arXiv subjects

Jennifer D'Souza

Publications and source records attributed to Jennifer D'Souza.

At least 19 recordsLinked to original sources

arXiv2026

Mined from Scientific Literature: Process Schemas for Atomic Layer Deposition and Etching in Materials Science

Atomic layer deposition (ALD) and atomic layer etching (ALE) are reported heterogeneously across experimental and simulation literature in materials science, hindering comparison and machine-actionable reuse. We present four domain-expert-reviewed JSON Schemas for ALD and ALE experimental and simulation processes. Curated with schema-miner and grounded in QUDT using schema-miner pro, the schemas structure materials, process conditions, configurations , and measured or predicted results. We compare their scope, structure, and semantic grounding, and demonstrate their use for schema-guided literature extraction and publication of structured records through ORKG templates.

cs.AI↗

arXiv2026

When Does Bigger Help? A Controlled Study of LLM Scale for Ontology Learning

The effect of Large Language Model (LLM) scale on ontology learning (OL) performance remains insufficiently characterized. We present a controlled evaluation of 13 models spanning dense and Mixture-of-Experts variants from the Qwen3.5 and Qwen3.6 lineages, together with proprietary GPT release variants, using the OntoLearner retrieval-augmented generation pipeline. All models are evaluated with the same embedding model, retrieval configuration, prompt templates, decoding settings, datasets, and metrics on term typing, taxonomy discovery, and non-taxonomic relationship extraction across four biomedical and materials science and engineering ontologies. Within the dense Qwen3.5 lineage, increasing parameter count primarily improves precision rather than recall, with the largest gains occurring between 9B and 27B parameters. However, the effect of scale is neither monotonic nor uniform across tasks and domains. Dense 27B models outperform substantially larger sparse models on term typing, whereas larger Mixture-of-Experts models achieve the strongest open-weight results on taxonomy discovery. Non-taxonomic relationship extraction remains difficult across model scales, particularly for the Materials Data Science ontology. Performance differences across matched Qwen variants and proprietary GPT releases further indicate that architecture and model lineage can outweigh nominal parameter count. These findings show that model size alone is an insufficient selection criterion for OL and provide empirical guidance for reproducible LLM-assisted ontology engineering.

cs.AI↗

arXiv2026

OntoAligner-Ensemble: Voting-Based Fusion across Heterogeneous Ontology Alignment Techniques

Ontology alignment (OA) has evolved through several methodological paradigms, ranging from lexical and structural aligners to knowledge graph embedding (KGE) models and, more recently, Large Language Model (LLM)-based approaches. Although modern OA frameworks provide unified ecosystems for deploying these heterogeneous aligners, mechanisms for systematically reconciling their complementary and sometimes conflicting predictions remain relatively underexplored. We present OntoAligner-Ensemble, a modular and aligner-agnostic framework that combines candidate correspondences through a configurable two-stage process comprising voting-based fusion strategies followed by post-fusion selection policies. The framework supports any aligner implemented within OntoAligner that produces candidate correspondences, enabling diverse alignment paradigms to be integrated through a unified decision process. To demonstrate its effectiveness, we instantiate the framework using representative lightweight string-aligner, KGE-based, and Retrieval-Augmented Generation aligners powered by both open-weight and API-based LLMs. We evaluate individual aligners and ensemble configurations across eight benchmark tasks from five OAEI tracks spanning biomedical to beyond-equivalence. The results show that ensemble fusion consistently improves the balance between precision and recall and frequently outperforms standalone aligners across diverse domains. Furthermore, our analysis reveals that ensemble composition directly affects the precision-recall trade-off: heterogeneous cross-paradigm ensembles generally improve precision, whereas homogeneous LLM ensembles more often achieve higher overall F1-scores. These findings demonstrate that systematic ensemble learning offers a robust and reproducible strategy for OA while providing practical guidance for selecting ensemble compositions under different alignment scenarios.

cs.AI↗

arXiv2026

Do General NLP Embeddings Capture Ontological Reasoning?

General-purpose NLP embedding models perform well on linguistic tasks, but their ability to capture symbolic ontological structure remains unclear. We introduce AVA, a systematic framework for evaluating whether embeddings distinguish logic-sensitive relational semantics in ontologies and knowledge graphs. AVA comprises 171,007 contrastive triplets derived from 163 heterogeneous ontologies using hierarchy inversion, relation substitution, and disjointness injection. Each triplet contains an ontology statement, a semantically equivalent paraphrase, and a logic-sensitive hard negative with contradictory relational meaning. We evaluate more than 25 state-of-the-art embedding models and find substantial limitations: the best model achieves only 0.739 triplet accuracy, while hard negative accuracy falls to 0.135. Fine-tuning improves discrimination by a large margin but transfers poorly to downstream Semantic Web tasks, including taxonomy discovery and ontology alignment. Further analysis suggests that improvements stem partly from perturbation-specific pattern recognition rather than robust ontological understanding. These findings reveal a persistent gap between linguistic representation learning and ontology-level discrimination, challenging the assumption that strong NLP benchmark performance translates to Semantic Web competence.

cs.CL↗

arXiv2026

A Pathway to General-Purpose Scientific AI: Multimodal Comprehension of Scientific Images

Scientific figures and tables encode essential experimental evidence, yet remain difficult for digital libraries and multimodal AI systems to retrieve and interpret. The ALD/E-ImageMiner benchmark and ICDAR 2026 Competition on Information Extraction from Atomic Layer Deposition/Etching Scientific Figures provide 1,951 figures from 205 publications, expert-annotated for classification, data table extraction, summarization, and visual question answering. In these companion proceedings, we present a forward-looking perspective on how the benchmark can guide future scientific-image challenges. We examine how its tasks probe capabilities from visual and quantitative reading to domain-grounded reasoning and evidential justification, and how Bloom-informed question design can support deeper scientific understanding. We propose "scientific conceptual understanding from images" as a long-term benchmark objective, with future directions including broader domains and figure types, contextual and cross-document synthesis, hypothesis evaluation, provenance, uncertainty, counterfactual grounding, and open-ended multimodal research. This perspective connects the ICDAR 2026 challenge to a broader agenda for machine-actionable scientific visual knowledge and verifiable multimodal scientific AI.

cs.AI↗

arXiv2026

SciSchema.org: A Multidisciplinary Collection of Schemas for Structured Scientific Process Descriptions

Scientific processes are often described in heterogeneous article discourse, with details needed for comparison, reproducibility, reuse, and automation dispersed across prose, tables, figures, protocols, and supplementary files. We present the first release of SciSchema.org, a multidisciplinary collection of 16 expert-annotated schemas spanning Biology & Biotechnology, Materials & Chemistry, Imaging & Measurement, Physics, and Psychology. Each schema defines reusable fields for describing process instances, including inputs, outputs, materials, instruments or software, parameters, conditions, procedural steps, measurements, and provenance-related information. The schemas were created through a human-in-the-loop schema-mining workflow in which large language models generated candidate structures from process specifications, scientific articles, and expert feedback, followed by domain-expert construction of final master schemas. The dataset contains final schemas in JSON Schema and SHACL formats, intermediate model-generated schemas, expert-feedback records, source-paper metadata, community-development materials, and analysis scripts. Technical validation assessed schema structure, development provenance, expert review, and syntactic conformance. The collection supports structured annotation, metadata enrichment, scientific knowledge graphs, information extraction, semantic publishing, and cross-study comparison.

cs.DL↗

arXiv2026

ICDAR 2026 Competition on Information Extraction from Atomic Layer Deposition/Etching (ALD/E) Scientific Figures

Scientific figure comprehension and reasoning using multimodal AI requires integrating visual perception with domain-specific reasoning to extract meaningful knowledge, often not presented in the text of a research publication. The Sci-ImageMiner benchmark dataset, accompanied by a community-driven competition, raises the bar over prior scientific competitions by curating a comprehensive, expert-annotated dataset across four end-to-end complementary tasks. The competition attracted 68 active participants and 1,263 public/private submissions from 9th January 2026 to 8th April 2026. Our results show that state-of-the-art multimodal models perform well on classification and summarization tasks but struggle with data extraction and scientific reasoning, particularly in visual question-answering. These findings reveal key limitations and highlight challenges and opportunities for improving domain-aware multimodal AI systems. Overall, the Sci-ImageMiner benchmark and competition establish a rigorous platform for advancing research in scientific figure comprehension and reasoning and demonstrate the potential of state-of-the-art approaches for a challenging and complex research area.

cs.CV↗

arXiv2026

OntoLearner: A Modular Python Library for Ontology Learning with Large Language Models

Ontology learning (OL) aims to automatically construct structured knowledge models from text, yet progress remains fragmented across methods, domains, and evaluation practices. Despite decades of research, OL lacks a shared infrastructure for systematic evaluation and ontology access. This absence has hindered progress and fragmented research, leaving the central challenges of OL largely unaddressed. We introduce OntoLearner, a modular, cross-domain, and first-of-its-kind framework that unifies ontology access, large language model (LLM)-driven learning pipelines, and standardized benchmarking. OntoLearner releases 180 machine-readable ontologies spanning 22 domains and provides pipeline-ready datasets with train/dev/test splits for three core OL tasks: term typing, taxonomy discovery, and non-taxonomic relation extraction. Using this infrastructure, we conduct a large-scale empirical study of OL, evaluating 22 retrieval models and 12 LLMs across domains and tasks. The results converge on a finding that reframes the central challenge of OL: failure modes scale with ontological complexity rather than model size or architectural sophistication. The primary bottleneck is not model capability, but a structural mismatch between how models encode knowledge and how ontologies organize it. These findings establish that effective OL is reachable through the cross-domain, multi-task benchmarking enabled by OntoLearner. OntoLearner is open-source (MIT license) at https://github.com/sciknoworg/OntoLearner/.

cs.AI↗

arXiv2026

An Extreme Multi-label Text Classification (XMTC) Library Dataset: What if we took "Use of Practical AI in Digital Libraries" seriously?

Subject indexing is vital for discovery but hard to sustain at scale and across languages. We release a large bilingual (English/German) corpus of catalog records annotated with the Integrated Authority File (GND), plus a machine-actionable GND taxonomy. The resource enables ontology-aware multi-label classification, mapping text to authority terms, and agent-assisted cataloging with reproducible, authority-grounded evaluation. We provide a brief statistical profile and qualitative error analyses of three systems. We invite the community to assess not only accuracy but usefulness and transparency, toward authority-anchored AI co-pilots that amplify catalogers' work.

cs.CL↗

arXiv2026

Transforming Science with Large Language Models: A Survey on AI-assisted Scientific Discovery, Experimentation, Content Generation, and Evaluation

With the advent of large multimodal language models, science is now at a threshold of an AI-based technological transformation. An emerging ecosystem of models and tools aims to support researchers throughout the scientific lifecycle, including (1) searching for relevant literature, (2) generating research ideas and conducting experiments, (3) producing text-based content, (4) creating multimodal artifacts such as figures and diagrams, and (5) evaluating scientific work, as in peer review. In this survey, we provide a curated overview of literature representative of the core techniques, evaluation practices, and emerging trends in AI-assisted scientific discovery. Across the five tasks outlined above, we discuss datasets, methods, results, evaluation strategies, limitations, and ethical concerns, including risks to research integrity through the misuse of generative models. We aim for this survey to serve both as an accessible, structured orientation for newcomers to the field, as well as a catalyst for new AI-based initiatives and their integration into future ``AI4Science'' systems.

cs.CL↗

arXiv2026

Diagnosing Structural Failures in LLM-Based Evidence Extraction for Meta-Analysis

Systematic reviews and meta-analyses rely on converting narrative articles into structured, numerically grounded study records. Despite rapid advances in large language models (LLMs), it remains unclear whether they can meet the structural requirements of this process, which hinge on preserving roles, methods, and effect-size attribution across documents rather than on recognizing isolated entities. We propose a structural, diagnostic framework that evaluates LLM-based evidence extraction as a progression of schema-constrained queries with increasing relational and numerical complexity, enabling precise identification of failure points beyond atom-level extraction. Using a manually curated corpus spanning five scientific domains, together with a unified query suite and evaluation protocol, we evaluate two state-of-the-art LLMs under both per-document and long-context, multi-document input regimes. Across domains and models, performance remains moderate for single-property queries but degrades sharply once tasks require stable binding between variables, roles, statistical methods, and effect sizes. Full meta-analytic association tuples are extracted with near-zero reliability, and long-context inputs further exacerbate these failures. Downstream aggregation amplifies even minor upstream errors, rendering corpus-level statistics unreliable. Our analysis shows that these limitations stem not from entity recognition errors, but from systematic structural breakdowns, including role reversals, cross-analysis binding drift, instance compression in dense result sections, and numeric misattribution, indicating that current LLMs lack the structural fidelity, relational binding, and numerical grounding required for automated meta-analysis. The code and data are publicly available at GitHub (https://github.com/zhiyintan/LLM-Meta-Analysis).

cs.CL↗

arXiv2026

Publishing FAIR and Machine-actionable Reviews in Materials Science: The Case for Symbolic Knowledge in Neuro-symbolic Artificial Intelligence

Scientific reviews are central to knowledge integration in materials science, yet their key insights remain locked in narrative text and static PDF tables, limiting reuse by humans and machines alike. This article presents a case study in atomic layer deposition and etching (ALD/E) where we publish review tables as FAIR, machine-actionable comparisons in the Open Research Knowledge Graph (ORKG), turning them into structured, queryable knowledge. Building on this, we contrast symbolic querying over ORKG with large language model-based querying, and argue that a curated symbolic layer should remain the backbone of reliable neurosymbolic AI in materials science, with LLMs serving as complementary, symbolically grounded interfaces rather than standalone sources of truth.

cs.AI↗

arXiv2025

Towards AI-Supported Research: a Vision of the TIB AIssistant

The rapid advancements in Generative AI and Large Language Models promise to transform the way research is conducted, potentially offering unprecedented opportunities to augment scholarly workflows. However, effectively integrating AI into research remains a challenge due to varying domain requirements, limited AI literacy, the complexity of coordinating tools and agents, and the unclear accuracy of Generative AI in research. We present the vision of the TIB AIssistant, a domain-agnostic human-machine collaborative platform designed to support researchers across disciplines in scientific discovery, with AI assistants supporting tasks across the research life cycle. The platform offers modular components - including prompt and tool libraries, a shared data store, and a flexible orchestration framework - that collectively facilitate ideation, literature analysis, methodology development, data analysis, and scholarly writing. We describe the conceptual framework, system architecture, and implementation of an early prototype that demonstrates the feasibility and potential impact of our approach.

cs.AI↗

arXiv2025

OntoAligner Meets Knowledge Graph Embedding Aligners

Ontology Alignment (OA) is essential for enabling semantic interoperability across heterogeneous knowledge systems. While recent advances have focused on large language models (LLMs) for capturing contextual semantics, this work revisits the underexplored potential of Knowledge Graph Embedding (KGE) models, which offer scalable, structure-aware representations well-suited to ontology-based tasks. Despite their effectiveness in link prediction, KGE methods remain underutilized in OA, with most prior work focusing narrowly on a few models. To address this gap, we reformulate OA as a link prediction problem over merged ontologies represented as RDF-style triples and develop a modular framework, integrated into the OntoAligner library, that supports 17 diverse KGE models. The system learns embeddings from a combined ontology and aligns entities by computing cosine similarity between their representations. We evaluate our approach using standard metrics across seven benchmark datasets spanning five domains: Anatomy, Biodiversity, Circular Economy, Material Science and Engineering, and Biomedical Machine Learning. Two key findings emerge: first, KGE models like ConvE and TransF consistently produce high-precision alignments, outperforming traditional systems in structure-rich and multi-relational domains; second, while their recall is moderate, this conservatism makes KGEs well-suited for scenarios demanding high-confidence mappings. Unlike LLM-based methods that excel at contextual reasoning, KGEs directly preserve and exploit ontology structure, offering a complementary and computationally efficient strategy. These results highlight the promise of embedding-based OA and open pathways for further work on hybrid models and adaptive strategies.

cs.AI↗

arXiv2025

Toward Purpose-oriented Topic Model Evaluation enabled by Large Language Models

This study presents a framework for automated evaluation of dynamically evolving topic models using Large Language Models (LLMs). Topic modeling is essential for organizing and retrieving scholarly content in digital library systems, helping users navigate complex and evolving knowledge domains. However, widely used automated metrics, such as coherence and diversity, often capture only narrow statistical patterns and fail to explain semantic failures in practice. We introduce a purpose-oriented evaluation framework that employs nine LLM-based metrics spanning four key dimensions of topic quality: lexical validity, intra-topic semantic soundness, inter-topic structural soundness, and document-topic alignment soundness. The framework is validated through adversarial and sampling-based protocols, and is applied across datasets spanning news articles, scholarly publications, and social media posts, as well as multiple topic modeling methods and open-source LLMs. Our analysis shows that LLM-based metrics provide interpretable, robust, and task-relevant assessments, uncovering critical weaknesses in topic models such as redundancy and semantic drift, which are often missed by traditional metrics. These results support the development of scalable, fine-grained evaluation tools for maintaining topic relevance in dynamic datasets. All code and data supporting this work are accessible at https://github.com/zhiyintan/topic-model-LLMjudgment.

cs.CL↗

arXiv2025

DeepResearch$^{\text{Eco}}$: A Recursive Agentic Workflow for Complex Scientific Question Answering in Ecology

We introduce DeepResearch$^{\text{Eco}}$, a novel agentic LLM-based system for automated scientific synthesis that supports recursive, depth- and breadth-controlled exploration of original research questions -- enhancing search diversity and nuance in the retrieval of relevant scientific literature. Unlike conventional retrieval-augmented generation pipelines, DeepResearch enables user-controllable synthesis with transparent reasoning and parameter-driven configurability, facilitating high-throughput integration of domain-specific evidence while maintaining analytical rigor. Applied to 49 ecological research questions, DeepResearch achieves up to a 21-fold increase in source integration and a 14.9-fold rise in sources integrated per 1,000 words. High-parameter settings yield expert-level analytical depth and contextual diversity. Source code available at: https://github.com/sciknoworg/deep-research.

cs.AI↗

arXiv2025

Research Knowledge Graphs: the Shifting Paradigm of Scholarly Information Representation

Sharing and reusing research artifacts, such as datasets, publications, or methods is a fundamental part of scientific activity, where heterogeneity of resources and metadata and the common practice of capturing information in unstructured publications pose crucial challenges. Reproducibility of research and finding state-of-the-art methods or data have become increasingly challenging. In this context, the concept of Research Knowledge Graphs (RKGs) has emerged, aiming at providing an easy to use and machine-actionable representation of research artifacts and their relations. That is facilitated through the use of established principles for data representation, the consistent adoption of globally unique persistent identifiers and the reuse and linking of vocabularies and data. This paper provides the first conceptualisation of the RKG vision, a categorisation of in-use RKGs together with a description of RKG building blocks and principles. We also survey real-world RKG implementations differing with respect to scale, schema, data, used vocabulary, and reliability of the contained data. We also characterise different RKG construction methodologies and provide a forward-looking perspective on the diverse applications, opportunities, and challenges associated with the RKG vision.

cs.IR↗

arXiv2025

YESciEval: Robust LLM-as-a-Judge for Scientific Question Answering

Large Language Models (LLMs) drive scientific question-answering on modern search engines, yet their evaluation robustness remains underexplored. We introduce YESciEval, an open-source framework that combines fine-grained rubric-based assessment with reinforcement learning to mitigate optimism bias in LLM evaluators. We release multidisciplinary scienceQ&A datasets, including adversarial variants, with evaluation scores from multiple LLMs. Independent of proprietary models and human feedback, our approach enables scalable, cost-free evaluation. By advancing reliable LLM-as-a-judge models, this work supports AI alignment and fosters robust, transparent evaluation essential for scientific inquiry.

cs.CL↗