlocked by coupling information extraction methods with Semantic Web techniques for the construction of full-fledged Knowledge Graphs, that are semantically transparent, explainable by design and interoperable. In this thesis, we experiment with the application of Natural Language Processing, Machine Learning and Generative AI methods, powered by Semantic Web best practices, to the automatic construction of Knowledge Graphs from large text corpora, in three use case applications: the analysis of the Digital Transformation discourse in the global news and social media platforms; the mapping and trend analysis of recent research in the Architecture, Engineering, Construction and Operations domain from a large corpus of publications; the generation of causal relation graphs of biomedical entities from electronic health records and patient-authored drug reviews. The contributions of this thesis to the research community are in terms of benchmark evaluation results, the design of customized algorithms and the creation of data resources in the form of Knowledge Graphs, together with data analysis results built on top of them.

Bridging Pixels and Words: Mask-Aware Local Semantic Fusion for Multimodal Media Verification

As multimodal misinformation becomes more sophisticated, its detection and grounding are crucial. However, current multimodal verification methods, relying on passive holistic fusion, struggle with sophisticated misinformation. Due to 'feature dilution,' global alignments tend to average out subtle local semantic inconsistencies, effectively masking the very conflicts they are designed to find. We introduce MaLSF (Mask-aware Local Semantic Fusion), a novel framework that shifts the paradigm to active, bidirectional verification, mimicking human cognitive cross-referencing. MaLSF utilizes mask-label pairs as semantic anchors to bridge pixels and words. Its core mechanism features two innovations: 1) a Bidirectional Cross-modal Verification (BCV) module that acts as an interrogator, using parallel query streams (Text-as-Query and Image-as-Query) to explicitly pinpoint conflicts; and 2) a Hierarchical Semantic Aggregation (HSA) module that intelligently aggregates these multi-granularity conflict signals for task-specific reasoning. In addition, to extract fine-grained mask-label pairs, we introduce a set of diverse mask-label pair extraction parsers. MaLSF achieves state-of-the-art performance on both the DGM4 and multimodal fake news detection tasks. Extensive ablation studies and visualization results further verify its effectiveness and interpretability.

Estimating near-verbatim extraction risk in language models with decoding-constrained beam search

Recent work shows that standard greedy-decoding extraction methods for quantifying memorization in LLMs miss how extraction risk varies across sequences. Probabilistic extraction -- computing the probability of generating a target suffix given a prefix under a decoding scheme -- addresses this, but is tractable only for verbatim memorization, missing near-verbatim instances that pose similar privacy and copyright risks. Quantifying near-verbatim extraction risk is expensive: the set of near-verbatim suffixes is combinatorially large, and reliable Monte Carlo (MC) estimation can require ~100,000 samples per sequence. To mitigate this cost, we introduce decoding-constrained beam search, which yields deterministic lower bounds on near-verbatim extraction risk at a cost comparable to ~20 MC samples per sequence. Across experiments, our approach surfaces information invisible to verbatim methods: many more extractable sequences, substantially larger per-sequence extraction mass, and patterns in how near-verbatim extraction risk manifests across model sizes and types of text.

Sketch2Simulation: Automating Flowsheet Generation via Multi Agent Large Language Models

Converting process sketches into executable simulation models remains a major bottleneck in process systems engineering, requiring substantial manual effort and simulator-specific expertise. Recent advances in generative AI have improved both engineering-diagram interpretation and LLM-assisted flowsheet generation, but these remain largely disconnected: diagram-understanding methods often stop at extracted graphs, while text-to-simulation workflows assume structured inputs rather than raw visual artifacts. To bridge this gap, we present an end-to-end multi-agent large language model system that converts process diagrams directly into executable Aspen HYSYS flowsheets. The framework decomposes the task into three coordinated layers: diagram parsing and interpretation, simulation model synthesis, and multi-level validation. Specialized agents handle visual interpretation, graph-based intermediate representation construction, code generation for the HYSYS COM interface, execution, and structural verification. We evaluate the framework on four chemical engineering case studies of increasing complexity, from a simple desalting process to an industrial aromatic production flowsheet with multiple recycle loops. The system produces executable HYSYS models in all cases, achieving complete structural fidelity on the two simpler cases and strong performance on the more complex ones, with connection consistency above 0.93 and stream consistency above 0.96. These results demonstrate a viable end-to-end sketch-to-simulation workflow while highlighting remaining challenges in dense recycle structures, implicit diagram semantics, and simulator-interface constraints.

VILLA: Versatile Information Retrieval From Scientific Literature Using Large LAnguage Models

The lack of high-quality ground truth datasets to train machine learning (ML) models impedes the potential of artificial intelligence (AI) for science research. Scientific information extraction (SIE) from the literature using LLMs is emerging as a powerful approach to automate the creation of these datasets. However, existing LLM-based approaches and benchmarking studies for SIE focus on broad topics such as biomedicine and chemistry, are limited to choice-based tasks, and focus on extracting information from short and well-formatted text. The potential of SIE methods in complex, open-ended tasks is considerably under-explored. In this study, we used a domain that has been virtually ignored in SIE, namely virology, to address these research gaps. We design a unique, open-ended SIE task of extracting mutations in a given virus that modify its interaction with the host. We develop a new, multi-step retrieval augmented generation (RAG) framework called VILLA for SIE. In parallel, we curate a novel dataset of 629 mutations in ten influenza A virus proteins obtained from 239 scientific publications to serve as ground truth for the mutation extraction task. Finally, we demonstrate VILLA's superior performance using a novel and comprehensive evaluation and comparison with vanilla RAG and other state-of-the art RAG- and agent-based tools for SIE.

Language-Guided Structure-Aware Network for Camouflaged Object Detection

Camouflaged Object Detection (COD) aims to segment objects that are highly integrated with the background in terms of color, texture, and structure, making it a highly challenging task in computer vision. Although existing methods introduce multi-scale fusion and attention mechanisms to alleviate the above issues, they generally lack the guidance of textual semantic priors, which limits the model's ability to focus on camouflaged regions in complex scenes. To address this issue, this paper proposes a Language-Guided Structure-Aware Network (LGSAN). Specifically, based on the visual backbone PVT-v2, we introduce CLIP to generate masks from text prompts and RGB images, thereby guiding the multi-scale features extracted by PVT-v2 to focus on potential target regions. On this foundation, we further design a Fourier Edge Enhancement Module (FEEM), which integrates multi-scale features with high-frequency information in the frequency domain to extract edge enhancement features. Furthermore, we propose a Structure-Aware Attention Module (SAAM) to effectively enhance the model's perception of object structures and boundaries. Finally, we introduce a Coarse-Guided Local Refinement Module (CGLRM) to enhance fine-grained reconstruction and boundary integrity of camouflaged object regions. Extensive experiments demonstrate that our method consistently achieves highly competitive performance across multiple COD datasets, validating its effectiveness and robustness.

Ran Score: a LLM-based Evaluation Score for Radiology Report Generation

Chest X-ray report generation and automated evaluation are limited by poor recognition of low-prevalence abnormalities and inadequate handling of clinically important language, including negation and ambiguity. We develop a clinician-guided framework combining human expertise and large language models for multi-label finding extraction from free-text chest X-ray reports and use it to define Ran Score, a finding-level metric for report evaluation. Using three non-overlapping MIMIC-CXR-EN cohorts from a public chest X-ray dataset and an independent ChestX-CN validation cohort, we optimize prompts, establish radiologist-derived reference labels and evaluate report generation models. The optimized framework improves the macro-averaged score from 0.753 to 0.956 on the MIMIC-CXR-EN development cohort, exceeds the CheXbert benchmark by 15.7 percentage points on directly comparable labels, and shows robust generalization on the ChestX-CN validation cohort. Here we show that clinician-guided prompt optimization improves agreement with a radiologist-derived reference standard and that Ran Score enables finding-level evaluation of report fidelity, particularly for low-prevalence abnormalities.

Context Selection for Hypothesis and Statistical Evidence Extraction from Full-Text Scientific Articles

Extracting hypotheses and their supporting statistical evidence from full-text scientific articles is central to the synthesis of empirical findings, but remains difficult due to document length and the distribution of scientific arguments across sections of the paper. The work studies a sequential full-text extraction setting, where the statement of a primary finding in an article's abstract is linked to (i) a corresponding hypothesis statement in the paper body and (ii) the statistical evidence that supports or refutes that hypothesis. This formulation induces a challenging within-document retrieval setting in which many candidate paragraphs are topically related to the finding but differ in rhetorical role, creating hard negatives for retrieval and extraction. Using a two-stage retrieve-and-extract framework, we conduct a controlled study of retrieval design choices, varying context quantity, context quality (standard Retrieval Augmented Generation, reranking, and a fine-tuned retriever paired with reranking), as well as an oracle paragraph setting to separate retrieval failures from extraction limits across four Large Language Model extractors. We find that targeted context selection consistently improves hypothesis extraction relative to full-text prompting, with gains concentrated in configurations that optimize retrieval quality and context cleanliness. In contrast, statistical evidence extraction remains substantially harder. Even with oracle paragraphs, performance remains moderate, indicating persistent extractor limitations in handling hybrid numeric-textual statements rather than retrieval failures alone.

CoCR-RAG: Enhancing Retrieval-Augmented Generation in Web Q&A via Concept-oriented Context Reconstruction

Retrieval-augmented generation (RAG) has shown promising results in enhancing Q&A by incorporating information from the web and other external sources. However, the supporting documents retrieved from the heterogeneous web often originate from multiple sources with diverse writing styles, varying formats, and inconsistent granularity. Fusing such multi-source documents into a coherent and knowledge-intensive context remains a significant challenge, as the presence of irrelevant and redundant information can compromise the factual consistency of the inferred answers. This paper proposes the Concept-oriented Context Reconstruction RAG (CoCR-RAG), a framework that addresses the multi-source information fusion problem in RAG through linguistically grounded concept-level integration. Specifically, we introduce a concept distillation algorithm that extracts essential concepts from Abstract Meaning Representation (AMR), a stable semantic representation that structures the meaning of texts as logical graphs. The distilled concepts from multiple retrieved documents are then fused and reconstructed into a unified, information-intensive context by Large Language Models, which supplement only the necessary sentence elements to highlight the core knowledge. Experiments on the PopQA and EntityQuestions datasets demonstrate that CoCR-RAG significantly outperforms existing context-reconstruction methods across these Web Q&A benchmarks. Furthermore, CoCR-RAG shows robustness across various backbone LLMs, establishing itself as a flexible, plug-and-play component adaptable to different RAG frameworks.