Daily Papers

Domain ontologies are important information sources for knowledge-based systems. Yet, building domain ontologies from scratch is known to be a very labor-intensive process. In this study, we present our semi-automatic approach to building an ontology for the domain of wind energy which is an important type of renewable energy with a growing share in electricity generation all over the world. Related Wikipedia articles are first processed in an automated manner to determine the basic concepts of the domain together with their properties and next the concepts, properties, and relationships are organized to arrive at the ultimate ontology. We also provide pointers to other engineering ontologies which could be utilized together with the proposed wind energy ontology in addition to its prospective application areas. The current study is significant as, to the best of our knowledge, it proposes the first considerably wide-coverage ontology for the wind energy domain and the ontology is built through a semi-automatic process which makes use of the related Web resources, thereby reducing the overall cost of the ontology building process.

Large Language Model agents demonstrate potential in solving real-world problems via tools, yet generalist intelligence is bottlenecked by scarce high-quality, long-horizon data. Existing methods collect privacy-constrained API logs or generate scripted interactions lacking diversity, which struggle to produce data requisite for scaling capabilities. We propose AgentSkiller, a fully automated framework synthesizing multi-turn interaction data across realistic, semantically linked domains. It employs a DAG-based architecture with explicit state transitions to ensure determinism and recoverability. The pipeline builds a domain ontology and Person-Centric Entity Graph, defines tool interfaces via Service Blueprints for Model Context Protocol servers, and populates environments with consistent databases and strict Domain Policies. A cross-domain fusion mechanism links services to simulate complex tasks. Finally, the pipeline creates user tasks by verifying solution paths, filtering via execution-based validation, and generating queries using a Persona-based Simulator for automated rollout. This produces reliable environments with clear state changes. To demonstrate effectiveness, we synthesized approx 11K interaction samples; experimental results indicate that models trained on this dataset achieve significant improvements on function calling over baselines, particularly in larger parameter regimes.

This paper introduces a new ontology for Materials Science Laboratory Equipment, termed MSLE. A fundamental issue with materials science laboratory (hereafter lab) equipment in the real world is that scientists work with various types of equipment with multiple specifications. For example, there are many electron microscopes with different parameters in chemical and physical labs. A critical development to unify the description is to build an equipment domain ontology as basic semantic knowledge and to guide the user to work with the equipment appropriately. Here, we propose to develop a consistent ontology for equipment, the MSLE ontology. In the MSLE, two main existing ontologies, the Semantic Sensor Network (SSN) and the Material Vocabulary (MatVoc), have been integrated into the MSLE core to build a coherent ontology. Since various acronyms and terms have been used for equipment, this paper proposes an approach to use a Simple Knowledge Organization System (SKOS) to represent the hierarchical structure of equipment terms. Equipment terms were collected in various languages and abbreviations and coded into the MSLE using the SKOS model. The ontology development was conducted in close collaboration with domain experts and focused on the large-scale devices for materials characterization available in our research group. Competency questions are expected to be addressed through the MSLE ontology. Constraints are modeled in the Shapes Query Language (SHACL); a prototype is shown and validated to show the value of the modeling constraints.

Entity linking faces significant challenges such as prolific variations and prevalent ambiguities, especially in high-value domains with myriad entities. Standard classification approaches suffer from the annotation bottleneck and cannot effectively handle unseen entities. Zero-shot entity linking has emerged as a promising direction for generalizing to new entities, but it still requires example gold entity mentions during training and canonical descriptions for all entities, both of which are rarely available outside of Wikipedia. In this paper, we explore Knowledge-RIch Self-Supervision (tt KRISS) for biomedical entity linking, by leveraging readily available domain knowledge. In training, it generates self-supervised mention examples on unlabeled text using a domain ontology and trains a contextual encoder using contrastive learning. For inference, it samples self-supervised mentions as prototypes for each entity and conducts linking by mapping the test mention to the most similar prototype. Our approach can easily incorporate entity descriptions and gold mention labels if available. We conducted extensive experiments on seven standard datasets spanning biomedical literature and clinical notes. Without using any labeled information, our method produces tt KRISSBERT, a universal entity linker for four million UMLS entities that attains new state of the art, outperforming prior self-supervised methods by as much as 20 absolute points in accuracy.

This study introduces a novel knowledge enhanced tokenisation mechanism, K-Tokeniser, for clinical text processing. Technically, at initialisation stage, K-Tokeniser populates global representations of tokens based on semantic types of domain concepts (such as drugs or diseases) from either a domain ontology like Unified Medical Language System or the training data of the task related corpus. At training or inference stage, sentence level localised context will be utilised for choosing the optimal global token representation to realise the semantic-based tokenisation. To avoid pretraining using the new tokeniser, an embedding initialisation approach is proposed to generate representations for new tokens. Using three transformer-based language models, a comprehensive set of experiments are conducted on four real-world datasets for evaluating K-Tokeniser in a wide range of clinical text analytics tasks including clinical concept and relation extraction, automated clinical coding, clinical phenotype identification, and clinical research article classification. Overall, our models demonstrate consistent improvements over their counterparts in all tasks. In particular, substantial improvements are observed in the automated clinical coding task with 13\% increase on Micro F_1 score. Furthermore, K-Tokeniser also shows significant capacities in facilitating quicker converge of language models. Specifically, using K-Tokeniser, the language models would only require 50\% of the training data to achieve the best performance of the baseline tokeniser using all training data in the concept extraction task and less than 20\% of the data for the automated coding task. It is worth mentioning that all these improvements require no pre-training process, making the approach generalisable.

This paper presents OG-RAG, an Ontology-Grounded Retrieval Augmented Generation method designed to enhance LLM-generated responses by anchoring retrieval processes in domain-specific ontologies. While LLMs are widely used for tasks like question answering and search, they struggle to adapt to specialized knowledge, such as industrial workflows or knowledge work, without expensive fine-tuning or sub-optimal retrieval methods. Existing retrieval-augmented models, such as RAG, offer improvements but fail to account for structured domain knowledge, leading to suboptimal context generation. Ontologies, which conceptually organize domain knowledge by defining entities and their interrelationships, offer a structured representation to address this gap. OG-RAG constructs a hypergraph representation of domain documents, where each hyperedge encapsulates clusters of factual knowledge grounded using domain-specific ontology. An optimization algorithm then retrieves the minimal set of hyperedges that constructs a precise, conceptually grounded context for the LLM. This method enables efficient retrieval while preserving the complex relationships between entities. OG-RAG applies to domains where fact-based reasoning is essential, particularly in tasks that require workflows or decision-making steps to follow predefined rules and procedures. These include industrial workflows in healthcare, legal, and agricultural sectors, as well as knowledge-driven tasks such as news journalism, investigative research, consulting and more. Our evaluations demonstrate that OG-RAG increases the recall of accurate facts by 55% and improves response correctness by 40% across four different LLMs. Additionally, OG-RAG enables 30% faster attribution of responses to context and boosts fact-based reasoning accuracy by 27% compared to baseline methods.

Traditional ontologies describe domain structure but cannot generate novel artifacts. Large language models generate fluently but produce outputs lacking structural validity, hallucinating mechanisms without components, goals without end conditions. We introduce Generative Ontology, a framework synthesizing these complementary strengths: ontology provides the grammar; the LLM provides the creativity. Generative Ontology encodes domain knowledge as executable Pydantic schemas constraining LLM generation via DSPy signatures. A multi-agent pipeline assigns specialized roles: a Mechanics Architect designs game systems, a Theme Weaver integrates narrative, a Balance Critic identifies exploits, each carrying a professional "anxiety" that prevents shallow outputs. Retrieval-augmented generation grounds designs in precedents from existing exemplars. We demonstrate the framework through GameGrammar, generating complete tabletop game designs, and present three empirical studies. An ablation study (120 designs, 4 conditions) shows multi-agent specialization produces the largest quality gains (fun d=1.12, depth d=1.59; p<.001), while schema validation eliminates structural errors (d=4.78). A benchmark against 20 published board games reveals structural parity but a bounded creative gap (fun d=1.86): generated designs score 7-8 while published games score 8-9. A test-retest study (50 evaluations) validates the LLM-based evaluator, with 7/9 metrics achieving Good-to-Excellent reliability (ICC 0.836-0.989). The pattern generalizes beyond games. Any domain with expert vocabulary, validity constraints, and accumulated exemplars is a candidate for Generative Ontology.

Ontologies and taxonomies of research fields are critical for managing and organising scientific knowledge, as they facilitate efficient classification, dissemination and retrieval of information. However, the creation and maintenance of such ontologies are expensive and time-consuming tasks, usually requiring the coordinated effort of multiple domain experts. Consequently, ontologies in this space often exhibit uneven coverage across different disciplines, limited inter-domain connectivity, and infrequent updating cycles. In this study, we investigate the capability of several large language models to identify semantic relationships among research topics within three academic domains: biomedicine, physics, and engineering. The models were evaluated under three distinct conditions: zero-shot prompting, chain-of-thought prompting, and fine-tuning on existing ontologies. Additionally, we assessed the cross-domain transferability of fine-tuned models by measuring their performance when trained in one domain and subsequently applied to a different one. To support this analysis, we introduce PEM-Rel-8K, a novel dataset consisting of over 8,000 relationships extracted from the most widely adopted taxonomies in the three disciplines considered in this study: MeSH, PhySH, and IEEE. Our experiments demonstrate that fine-tuning LLMs on PEM-Rel-8K yields excellent performance across all disciplines.

We present KNOW--the Knowledge Navigator Ontology for the World--the first ontology designed to capture everyday knowledge to augment large language models (LLMs) in real-world generative AI use cases such as personal AI assistants. Our domain is human life, both its everyday concerns and its major milestones. We have limited the initial scope of the modeled concepts to only established human universals: spacetime (places, events) plus social (people, groups, organizations). The inclusion criteria for modeled concepts are pragmatic, beginning with universality and utility. We compare and contrast previous work such as Schema.org and Cyc--as well as attempts at a synthesis of knowledge graphs and language models--noting how LLMs already encode internally much of the commonsense tacit knowledge that took decades to capture in the Cyc project. We also make available code-generated software libraries for the 12 most popular programming languages, enabling the direct use of ontology concepts in software engineering. We emphasize simplicity and developer experience in promoting AI interoperability.

With the web getting bigger and assimilating knowledge about different concepts and domains, it is becoming very difficult for simple database driven applications to capture the data for a domain. Thus developers have come out with ontology based systems which can store large amount of information and can apply reasoning and produce timely information. Thus facilitating effective knowledge management. Though this approach has made our lives easier, but at the same time has given rise to another problem. Two different ontologies assimilating same knowledge tend to use different terms for the same concepts. This creates confusion among knowledge engineers and workers, as they do not know which is a better term then the other. Thus we need to merge ontologies working on same domain so that the engineers can develop a better application over it. This paper shows the development of one such matcher which merges the concepts available in two ontologies at two levels; 1) at string level and 2) at semantic level; thus producing better merged ontologies. We have used a graph matching technique which works at the core of the system. We have also evaluated the system and have tested its performance with its predecessor which works only on string matching. Thus current approach produces better results.

Since long, corporations are looking for knowledge sources which can provide structured description of data and can focus on meaning and shared understanding. Structures which can facilitate open world assumptions and can be flexible enough to incorporate and recognize more than one name for an entity. A source whose major purpose is to facilitate human communication and interoperability. Clearly, databases fail to provide these features and ontologies have emerged as an alternative choice, but corporations working on same domain tend to make different ontologies. The problem occurs when they want to share their data/knowledge. Thus we need tools to merge ontologies into one. This task is termed as ontology matching. This is an emerging area and still we have to go a long way in having an ideal matcher which can produce good results. In this paper we have shown a framework to matching ontologies using graphs.

The ability to summarize and organize knowledge into abstract concepts is key to learning and reasoning. Many industrial applications rely on the consistent and systematic use of concepts, especially when dealing with decision-critical knowledge. However, we demonstrate that, when methodically questioned, large language models (LLMs) often display and demonstrate significant inconsistencies in their knowledge. Computationally, the basic aspects of the conceptualization of a given domain can be represented as Is-A hierarchies in a knowledge graph (KG) or ontology, together with a few properties or axioms that enable straightforward reasoning. We show that even simple ontologies can be used to reveal conceptual inconsistencies across several LLMs. We also propose strategies that domain experts can use to evaluate and improve the coverage of key domain concepts in LLMs of various sizes. In particular, we have been able to significantly enhance the performance of LLMs of various sizes with openly available weights using simple knowledge-graph (KG) based prompting strategies.

OWL (Web Ontology Language) ontologies which are able to formally represent complex knowledge and support semantic reasoning have been widely adopted across various domains such as healthcare and bioinformatics. Recently, ontology embeddings have gained wide attention due to its potential to infer plausible new knowledge and approximate complex reasoning. However, existing methods face notable limitations: geometric model-based embeddings typically overlook valuable textual information, resulting in suboptimal performance, while the approaches that incorporate text, which are often based on language models, fail to preserve the logical structure. In this work, we propose a new ontology embedding method OnT, which tunes a Pretrained Language Model (PLM) via geometric modeling in a hyperbolic space for effectively incorporating textual labels and simultaneously preserving class hierarchies and other logical relationships of Description Logic EL. Extensive experiments on four real-world ontologies show that OnT consistently outperforms the baselines including the state-of-the-art across both tasks of prediction and inference of axioms. OnT also demonstrates strong potential in real-world applications, indicated by its robust transfer learning abilities and effectiveness in real cases of constructing a new ontology from SNOMED CT. Data and code are available at https://github.com/HuiYang1997/OnT.

In this paper we introduce the olog, or ontology log, a category-theoretic model for knowledge representation (KR). Grounded in formal mathematics, ologs can be rigorously formulated and cross-compared in ways that other KR models (such as semantic networks) cannot. An olog is similar to a relational database schema; in fact an olog can serve as a data repository if desired. Unlike database schemas, which are generally difficult to create or modify, ologs are designed to be user-friendly enough that authoring or reconfiguring an olog is a matter of course rather than a difficult chore. It is hoped that learning to author ologs is much simpler than learning a database definition language, despite their similarity. We describe ologs carefully and illustrate with many examples. As an application we show that any primitive recursive function can be described by an olog. We also show that ologs can be aligned or connected together into a larger network using functors. The various methods of information flow and institutions can then be used to integrate local and global world-views. We finish by providing several different avenues for future research.

Existing domain-specific Large Language Models (LLMs) are typically developed by fine-tuning general-purposed LLMs with large-scale domain-specific corpora. However, training on large-scale corpora often fails to effectively organize domain knowledge of LLMs, leading to fragmented understanding. Inspired by how humans connect concepts and organize knowledge through mind maps, we aim to emulate this approach by using ontology with hierarchical conceptual knowledge to reorganize LLM's domain knowledge. From this perspective, we propose an ontology-driven self-training framework called OntoTune, which aims to align LLMs with ontology through in-context learning, enabling the generation of responses guided by the ontology. We leverage in-context learning to identify whether the LLM has acquired the specific concept's ontology knowledge, and select the entries not yet mastered by LLM as the training set to further align the LLM with ontology. Compared to existing domain LLMs based on newly collected large-scale domain-specific corpora, our OntoTune, which relies on the existing, long-term developed ontology and LLM itself, significantly reduces data maintenance costs and offers improved generalization ability. We conduct our study in the medical domain to evaluate the effectiveness of OntoTune, utilizing a standardized medical ontology, SNOMED CT as our ontology source. Experimental results demonstrate that OntoTune achieves state-of-the-art performance in both in-ontology task hypernym discovery and out-of-ontology task medical domain QA. Moreover, compared to the latest direct ontology injection method TaxoLLaMA, our OntoTune better preserves original knowledge of LLM. The code and data are available at https://github.com/zjukg/OntoTune.

In this paper, we present a new theoretical approach for enabling domain knowledge acquisition by intelligent systems. We introduce a hybrid model that starts with minimal input knowledge in the form of an upper ontology of concepts, stores and reasons over this knowledge through a knowledge graph database and learns new information through a Logic Neural Network. We study the behavior of this architecture when handling new data and show that the final system is capable of enriching its current knowledge as well as extending it to new domains.

We present NLU++, a novel dataset for natural language understanding (NLU) in task-oriented dialogue (ToD) systems, with the aim to provide a much more challenging evaluation environment for dialogue NLU models, up to date with the current application and industry requirements. NLU++ is divided into two domains (BANKING and HOTELS) and brings several crucial improvements over current commonly used NLU datasets. 1) NLU++ provides fine-grained domain ontologies with a large set of challenging multi-intent sentences, introducing and validating the idea of intent modules that can be combined into complex intents that convey complex user goals, combined with finer-grained and thus more challenging slot sets. 2) The ontology is divided into domain-specific and generic (i.e., domain-universal) intent modules that overlap across domains, promoting cross-domain reusability of annotated examples. 3) The dataset design has been inspired by the problems observed in industrial ToD systems, and 4) it has been collected, filtered and carefully annotated by dialogue NLU experts, yielding high-quality annotated data. Finally, we benchmark a series of current state-of-the-art NLU models on NLU++; the results demonstrate the challenging nature of the dataset, especially in low-data regimes, the validity of `intent modularisation', and call for further research on ToD NLU.

Large language models (LLMs) have significantly advanced the field of natural language processing (NLP), providing a highly useful, task-agnostic foundation for a wide range of applications. However, directly applying LLMs to solve sophisticated problems in specific domains meets many hurdles, caused by the heterogeneity of domain data, the sophistication of domain knowledge, the uniqueness of domain objectives, and the diversity of the constraints (e.g., various social norms, cultural conformity, religious beliefs, and ethical standards in the domain applications). Domain specification techniques are key to make large language models disruptive in many applications. Specifically, to solve these hurdles, there has been a notable increase in research and practices conducted in recent years on the domain specialization of LLMs. This emerging field of study, with its substantial potential for impact, necessitates a comprehensive and systematic review to better summarize and guide ongoing work in this area. In this article, we present a comprehensive survey on domain specification techniques for large language models, an emerging direction critical for large language model applications. First, we propose a systematic taxonomy that categorizes the LLM domain-specialization techniques based on the accessibility to LLMs and summarizes the framework for all the subcategories as well as their relations and differences to each other. Second, we present an extensive taxonomy of critical application domains that can benefit dramatically from specialized LLMs, discussing their practical significance and open challenges. Last, we offer our insights into the current research status and future trends in this area.

Ontologies comprising of concepts, their attributes, and relationships are used in many knowledge based AI systems. While there have been efforts towards populating domain specific ontologies, we examine the role of document structure in learning ontological relationships between concepts in any document corpus. Inspired by ideas from hypernym discovery and explainability, our method performs about 15 points more accurate than a stand-alone R-GCN model for this task.

Language models exhibit fundamental limitations -- hallucination, brittleness, and lack of formal grounding -- that are particularly problematic in high-stakes specialist fields requiring verifiable reasoning. I investigate whether formal domain ontologies can enhance language model reliability through retrieval-augmented generation. Using mathematics as proof of concept, I implement a neuro-symbolic pipeline leveraging the OpenMath ontology with hybrid retrieval and cross-encoder reranking to inject relevant definitions into model prompts. Evaluation on the MATH benchmark with three open-source models reveals that ontology-guided context improves performance when retrieval quality is high, but irrelevant context actively degrades it -- highlighting both the promise and challenges of neuro-symbolic approaches.

We propose the LLMs4OL approach, which utilizes Large Language Models (LLMs) for Ontology Learning (OL). LLMs have shown significant advancements in natural language processing, demonstrating their ability to capture complex language patterns in different knowledge domains. Our LLMs4OL paradigm investigates the following hypothesis: Can LLMs effectively apply their language pattern capturing capability to OL, which involves automatically extracting and structuring knowledge from natural language text? To test this hypothesis, we conduct a comprehensive evaluation using the zero-shot prompting method. We evaluate nine different LLM model families for three main OL tasks: term typing, taxonomy discovery, and extraction of non-taxonomic relations. Additionally, the evaluations encompass diverse genres of ontological knowledge, including lexicosemantic knowledge in WordNet, geographical knowledge in GeoNames, and medical knowledge in UMLS.

We present M2D2, a fine-grained, massively multi-domain corpus for studying domain adaptation in language models (LMs). M2D2 consists of 8.5B tokens and spans 145 domains extracted from Wikipedia and Semantic Scholar. Using ontologies derived from Wikipedia and ArXiv categories, we organize the domains in each data source into 22 groups. This two-level hierarchy enables the study of relationships between domains and their effects on in- and out-of-domain performance after adaptation. We also present a number of insights into the nature of effective domain adaptation in LMs, as examples of the new types of studies M2D2 enables. To improve in-domain performance, we show the benefits of adapting the LM along a domain hierarchy; adapting to smaller amounts of fine-grained domain-specific data can lead to larger in-domain performance gains than larger amounts of weakly relevant data. We further demonstrate a trade-off between in-domain specialization and out-of-domain generalization within and across ontologies, as well as a strong correlation between out-of-domain performance and lexical overlap between domains.

The core obstacle towards a large-scale deployment of autonomous vehicles currently lies in the long tail of rare events. These are extremely challenging since they do not occur often in the utilized training data for deep neural networks. To tackle this problem, we propose the generation of additional synthetic training data, covering a wide variety of corner case scenarios. As ontologies can represent human expert knowledge while enabling computational processing, we use them to describe scenarios. Our proposed master ontology is capable to model scenarios from all common corner case categories found in the literature. From this one master ontology, arbitrary scenario-describing ontologies can be derived. In an automated fashion, these can be converted into the OpenSCENARIO format and subsequently executed in simulation. This way, also challenging test and evaluation scenarios can be generated.

Textual domain is a crucial property within the Natural Language Processing (NLP) community due to its effects on downstream model performance. The concept itself is, however, loosely defined and, in practice, refers to any non-typological property, such as genre, topic, medium or style of a document. We investigate the core notion of domains via human proficiency in identifying related intrinsic textual properties, specifically the concepts of genre (communicative purpose) and topic (subject matter). We publish our annotations in *TGeGUM*: A collection of 9.1k sentences from the GUM dataset (Zeldes, 2017) with single sentence and larger context (i.e., prose) annotations for one of 11 genres (source type), and its topic/subtopic as per the Dewey Decimal library classification system (Dewey, 1979), consisting of 10/100 hierarchical topics of increased granularity. Each instance is annotated by three annotators, for a total of 32.7k annotations, allowing us to examine the level of human disagreement and the relative difficulty of each annotation task. With a Fleiss' kappa of at most 0.53 on the sentence level and 0.66 at the prose level, it is evident that despite the ubiquity of domains in NLP, there is little human consensus on how to define them. By training classifiers to perform the same task, we find that this uncertainty also extends to NLP models.

Emotions have played an important part in many sectors, including psychology, medicine, mental health, computer science, and so on, and categorizing them has proven extremely useful in separating one emotion from another. Emotions can be classified using the following two methods: (1) The supervised method's efficiency is strongly dependent on the size and domain of the data collected. A categorization established using relevant data from one domain may not work well in another. (2) An unsupervised method that uses either domain expertise or a knowledge base of emotion types already exists. Though this second approach provides a suitable and generic categorization of emotions and is cost-effective, the literature doesn't possess a publicly available knowledge base that can be directly applied to any emotion categorization-related task. This pushes us to create a knowledge base that can be used for emotion classification across domains, and ontology is often used for this purpose. In this study, we provide TONE, an emotion-based ontology that effectively creates an emotional hierarchy based on Dr. Gerrod Parrot's group of emotions. In addition to ontology development, we introduce a semi-automated vocabulary construction process to generate a detailed collection of terms for emotions at each tier of the hierarchy. We also demonstrate automated methods for establishing three sorts of dependencies in order to develop linkages between different emotions. Our human and automatic evaluation results show the ontology's quality. Furthermore, we describe three distinct use cases that demonstrate the applicability of our ontology.

Knowledge Graph-to-Text (G2T) generation involves verbalizing structured knowledge graphs into natural language text. Recent advancements in Pretrained Language Models (PLMs) have improved G2T performance, but their effectiveness depends on datasets with precise graph-text alignment. However, the scarcity of high-quality, general-domain G2T generation datasets restricts progress in the general-domain G2T generation research. To address this issue, we introduce Wikipedia Ontology-Free Graph-text dataset (WikiOFGraph), a new large-scale G2T dataset generated using a novel method that leverages Large Language Model (LLM) and Data-QuestEval. Our new dataset, which contains 5.85M general-domain graph-text pairs, offers high graph-text consistency without relying on external ontologies. Experimental results demonstrate that PLM fine-tuned on WikiOFGraph outperforms those trained on other datasets across various evaluation metrics. Our method proves to be a scalable and effective solution for generating high-quality G2T data, significantly advancing the field of G2T generation.

We introduce semantic towers, an extrinsic knowledge representation method, and compare it to intrinsic knowledge in large language models for ontology learning. Our experiments show a trade-off between performance and semantic grounding for extrinsic knowledge compared to a fine-tuned model intrinsic knowledge. We report our findings on the Large Language Models for Ontology Learning (LLMs4OL) 2024 challenge.

This paper introduces a novel method for merging open-domain terminological knowledge. It takes advantage of the Region Connection Calculus (RCC5), a formalism used to represent regions in a topological space and to reason about their set-theoretic relationships. To this end, we first propose a faithful translation of terminological knowledge provided by several and potentially conflicting sources into region spaces. The merging is then performed on these spaces, and the result is translated back into the underlying language of the input sources. Our approach allows us to benefit from the expressivity and the flexibility of RCC5 while dealing with conflicting knowledge in a principled way.

Large Language Models (LLMs) are widely applied to downstream domains. However, current LLMs for high-stakes domain tasks, such as financial investment and legal QA, typically generate brief answers without reasoning processes and explanations. This limits users' confidence in making decisions based on their responses. While original CoT shows promise, it lacks self-correction mechanisms during reasoning. This work introduces Domaino1s, which enhances LLMs' reasoning capabilities on domain tasks through supervised fine-tuning and tree search. We construct CoT-stock-2k and CoT-legal-2k datasets for fine-tuning models that activate domain-specific reasoning steps based on their judgment. Additionally, we propose Selective Tree Exploration to spontaneously explore solution spaces and sample optimal reasoning paths to improve performance. We also introduce PROOF-Score, a new metric for evaluating domain models' explainability, complementing traditional accuracy metrics with richer assessment dimensions. Extensive experiments on stock investment recommendation and legal reasoning QA tasks demonstrate Domaino1s's leading performance and explainability. Our code is available at https://anonymous.4open.science/r/Domaino1s-006F/.

Investigating whether pre-trained language models (LMs) can function as knowledge bases (KBs) has raised wide research interests recently. However, existing works focus on simple, triple-based, relational KBs, but omit more sophisticated, logic-based, conceptualised KBs such as OWL ontologies. To investigate an LM's knowledge of ontologies, we propose OntoLAMA, a set of inference-based probing tasks and datasets from ontology subsumption axioms involving both atomic and complex concepts. We conduct extensive experiments on ontologies of different domains and scales, and our results demonstrate that LMs encode relatively less background knowledge of Subsumption Inference (SI) than traditional Natural Language Inference (NLI) but can improve on SI significantly when a small number of samples are given. We will open-source our code and datasets.

A person ontology comprising concepts, attributes and relationships of people has a number of applications in data protection, didentification, population of knowledge graphs for business intelligence and fraud prevention. While artificial neural networks have led to improvements in Entity Recognition, Entity Classification, and Relation Extraction, creating an ontology largely remains a manual process, because it requires a fixed set of semantic relations between concepts. In this work, we present a system for automatically populating a person ontology graph from unstructured data using neural models for Entity Classification and Relation Extraction. We introduce a new dataset for these tasks and discuss our results.

We propose a framework for classifying the capabilities and behavior of Artificial General Intelligence (AGI) models and their precursors. This framework introduces levels of AGI performance, generality, and autonomy, providing a common language to compare models, assess risks, and measure progress along the path to AGI. To develop our framework, we analyze existing definitions of AGI, and distill six principles that a useful ontology for AGI should satisfy. With these principles in mind, we propose "Levels of AGI" based on depth (performance) and breadth (generality) of capabilities, and reflect on how current systems fit into this ontology. We discuss the challenging requirements for future benchmarks that quantify the behavior and capabilities of AGI models against these levels. Finally, we discuss how these levels of AGI interact with deployment considerations such as autonomy and risk, and emphasize the importance of carefully selecting Human-AI Interaction paradigms for responsible and safe deployment of highly capable AI systems.

This paper analyzes the proliferation of cybersecurity ontologies, arguing that this surge cannot be explained solely by technical shortcomings related to quality, but also by a credibility deficit - a lack of trust, endorsement, and adoption by users. This conclusion is based on our first contribution, which is a state-of-the-art review and categorization of cybersecurity ontologies using the Framework for Ontologies Classification framework. To address this gap, we propose a revised framework for assessing credibility, introducing indicators such as institutional support, academic recognition, day-to-day practitioner validation, and industrial adoption. Based on these new credibility indicators, we construct a classification scheme designed to guide the selection of ontologies that are relevant to specific security needs. We then apply this framework to a concrete use case: the Franco-Luxembourgish research project ANCILE, which illustrates how a credibility-aware evaluation can reshape ontology selection for operational contexts.

Ontology engineering (OE) in large projects poses a number of challenges arising from the heterogeneous backgrounds of the various stakeholders, domain experts, and their complex interactions with ontology designers. This multi-party interaction often creates systematic ambiguities and biases from the elicitation of ontology requirements, which directly affect the design, evaluation and may jeopardise the target reuse. Meanwhile, current OE methodologies strongly rely on manual activities (e.g., interviews, discussion pages). After collecting evidence on the most crucial OE activities, we introduce OntoChat, a framework for conversational ontology engineering that supports requirement elicitation, analysis, and testing. By interacting with a conversational agent, users can steer the creation of user stories and the extraction of competency questions, while receiving computational support to analyse the overall requirements and test early versions of the resulting ontologies. We evaluate OntoChat by replicating the engineering of the Music Meta Ontology, and collecting preliminary metrics on the effectiveness of each component from users. We release all code at https://github.com/King-s-Knowledge-Graph-Lab/OntoChat.

Large Language Models (LLMs) assist in specialized tasks but struggle to align with evolving domain knowledge without costly fine-tuning. Domain knowledge consists of: Knowledge: Immutable facts (e.g., 'A stone is solid') and generally accepted principles (e.g., ethical standards); Refined Memory: Evolving insights shaped by business needs and real-world changes. However, a significant gap often exists between a domain expert's deep, nuanced understanding and the system's domain knowledge, which can hinder accurate information retrieval and application. Our Memory-Augmented Refinement of Knowledge (MARK) framework enables LLMs to continuously learn without retraining by leveraging structured refined memory, inspired by the Society of Mind. MARK operates through specialized agents, each serving a distinct role: Residual Refined Memory Agent: Stores and retrieves domain-specific insights to maintain context over time; User Question Refined Memory Agent: Captures user-provided facts, abbreviations, and terminology for better comprehension; LLM Response Refined Memory Agent: Extracts key elements from responses for refinement and personalization. These agents analyse stored refined memory, detect patterns, resolve contradictions, and improve response accuracy. Temporal factors like recency and frequency prioritize relevant information while discarding outdated insights. MARK enhances LLMs in multiple ways: Ground Truth Strategy: Reduces hallucinations by establishing a structured reference; Domain-Specific Adaptation: Essential for fields like healthcare, law, and manufacturing, where proprietary insights are absent from public datasets; Personalized AI Assistants: Improves virtual assistants by remembering user preferences, ensuring coherent responses over time.

We present a comprehensive system for addressing Tasks A, B, and C of the LLMs4OL 2025 challenge, which together span the full ontology construction pipeline: term extraction, typing, and taxonomy discovery. Our approach combines retrieval-augmented prompting, zero-shot classification, and attention-based graph modeling -- each tailored to the demands of the respective task. For Task A, we jointly extract domain-specific terms and their ontological types using a retrieval-augmented generation (RAG) pipeline. Training data was reformulated into a document to terms and types correspondence, while test-time inference leverages semantically similar training examples. This single-pass method requires no model finetuning and improves overall performance through lexical augmentation Task B, which involves assigning types to given terms, is handled via a dual strategy. In the few-shot setting (for domains with labeled training data), we reuse the RAG scheme with few-shot prompting. In the zero-shot setting (for previously unseen domains), we use a zero-shot classifier that combines cosine similarity scores from multiple embedding models using confidence-based weighting. In Task C, we model taxonomy discovery as graph inference. Using embeddings of type labels, we train a lightweight cross-attention layer to predict is-a relations by approximating a soft adjacency matrix. These modular, task-specific solutions enabled us to achieve top-ranking results in the official leaderboard across all three tasks. Taken together these strategies showcase the scalability, adaptability, and robustness of LLM-based architectures for ontology learning across heterogeneous domains. Code is available at: https://github.com/BelyaevaAlex/LLMs4OL-Challenge-Alexbek

Recent advances in Language Models (LMs) have failed to mask their shortcomings particularly in the domain of reasoning. This limitation impacts several tasks, most notably those involving ontology engineering. As part of a PhD research, we investigate the consequences of incorporating formal methods on the performance of Small Language Models (SLMs) on reasoning tasks. Specifically, we aim to orient our work toward using SLMs to bootstrap ontology construction and set up a series of preliminary experiments to determine the impact of expressing logical problems with different grammars on the performance of SLMs on a predefined reasoning task. Our findings show that it is possible to substitute Natural Language (NL) with a more compact logical language while maintaining a strong performance on reasoning tasks and hope to use these results to further refine the role of SLMs in ontology engineering.

There has been an influx of biomedical domain-specific language models, showing language models pre-trained on biomedical text perform better on biomedical domain benchmarks than those trained on general domain text corpora such as Wikipedia and Books. Yet, most works do not study the factors affecting each domain language application deeply. Additionally, the study of model size on domain-specific models has been mostly missing. We empirically study and evaluate several factors that can affect performance on domain language applications, such as the sub-word vocabulary set, model size, pre-training corpus, and domain transfer. We show consistent improvements on benchmarks with our larger BioMegatron model trained on a larger domain corpus, contributing to our understanding of domain language model applications. We demonstrate noticeable improvements over the previous state-of-the-art (SOTA) on standard biomedical NLP benchmarks of named entity recognition, relation extraction, and question answering. Model checkpoints and code are available at [https://ngc.nvidia.com] and [https://github.com/NVIDIA/NeMo].

Can one inject new concepts into an already trained generative model, while respecting its existing structure and knowledge? We propose a new task - domain expansion - to address this. Given a pretrained generator and novel (but related) domains, we expand the generator to jointly model all domains, old and new, harmoniously. First, we note the generator contains a meaningful, pretrained latent space. Is it possible to minimally perturb this hard-earned representation, while maximally representing the new domains? Interestingly, we find that the latent space offers unused, "dormant" directions, which do not affect the output. This provides an opportunity: By "repurposing" these directions, we can represent new domains without perturbing the original representation. In fact, we find that pretrained generators have the capacity to add several - even hundreds - of new domains! Using our expansion method, one "expanded" model can supersede numerous domain-specific models, without expanding the model size. Additionally, a single expanded generator natively supports smooth transitions between domains, as well as composition of domains. Code and project page available at https://yotamnitzan.github.io/domain-expansion/.

Developing domain models is one of the few remaining places that require manual human labor in AI planning. Thus, in order to make planning more accessible, it is desirable to automate the process of domain model generation. To this end, we investigate if large language models (LLMs) can be used to generate planning domain models from simple textual descriptions. Specifically, we introduce a framework for automated evaluation of LLM-generated domains by comparing the sets of plans for domain instances. Finally, we perform an empirical analysis of 7 large language models, including coding and chat models across 9 different planning domains, and under three classes of natural language domain descriptions. Our results indicate that LLMs, particularly those with high parameter counts, exhibit a moderate level of proficiency in generating correct planning domains from natural language descriptions. Our code is available at https://github.com/IBM/NL2PDDL.

The recent advances in large language models (LLM) and foundation models with emergent capabilities have been shown to improve the performance of many NLP tasks. LLMs and Knowledge Graphs (KG) can complement each other such that LLMs can be used for KG construction or completion while existing KGs can be used for different tasks such as making LLM outputs explainable or fact-checking in Neuro-Symbolic manner. In this paper, we present Text2KGBench, a benchmark to evaluate the capabilities of language models to generate KGs from natural language text guided by an ontology. Given an input ontology and a set of sentences, the task is to extract facts from the text while complying with the given ontology (concepts, relations, domain/range constraints) and being faithful to the input sentences. We provide two datasets (i) Wikidata-TekGen with 10 ontologies and 13,474 sentences and (ii) DBpedia-WebNLG with 19 ontologies and 4,860 sentences. We define seven evaluation metrics to measure fact extraction performance, ontology conformance, and hallucinations by LLMs. Furthermore, we provide results for two baseline models, Vicuna-13B and Alpaca-LoRA-13B using automatic prompt generation from test cases. The baseline results show that there is room for improvement using both Semantic Web and Natural Language Processing techniques.

In applications such as personal assistants, large language models (LLMs) must consider the user's personal information and preferences. However, LLMs lack the inherent ability to learn from user interactions. This paper explores capturing personal information from user prompts using ontology and knowledge-graph approaches. We use a subset of the KNOW ontology, which models personal information, to train the language model on these concepts. We then evaluate the success of knowledge capture using a specially constructed dataset. Our code and datasets are publicly available at https://github.com/HaltiaAI/paper-PTODSKC

Ontologies and knowledge graphs (KGs) are general-purpose computable representations of some domain, such as human anatomy, and are frequently a crucial part of modern information systems. Most of these structures change over time, incorporating new knowledge or information that was previously missing. Managing these changes is a challenge, both in terms of communicating changes to users, and providing mechanisms to make it easier for multiple stakeholders to contribute. To fill that need, we have created KGCL, the Knowledge Graph Change Language, a standard data model for describing changes to KGs and ontologies at a high level, and an accompanying human-readable controlled natural language. This language serves two purposes: a curator can use it to request desired changes, and it can also be used to describe changes that have already happened, corresponding to the concepts of "apply patch" and "diff" commonly used for managing changes in text documents and computer programs. Another key feature of KGCL is that descriptions are at a high enough level to be useful and understood by a variety of stakeholders--for example, ontology edits can be specified by commands like "add synonym 'arm' to 'forelimb'" or "move 'Parkinson disease' under 'neurodegenerative disease'". We have also built a suite of tools for managing ontology changes. These include an automated agent that integrates with and monitors GitHub ontology repositories and applies any requested changes, and a new component in the BioPortal ontology resource that allows users to make change requests directly from within the BioPortal user interface. Overall, the KGCL data model, its controlled natural language, and associated tooling allow for easier management and processing of changes associated with the development of ontologies and KGs.

Domain Large Language Models (LLMs) are developed for domain-specific tasks based on general LLMs. But it still requires professional knowledge to facilitate the expertise for some domain-specific tasks. In this paper, we investigate into knowledge-intensive calculation problems. We find that the math problems to be challenging for LLMs, when involving complex domain-specific rules and knowledge documents, rather than simple formulations of terminologies. Therefore, we propose a pipeline to solve the domain-specific calculation problems with Knowledge-Intensive Programs Generator more effectively, named as KIPG. It generates knowledge-intensive programs according to the domain-specific documents. For each query, key variables are extracted, then outcomes which are dependent on domain knowledge are calculated with the programs. By iterative preference alignment, the code generator learns to improve the logic consistency with the domain knowledge. Taking legal domain as an example, we have conducted experiments to prove the effectiveness of our pipeline, and extensive analysis on the modules. We also find that the code generator is also adaptable to other domains, without training on the new knowledge.

Scientific machine learning research spans diverse domains and data modalities, yet existing benchmark efforts remain siloed and lack standardization. This makes novel and transformative applications of machine learning to critical scientific use-cases more fragmented and less clear in pathways to impact. This paper introduces an ontology for scientific benchmarking developed through a unified, community-driven effort that extends the MLCommons ecosystem to cover physics, chemistry, materials science, biology, climate science, and more. Building on prior initiatives such as XAI-BENCH, FastML Science Benchmarks, PDEBench, and the SciMLBench framework, our effort consolidates a large set of disparate benchmarks and frameworks into a single taxonomy of scientific, application, and system-level benchmarks. New benchmarks can be added through an open submission workflow coordinated by the MLCommons Science Working Group and evaluated against a six-category rating rubric that promotes and identifies high-quality benchmarks, enabling stakeholders to select benchmarks that meet their specific needs. The architecture is extensible, supporting future scientific and AI/ML motifs, and we discuss methods for identifying emerging computing patterns for unique scientific workloads. The MLCommons Science Benchmarks Ontology provides a standardized, scalable foundation for reproducible, cross-domain benchmarking in scientific machine learning. A companion webpage for this work has also been developed as the effort evolves: https://mlcommons-science.github.io/benchmark/

Competency Questions (CQs) are widely used in ontology development by guiding, among others, the scoping and validation stages. However, very limited guidance exists for formulating CQs and assessing whether they are good CQs, leading to issues such as ambiguity and unusable formulations. To solve this, one requires insight into the nature of CQs for ontologies and their constituent parts, as well as which ones are not. We aim to contribute to such theoretical foundations in this paper, which is informed by analysing questions, their uses, and the myriad of ontology development tasks. This resulted in a first Model for Competency Questions, which comprises five main types of CQs, each with a different purpose: Scoping (SCQ), Validating (VCQ), Foundational (FCQ), Relationship (RCQ), and Metaproperty (MpCQ) questions. This model enhances the clarity of CQs and therewith aims to improve on the effectiveness of CQs in ontology development, thanks to their respective identifiable distinct constituent elements. We illustrate and evaluate them with a user story and demonstrate where which type can be used in ontology development tasks. To foster use and research, we created an annotated repository of 438 CQs, the Repository of Ontology Competency QuestionS (ROCQS), incorporating an existing CQ dataset and new CQs and CQ templates, which further demonstrate distinctions among types of CQs.

Large language models have demonstrated remarkable potential in various tasks, however, there remains a significant scarcity of open-source models and data for specific domains. Previous works have primarily focused on manually specifying resources and collecting high-quality data on specific domains, which significantly consume time and effort. To address this limitation, we propose an efficient data collection method~Query of CC based on large language models. This method bootstraps seed information through a large language model and retrieves related data from public corpora. It not only collects knowledge-related data for specific domains but unearths the data with potential reasoning procedures. Through the application of this method, we have curated a high-quality dataset called~Knowledge Pile, encompassing four major domains, including stem and humanities sciences, among others. Experimental results demonstrate that~Knowledge Pile significantly improves the performance of large language models in mathematical and knowledge-related reasoning ability tests. To facilitate academic sharing, we open-source our dataset and code, providing valuable support to the academic community.

The ability to build and leverage world models is essential for a general-purpose AI agent. Testing such capabilities is hard, in part because the building blocks of world models are ill-defined. We present Elements of World Knowledge (EWOK), a framework for evaluating world modeling in language models by testing their ability to use knowledge of a concept to match a target text with a plausible/implausible context. EWOK targets specific concepts from multiple knowledge domains known to be vital for world modeling in humans. Domains range from social interactions (help/hinder) to spatial relations (left/right). Both, contexts and targets are minimal pairs. Objects, agents, and locations in the items can be flexibly filled in enabling easy generation of multiple controlled datasets. We then introduce EWOK-CORE-1.0, a dataset of 4,374 items covering 11 world knowledge domains. We evaluate 20 openweights large language models (1.3B--70B parameters) across a battery of evaluation paradigms along with a human norming study comprising 12,480 measurements. The overall performance of all tested models is worse than human performance, with results varying drastically across domains. These data highlight simple cases where even large models fail and present rich avenues for targeted research on LLM world modeling capabilities.

Scientific literature is growing exponentially, creating a critical bottleneck for researchers to efficiently synthesize knowledge. While general-purpose Large Language Models (LLMs) show potential in text processing, they often fail to capture scientific domain-specific nuances (e.g., technical jargon, methodological rigor) and struggle with complex scientific tasks, limiting their utility for interdisciplinary research. To address these gaps, this paper presents SciGPT, a domain-adapted foundation model for scientific literature understanding and ScienceBench, an open source benchmark tailored to evaluate scientific LLMs. Built on the Qwen3 architecture, SciGPT incorporates three key innovations: (1) low-cost domain distillation via a two-stage pipeline to balance performance and efficiency; (2) a Sparse Mixture-of-Experts (SMoE) attention mechanism that cuts memory consumption by 55\% for 32,000-token long-document reasoning; and (3) knowledge-aware adaptation integrating domain ontologies to bridge interdisciplinary knowledge gaps. Experimental results on ScienceBench show that SciGPT outperforms GPT-4o in core scientific tasks including sequence labeling, generation, and inference. It also exhibits strong robustness in unseen scientific tasks, validating its potential to facilitate AI-augmented scientific discovery.

This work introduces BioLORD, a new pre-training strategy for producing meaningful representations for clinical sentences and biomedical concepts. State-of-the-art methodologies operate by maximizing the similarity in representation of names referring to the same concept, and preventing collapse through contrastive learning. However, because biomedical names are not always self-explanatory, it sometimes results in non-semantic representations. BioLORD overcomes this issue by grounding its concept representations using definitions, as well as short descriptions derived from a multi-relational knowledge graph consisting of biomedical ontologies. Thanks to this grounding, our model produces more semantic concept representations that match more closely the hierarchical structure of ontologies. BioLORD establishes a new state of the art for text similarity on both clinical sentences (MedSTS) and biomedical concepts (MayoSRS).

Predictive process monitoring is a process mining task aimed at forecasting information about a running process trace, such as the most correct next activity to be executed. In medical domains, predictive process monitoring can provide valuable decision support in atypical and nontrivial situations. Decision support and quality assessment in medicine cannot ignore domain knowledge, in order to be grounded on all the available information (which is not limited to data) and to be really acceptable by end users. In this paper, we propose a predictive process monitoring approach relying on the use of a {\em transformer}, a deep learning architecture based on the attention mechanism. A major contribution of our work lies in the incorporation of ontological domain-specific knowledge, carried out through a graph positional encoding technique. The paper presents and discusses the encouraging experimental result we are collecting in the domain of stroke management.

Recently, there has been significant progress in studying neural networks for translating text descriptions into SQL queries under the zero-shot cross-domain setting. Despite achieving good performance on some public benchmarks, we observe that existing text-to-SQL models do not generalize when facing domain knowledge that does not frequently appear in the training data, which may render the worse prediction performance for unseen domains. In this work, we investigate the robustness of text-to-SQL models when the questions require rarely observed domain knowledge. In particular, we define five types of domain knowledge and introduce Spider-DK (DK is the abbreviation of domain knowledge), a human-curated dataset based on the Spider benchmark for text-to-SQL translation. NL questions in Spider-DK are selected from Spider, and we modify some samples by adding domain knowledge that reflects real-world question paraphrases. We demonstrate that the prediction accuracy dramatically drops on samples that require such domain knowledge, even if the domain knowledge appears in the training set, and the model provides the correct predictions for related training samples.

Data science plays a critical role in transforming complex data into actionable insights across numerous domains. Recent developments in large language models (LLMs) have significantly automated data science workflows, but a fundamental question persists: Can these agentic AI systems truly match the performance of human data scientists who routinely leverage domain-specific knowledge? We explore this question by designing a prediction task where a crucial latent variable is hidden in relevant image data instead of tabular features. As a result, agentic AI that generates generic codes for modeling tabular data cannot perform well, while human experts could identify the important hidden variable using domain knowledge. We demonstrate this idea with a synthetic dataset for property insurance. Our experiments show that agentic AI that relies on generic analytics workflow falls short of methods that use domain-specific insights. This highlights a key limitation of the current agentic AI for data science and underscores the need for future research to develop agentic AI systems that can better recognize and incorporate domain knowledge.

Problem-solving has been a fundamental driver of human progress in numerous domains. With advancements in artificial intelligence, Large Language Models (LLMs) have emerged as powerful tools capable of tackling complex problems across diverse domains. Unlike traditional computational systems, LLMs combine raw computational power with an approximation of human reasoning, allowing them to generate solutions, make inferences, and even leverage external computational tools. However, applying LLMs to real-world problem-solving presents significant challenges, including multi-step reasoning, domain knowledge integration, and result verification. This survey explores the capabilities and limitations of LLMs in complex problem-solving, examining techniques including Chain-of-Thought (CoT) reasoning, knowledge augmentation, and various LLM-based and tool-based verification techniques. Additionally, we highlight domain-specific challenges in various domains, such as software engineering, mathematical reasoning and proving, data analysis and modeling, and scientific research. The paper further discusses the fundamental limitations of the current LLM solutions and the future directions of LLM-based complex problems solving from the perspective of multi-step reasoning, domain knowledge integration and result verification.

Given appropriate representations of the semantic relations between carpenter and wood and between mason and stone (for example, vectors in a vector space model), a suitable algorithm should be able to recognize that these relations are highly similar (carpenter is to wood as mason is to stone; the relations are analogous). Likewise, with representations of dog, house, and kennel, an algorithm should be able to recognize that the semantic composition of dog and house, dog house, is highly similar to kennel (dog house and kennel are synonymous). It seems that these two tasks, recognizing relations and compositions, are closely connected. However, up to now, the best models for relations are significantly different from the best models for compositions. In this paper, we introduce a dual-space model that unifies these two tasks. This model matches the performance of the best previous models for relations and compositions. The dual-space model consists of a space for measuring domain similarity and a space for measuring function similarity. Carpenter and wood share the same domain, the domain of carpentry. Mason and stone share the same domain, the domain of masonry. Carpenter and mason share the same function, the function of artisans. Wood and stone share the same function, the function of materials. In the composition dog house, kennel has some domain overlap with both dog and house (the domains of pets and buildings). The function of kennel is similar to the function of house (the function of shelters). By combining domain and function similarities in various ways, we can model relations, compositions, and other aspects of semantics.

The emerging trend of advancing generalist artificial intelligence, such as GPTv4 and Gemini, has reshaped the landscape of research (academia and industry) in machine learning and many other research areas. However, domain-specific applications of such foundation models (e.g., in medicine) remain untouched or often at their very early stages. It will require an individual set of transfer learning and model adaptation techniques by further expanding and injecting these models with domain knowledge and data. The development of such technologies could be largely accelerated if the bundle of data, algorithms, and pre-trained foundation models were gathered together and open-sourced in an organized manner. In this work, we present OpenMEDLab, an open-source platform for multi-modality foundation models. It encapsulates not only solutions of pioneering attempts in prompting and fine-tuning large language and vision models for frontline clinical and bioinformatic applications but also building domain-specific foundation models with large-scale multi-modal medical data. Importantly, it opens access to a group of pre-trained foundation models for various medical image modalities, clinical text, protein engineering, etc. Inspiring and competitive results are also demonstrated for each collected approach and model in a variety of benchmarks for downstream tasks. We welcome researchers in the field of medical artificial intelligence to continuously contribute cutting-edge methods and models to OpenMEDLab, which can be accessed via https://github.com/openmedlab.

Scholarly data are largely fragmented across siloed databases with divergent metadata and missing linkages among them. We present the Science Data Lake, a locally-deployable infrastructure built on DuckDB and simple Parquet files that unifies eight open sources - Semantic Scholar, OpenAlex, SciSciNet, Papers with Code, Retraction Watch, Reliance on Science, a preprint-to-published mapping, and Crossref - via DOI normalization while preserving source-level schemas. The resource comprises approximately 960GB of Parquet files spanning ~293 million uniquely identifiable papers across ~22 schemas and ~153 SQL views. An embedding-based ontology alignment using BGE-large sentence embeddings maps 4,516 OpenAlex topics to 13 scientific ontologies (~1.3 million terms), yielding 16,150 mappings covering 99.8% of topics (geq 0.65 threshold) with F1 = 0.77 at the recommended geq 0.85 operating point, outperforming TF-IDF, BM25, and Jaro-Winkler baselines on a 300-pair gold-standard evaluation. We validate through 10 automated checks, cross-source citation agreement analysis (pairwise Pearson r = 0.76 - 0.87), and stratified manual annotation. Four vignettes demonstrate cross-source analyses infeasible with any single database. The resource is open source, deployable on a single drive or queryable remotely via HuggingFace, and includes structured documentation suitable for large language model (LLM) based research agents.

Complex hierarchical structures composed of simple nanoscale building blocks form the basis of most biological materials. Here we demonstrate how analogies between seemingly different fields enable the understanding of general principles by which functional properties in hierarchical systems emerge, similar to an analogy learning process. Specifically, natural hierarchical materials like spider silk exhibit properties comparable to classical music in terms of their hierarchical structure and function. As a comparative tool here we apply hierarchical ontology logs (olog) that follow a rigorous mathematical formulation based on category theory to provide an insightful system representation by expressing knowledge in a conceptual map. We explain the process of analogy creation, draw connections at several levels of hierarchy and identify similar patterns that govern the structure of the hierarchical systems silk and music and discuss the impact of the derived analogy for nanotechnology.

Background. In the last decades, several life science resources have structured data using the same framework and made these accessible using the same query language to facilitate interoperability. Knowledge graphs have seen increased adoption in bioinformatics due to their advantages for representing data in a generic graph format. For example, yummydata.org catalogs more than 60 knowledge graphs accessible through SPARQL, a technical query language. Although SPARQL allows powerful, expressive queries, even across physically distributed knowledge graphs, formulating such queries is a challenge for most users. Therefore, to guide users in retrieving the relevant data, many of these resources provide representative examples. These examples can also be an important source of information for machine learning, if a sufficiently large number of examples are provided and published in a common, machine-readable and standardized format across different resources. Findings. We introduce a large collection of human-written natural language questions and their corresponding SPARQL queries over federated bioinformatics knowledge graphs (KGs) collected for several years across different research groups at the SIB Swiss Institute of Bioinformatics. The collection comprises more than 1000 example questions and queries, including 65 federated queries. We propose a methodology to uniformly represent the examples with minimal metadata, based on existing standards. Furthermore, we introduce an extensive set of open-source applications, including query graph visualizations and smart query editors, easily reusable by KG maintainers who adopt the proposed methodology. Conclusions. We encourage the community to adopt and extend the proposed methodology, towards richer KG metadata and improved Semantic Web services.

We have witnessed promising progress led by large language models (LLMs) and further vision language models (VLMs) in handling various queries as a general-purpose assistant. VLMs, as a bridge to connect the visual world and language corpus, receive both visual content and various text-only user instructions to generate corresponding responses. Though great success has been achieved by VLMs in various fields, in this work, we ask whether the existing VLMs can act as domain experts, accurately answering marine questions, which require significant domain expertise and address special domain challenges/requirements. To comprehensively evaluate the effectiveness and explore the boundary of existing VLMs, we construct the first large-scale marine VLM dataset and benchmark called MarineEval, with 2,000 image-based question-answering pairs. During our dataset construction, we ensure the diversity and coverage of the constructed data: 7 task dimensions and 20 capacity dimensions. The domain requirements are specially integrated into the data construction and further verified by the corresponding marine domain experts. We comprehensively benchmark 17 existing VLMs on our MarineEval and also investigate the limitations of existing models in answering marine research questions. The experimental results reveal that existing VLMs cannot effectively answer the domain-specific questions, and there is still a large room for further performance improvements. We hope our new benchmark and observations will facilitate future research. Project Page: http://marineeval.hkustvgd.com/

Ontology Alignment (OA) is fundamental for achieving semantic interoperability across diverse knowledge systems. We present OntoAligner, a comprehensive, modular, and robust Python toolkit for ontology alignment, designed to address current limitations with existing tools faced by practitioners. Existing tools are limited in scalability, modularity, and ease of integration with recent AI advances. OntoAligner provides a flexible architecture integrating existing lightweight OA techniques such as fuzzy matching but goes beyond by supporting contemporary methods with retrieval-augmented generation and large language models for OA. The framework prioritizes extensibility, enabling researchers to integrate custom alignment algorithms and datasets. This paper details the design principles, architecture, and implementation of the OntoAligner, demonstrating its utility through benchmarks on standard OA tasks. Our evaluation highlights OntoAligner's ability to handle large-scale ontologies efficiently with few lines of code while delivering high alignment quality. By making OntoAligner open-source, we aim to provide a resource that fosters innovation and collaboration within the OA community, empowering researchers and practitioners with a toolkit for reproducible OA research and real-world applications.

Despite outstanding processes in many tasks, Large Language Models (LLMs) still lack accuracy when dealing with highly technical domains. Especially, telecommunications (telco) is a particularly challenging domain due the large amount of lexical, semantic and conceptual peculiarities. Yet, this domain holds many valuable use cases, directly linked to industrial needs. Hence, this paper studies how LLMs can be adapted to the telco domain. It reports our effort to (i) collect a massive corpus of domain-specific data (800M tokens, 80K instructions), (ii) perform adaptation using various methodologies, and (iii) benchmark them against larger generalist models in downstream tasks that require extensive knowledge of telecommunications. Our experiments on Llama-2-7b show that domain-adapted models can challenge the large generalist models. They also suggest that adaptation can be restricted to a unique instruction-tuning step, dicarding the need for any fine-tuning on raw texts beforehand.

The cybersecurity landscape evolves rapidly and poses threats to organizations. To enhance resilience, one needs to track the latest developments and trends in the domain. It has been demonstrated that standard bibliometrics approaches show their limits in such a fast-evolving domain. For this purpose, we use large language models (LLMs) to extract relevant knowledge entities from cybersecurity-related texts. We use a subset of arXiv preprints on cybersecurity as our data and compare different LLMs in terms of entity recognition (ER) and relevance. The results suggest that LLMs do not produce good knowledge entities that reflect the cybersecurity context, but our results show some potential for noun extractors. For this reason, we developed a noun extractor boosted with some statistical analysis to extract specific and relevant compound nouns from the domain. Later, we tested our model to identify trends in the LLM domain. We observe some limitations, but it offers promising results to monitor the evolution of emergent trends.

Recent work by (Richardson and Kuhn, 2017a,b; Richardson et al., 2018) looks at semantic parser induction and question answering in the domain of source code libraries and APIs. In this brief note, we formalize the representations being learned in these studies and introduce a simple domain specific language and a systematic translation from this language to first-order logic. By recasting the target representations in terms of classical logic, we aim to broaden the applicability of existing code datasets for investigating more complex natural language understanding and reasoning problems in the software domain.

Creating knowledge bases and ontologies is a time consuming task that relies on a manual curation. AI/NLP approaches can assist expert curators in populating these knowledge bases, but current approaches rely on extensive training data, and are not able to populate arbitrary complex nested knowledge schemas. Here we present Structured Prompt Interrogation and Recursive Extraction of Semantics (SPIRES), a Knowledge Extraction approach that relies on the ability of Large Language Models (LLMs) to perform zero-shot learning (ZSL) and general-purpose query answering from flexible prompts and return information conforming to a specified schema. Given a detailed, user-defined knowledge schema and an input text, SPIRES recursively performs prompt interrogation against GPT-3+ to obtain a set of responses matching the provided schema. SPIRES uses existing ontologies and vocabularies to provide identifiers for all matched elements. We present examples of use of SPIRES in different domains, including extraction of food recipes, multi-species cellular signaling pathways, disease treatments, multi-step drug mechanisms, and chemical to disease causation graphs. Current SPIRES accuracy is comparable to the mid-range of existing Relation Extraction (RE) methods, but has the advantage of easy customization, flexibility, and, crucially, the ability to perform new tasks in the absence of any training data. This method supports a general strategy of leveraging the language interpreting capabilities of LLMs to assemble knowledge bases, assisting manual knowledge curation and acquisition while supporting validation with publicly-available databases and ontologies external to the LLM. SPIRES is available as part of the open source OntoGPT package: https://github.com/ monarch-initiative/ontogpt.

In this work we explore the task of instance segmentation with attribute localization, which unifies instance segmentation (detect and segment each object instance) and fine-grained visual attribute categorization (recognize one or multiple attributes). The proposed task requires both localizing an object and describing its properties. To illustrate the various aspects of this task, we focus on the domain of fashion and introduce Fashionpedia as a step toward mapping out the visual aspects of the fashion world. Fashionpedia consists of two parts: (1) an ontology built by fashion experts containing 27 main apparel categories, 19 apparel parts, 294 fine-grained attributes and their relationships; (2) a dataset with everyday and celebrity event fashion images annotated with segmentation masks and their associated per-mask fine-grained attributes, built upon the Fashionpedia ontology. In order to solve this challenging task, we propose a novel Attribute-Mask RCNN model to jointly perform instance segmentation and localized attribute recognition, and provide a novel evaluation metric for the task. We also demonstrate instance segmentation models pre-trained on Fashionpedia achieve better transfer learning performance on other fashion datasets than ImageNet pre-training. Fashionpedia is available at: https://fashionpedia.github.io/home/index.html.

We propose Semantic Parser Localizer (SPL), a toolkit that leverages Neural Machine Translation (NMT) systems to localize a semantic parser for a new language. Our methodology is to (1) generate training data automatically in the target language by augmenting machine-translated datasets with local entities scraped from public websites, (2) add a few-shot boost of human-translated sentences and train a novel XLMR-LSTM semantic parser, and (3) test the model on natural utterances curated using human translators. We assess the effectiveness of our approach by extending the current capabilities of Schema2QA, a system for English Question Answering (QA) on the open web, to 10 new languages for the restaurants and hotels domains. Our models achieve an overall test accuracy ranging between 61% and 69% for the hotels domain and between 64% and 78% for restaurants domain, which compares favorably to 69% and 80% obtained for English parser trained on gold English data and a few examples from validation set. We show our approach outperforms the previous state-of-the-art methodology by more than 30% for hotels and 40% for restaurants with localized ontologies for the subset of languages tested. Our methodology enables any software developer to add a new language capability to a QA system for a new domain, leveraging machine translation, in less than 24 hours.

Large Language Models (LLMs) have demonstrated unprecedented prowess across various natural language processing tasks in various application domains. Recent studies show that LLMs can be leveraged to perform lexical semantic tasks, such as Knowledge Base Completion (KBC) or Ontology Learning (OL). However, it has not effectively been verified whether their success is due to their ability to reason over unstructured or semi-structured data, or their effective learning of linguistic patterns and senses alone. This unresolved question is particularly crucial when dealing with domain-specific data, where the lexical senses and their meaning can completely differ from what a LLM has learned during its training stage. This paper investigates the following question: Do LLMs really adapt to domains and remain consistent in the extraction of structured knowledge, or do they only learn lexical senses instead of reasoning? To answer this question and, we devise a controlled experiment setup that uses WordNet to synthesize parallel corpora, with English and gibberish terms. We examine the differences in the outputs of LLMs for each corpus in two OL tasks: relation extraction and taxonomy discovery. Empirical results show that, while adapting to the gibberish corpora, off-the-shelf LLMs do not consistently reason over semantic relationships between concepts, and instead leverage senses and their frame. However, fine-tuning improves the performance of LLMs on lexical semantic tasks even when the domain-specific terms are arbitrary and unseen during pre-training, hinting at the applicability of pre-trained LLMs for OL.

Goal-oriented chatbots are essential for automating user tasks, such as booking flights or making restaurant reservations. A key component of these systems is Dialogue State Tracking (DST), which interprets user intent and maintains the dialogue state. However, existing DST methods often rely on fixed ontologies and manually compiled slot values, limiting their adaptability to open-domain dialogues. We propose a novel approach that leverages instruction tuning and advanced prompt strategies to enhance DST performance, without relying on any predefined ontologies. Our method enables Large Language Model (LLM) to infer dialogue states through carefully designed prompts and includes an anti-hallucination mechanism to ensure accurate tracking in diverse conversation contexts. Additionally, we employ a Variational Graph Auto-Encoder (VGAE) to model and predict subsequent user intent. Our approach achieved state-of-the-art with a JGA of 42.57% outperforming existing ontology-less DST models, and performed well in open-domain real-world conversations. This work presents a significant advancement in creating more adaptive and accurate goal-oriented chatbots.

This research presents a comprehensive methodology for utilizing an ontology-driven structured prompts system in interplay with ChatGPT, a widely used large language model (LLM). The study develops formal models, both information and functional, and establishes the methodological foundations for integrating ontology-driven prompts with ChatGPT's meta-learning capabilities. The resulting productive triad comprises the methodological foundations, advanced information technology, and the OntoChatGPT system, which collectively enhance the effectiveness and performance of chatbot systems. The implementation of this technology is demonstrated using the Ukrainian language within the domain of rehabilitation. By applying the proposed methodology, the OntoChatGPT system effectively extracts entities from contexts, classifies them, and generates relevant responses. The study highlights the versatility of the methodology, emphasizing its applicability not only to ChatGPT but also to other chatbot systems based on LLMs, such as Google's Bard utilizing the PaLM 2 LLM. The underlying principles of meta-learning, structured prompts, and ontology-driven information retrieval form the core of the proposed methodology, enabling their adaptation and utilization in various LLM-based systems. This versatile approach opens up new possibilities for NLP and dialogue systems, empowering developers to enhance the performance and functionality of chatbot systems across different domains and languages.

Large Language Models (LLMs) have demonstrated remarkable success in various tasks such as natural language understanding, text summarization, and machine translation. However, their general-purpose nature often limits their effectiveness in domain-specific applications that require specialized knowledge, such as healthcare, chemistry, or legal analysis. To address this, researchers have explored diverse methods to enhance LLMs by integrating domain-specific knowledge. In this survey, we provide a comprehensive overview of these methods, which we categorize into four key approaches: dynamic knowledge injection, static knowledge embedding, modular adapters, and prompt optimization. Each approach offers unique mechanisms to equip LLMs with domain expertise, balancing trade-offs between flexibility, scalability, and efficiency. We discuss how these methods enable LLMs to tackle specialized tasks, compare their advantages and disadvantages, evaluate domain-specific LLMs against general LLMs, and highlight the challenges and opportunities in this emerging field. For those interested in delving deeper into this area, we also summarize the commonly used datasets and benchmarks. To keep researchers updated on the latest studies, we maintain an open-source at: https://github.com/abilliyb/Knowledge_Injection_Survey_Papers, dedicated to documenting research in the field of specialized LLM.

Retrieval-augmented learning based on radiology reports has emerged as a promising direction to improve performance on long-tail medical imaging tasks, such as rare disease detection in chest X-rays. Most existing methods rely on comparing high-dimensional text embeddings from models like CLIP or CXR-BERT, which are often difficult to interpret, computationally expensive, and not well-aligned with the structured nature of medical knowledge. We propose a novel, ontology-driven alternative for comparing radiology report texts based on clinically grounded concepts from the Unified Medical Language System (UMLS). Our method extracts standardised medical entities from free-text reports using an enhanced pipeline built on RadGraph-XL and SapBERT. These entities are linked to UMLS concepts (CUIs), enabling a transparent, interpretable set-based representation of each report. We then define a task-adaptive similarity measure based on a modified and weighted version of the Tversky Index that accounts for synonymy, negation, and hierarchical relationships between medical entities. This allows efficient and semantically meaningful similarity comparisons between reports. We demonstrate that our approach outperforms state-of-the-art embedding-based retrieval methods in a radiograph classification task on MIMIC-CXR, particularly in long-tail settings. Additionally, we use our pipeline to generate ontology-backed disease labels for MIMIC-CXR, offering a valuable new resource for downstream learning tasks. Our work provides more explainable, reliable, and task-specific retrieval strategies in clinical AI systems, especially when interpretability and domain knowledge integration are essential. Our code is available at https://github.com/Felix-012/ontology-concept-distillation

Virtual assistants such as Google Assistant, Alexa and Siri provide a conversational interface to a large number of services and APIs spanning multiple domains. Such systems need to support an ever-increasing number of services with possibly overlapping functionality. Furthermore, some of these services have little to no training data available. Existing public datasets for task-oriented dialogue do not sufficiently capture these challenges since they cover few domains and assume a single static ontology per domain. In this work, we introduce the the Schema-Guided Dialogue (SGD) dataset, containing over 16k multi-domain conversations spanning 16 domains. Our dataset exceeds the existing task-oriented dialogue corpora in scale, while also highlighting the challenges associated with building large-scale virtual assistants. It provides a challenging testbed for a number of tasks including language understanding, slot filling, dialogue state tracking and response generation. Along the same lines, we present a schema-guided paradigm for task-oriented dialogue, in which predictions are made over a dynamic set of intents and slots, provided as input, using their natural language descriptions. This allows a single dialogue system to easily support a large number of services and facilitates simple integration of new services without requiring additional training data. Building upon the proposed paradigm, we release a model for dialogue state tracking capable of zero-shot generalization to new APIs, while remaining competitive in the regular setting.

The impressive performance of ChatGPT and other foundation-model-based products in human language understanding has prompted both academia and industry to explore how these models can be tailored for specific industries and application scenarios. This process, known as the customization of domain-specific foundation models (FMs), addresses the limitations of general-purpose models, which may not fully capture the unique patterns and requirements of domain-specific data. Despite its importance, there is a notable lack of comprehensive overview papers on building domain-specific FMs, while numerous resources exist for general-purpose models. To bridge this gap, this article provides a timely and thorough overview of the methodology for customizing domain-specific FMs. It introduces basic concepts, outlines the general architecture, and surveys key methods for constructing domain-specific models. Furthermore, the article discusses various domains that can benefit from these specialized models and highlights the challenges ahead. Through this overview, we aim to offer valuable guidance and reference for researchers and practitioners from diverse fields to develop their own customized FMs.

The web provides a rich, open-domain environment with textual, structural, and spatial properties. We propose a new task for grounding language in this environment: given a natural language command (e.g., "click on the second article"), choose the correct element on the web page (e.g., a hyperlink or text box). We collected a dataset of over 50,000 commands that capture various phenomena such as functional references (e.g. "find who made this site"), relational reasoning (e.g. "article by john"), and visual reasoning (e.g. "top-most article"). We also implemented and analyzed three baseline models that capture different phenomena present in the dataset.

Identifying effective interventions from the scientific literature is challenging due to the high volume of publications, specialized terminology, and inconsistent reporting formats, making manual curation laborious and prone to oversight. To address this challenge, this paper proposes a novel framework leveraging large language models (LLMs), which integrates a progressive ontology prompting (POP) algorithm with a dual-agent system, named LLM-Duo. On the one hand, the POP algorithm conducts a prioritized breadth-first search (BFS) across a predefined ontology, generating structured prompt templates and action sequences to guide the automatic annotation process. On the other hand, the LLM-Duo system features two specialized LLM agents, an explorer and an evaluator, working collaboratively and adversarially to continuously refine annotation quality. We showcase the real-world applicability of our framework through a case study focused on speech-language intervention discovery. Experimental results show that our approach surpasses advanced baselines, achieving more accurate and comprehensive annotations through a fully automated process. Our approach successfully identified 2,421 interventions from a corpus of 64,177 research articles in the speech-language pathology domain, culminating in the creation of a publicly accessible intervention knowledge base with great potential to benefit the speech-language pathology community.

We present DART, an open domain structured DAta Record to Text generation dataset with over 82k instances (DARTs). Data-to-Text annotations can be a costly process, especially when dealing with tables which are the major source of structured data and contain nontrivial structures. To this end, we propose a procedure of extracting semantic triples from tables that encodes their structures by exploiting the semantic dependencies among table headers and the table title. Our dataset construction framework effectively merged heterogeneous sources from open domain semantic parsing and dialogue-act-based meaning representation tasks by utilizing techniques such as: tree ontology annotation, question-answer pair to declarative sentence conversion, and predicate unification, all with minimum post-editing. We present systematic evaluation on DART as well as new state-of-the-art results on WebNLG 2017 to show that DART (1) poses new challenges to existing data-to-text datasets and (2) facilitates out-of-domain generalization. Our data and code can be found at https://github.com/Yale-LILY/dart.

Recent proprietary large language models (LLMs), such as GPT-4, have achieved a milestone in tackling diverse challenges in the biomedical domain, ranging from multiple-choice questions to long-form generations. To address challenges that still cannot be handled with the encoded knowledge of LLMs, various retrieval-augmented generation (RAG) methods have been developed by searching documents from the knowledge corpus and appending them unconditionally or selectively to the input of LLMs for generation. However, when applying existing methods to different domain-specific problems, poor generalization becomes apparent, leading to fetching incorrect documents or making inaccurate judgments. In this paper, we introduce Self-BioRAG, a framework reliable for biomedical text that specializes in generating explanations, retrieving domain-specific documents, and self-reflecting generated responses. We utilize 84k filtered biomedical instruction sets to train Self-BioRAG that can assess its generated explanations with customized reflective tokens. Our work proves that domain-specific components, such as a retriever, domain-related document corpus, and instruction sets are necessary for adhering to domain-related instructions. Using three major medical question-answering benchmark datasets, experimental results of Self-BioRAG demonstrate significant performance gains by achieving a 7.2% absolute improvement on average over the state-of-the-art open-foundation model with a parameter size of 7B or less. Overall, we analyze that Self-BioRAG finds the clues in the question, retrieves relevant documents if needed, and understands how to answer with information from retrieved documents and encoded knowledge as a medical expert does. We release our data and code for training our framework components and model weights (7B and 13B) to enhance capabilities in biomedical and clinical domains.

Aspect-based summarization is the task of generating focused summaries based on specific points of interest. Such summaries aid efficient analysis of text, such as quickly understanding reviews or opinions from different angles. However, due to large differences in the type of aspects for different domains (e.g., sentiment, product features), the development of previous models has tended to be domain-specific. In this paper, we propose WikiAsp, a large-scale dataset for multi-domain aspect-based summarization that attempts to spur research in the direction of open-domain aspect-based summarization. Specifically, we build the dataset using Wikipedia articles from 20 different domains, using the section titles and boundaries of each article as a proxy for aspect annotation. We propose several straightforward baseline models for this task and conduct experiments on the dataset. Results highlight key challenges that existing summarization models face in this setting, such as proper pronoun handling of quoted sources and consistent explanation of time-sensitive events.

The emergence of open data portals necessitates more attention to protecting sensitive data before datasets get published and exchanged. While an abundance of methods for suppressing sensitive data exist, the conceptualization of sensitive data and methods to detect it, focus particularly on personal data that, if disclosed, may be harmful or violate privacy. We observe the need for refining and broadening our definitions of sensitive data, and argue that the sensitivity of data depends on its context. Based on this definition, we introduce two mechanisms for contextual sensitive data detection that consider the broader context of a dataset at hand. First, we introduce type contextualization, which first detects the semantic type of particular data values, then considers the overall context of the data values within the dataset or document. Second, we introduce domain contextualization which determines sensitivity of a given dataset in the broader context based on the retrieval of relevant rules from documents that specify data sensitivity (e.g., data topic and geographic origin). Experiments with these mechanisms, assisted by large language models (LLMs), confirm that: 1) type-contextualization significantly reduces the number of false positives for type-based sensitive data detection and reaches a recall of 94% compared to 63% with commercial tools, and 2) domain-contextualization leveraging sensitivity rule retrieval is effective for context-grounded sensitive data detection in non-standard data domains such as humanitarian datasets. Evaluation with humanitarian data experts also reveals that context-grounded LLM explanations provide useful guidance in manual data auditing processes, improving consistency. We open-source mechanisms and annotated datasets for contextual sensitive data detection at https://github.com/trl-lab/sensitive-data-detection.

Knowledge graphs (KGs) provide structured, verifiable grounding for large language models (LLMs), but current LLM-based systems commonly use KGs as auxiliary structures for text retrieval, leaving their intrinsic quality underexplored. In this work, we propose Wikontic, a multi-stage pipeline that constructs KGs from open-domain text by extracting candidate triplets with qualifiers, enforcing Wikidata-based type and relation constraints, and normalizing entities to reduce duplication. The resulting KGs are compact, ontology-consistent, and well-connected; on MuSiQue, the correct answer entity appears in 96% of generated triplets. On HotpotQA, our triplets-only setup achieves 76.0 F1, and on MuSiQue 59.8 F1, matching or surpassing several retrieval-augmented generation baselines that still require textual context. In addition, Wikontic attains state-of-the-art information-retention performance on the MINE-1 benchmark (86%), outperforming prior KG construction methods. Wikontic is also efficient at build time: KG construction uses less than 1,000 output tokens, about 3times fewer than AriGraph and <1/20 of GraphRAG. The proposed pipeline enhances the quality of the generated KG and offers a scalable solution for leveraging structured knowledge in LLMs.

While dense biomedical embeddings achieve strong performance, their black-box nature limits their utility in clinical decision-making. Recent question-based interpretable embeddings represent text as binary answers to natural-language questions, but these approaches often rely on heuristic or surface-level contrastive signals and overlook specialized domain knowledge. We propose QIME, an ontology-grounded framework for constructing interpretable medical text embeddings in which each dimension corresponds to a clinically meaningful yes/no question. By conditioning on cluster-specific medical concept signatures, QIME generates semantically atomic questions that capture fine-grained distinctions in biomedical text. Furthermore, QIME supports a training-free embedding construction strategy that eliminates per-question classifier training while further improving performance. Experiments across biomedical semantic similarity, clustering, and retrieval benchmarks show that QIME consistently outperforms prior interpretable embedding methods and substantially narrows the gap to strong black-box biomedical encoders, while providing concise and clinically informative explanations.

This work investigates the applicability of recent generative Large Language Models (LLMs), such as the GPT series and Flan-T5, to ontology alignment for identifying concept equivalence mappings across ontologies. To test the zero-shot performance of Flan-T5-XXL and GPT-3.5-turbo, we leverage challenging subsets from two equivalence matching datasets of the OAEI Bio-ML track, taking into account concept labels and structural contexts. Preliminary findings suggest that LLMs have the potential to outperform existing ontology alignment systems like BERTMap, given careful framework and prompt design.

MultiWOZ 2.0 (Budzianowski et al., 2018) is a recently released multi-domain dialogue dataset spanning 7 distinct domains and containing over 10,000 dialogues. Though immensely useful and one of the largest resources of its kind to-date, MultiWOZ 2.0 has a few shortcomings. Firstly, there is substantial noise in the dialogue state annotations and dialogue utterances which negatively impact the performance of state-tracking models. Secondly, follow-up work (Lee et al., 2019) has augmented the original dataset with user dialogue acts. This leads to multiple co-existent versions of the same dataset with minor modifications. In this work we tackle the aforementioned issues by introducing MultiWOZ 2.1. To fix the noisy state annotations, we use crowdsourced workers to re-annotate state and utterances based on the original utterances in the dataset. This correction process results in changes to over 32% of state annotations across 40% of the dialogue turns. In addition, we fix 146 dialogue utterances by canonicalizing slot values in the utterances to the values in the dataset ontology. To address the second problem, we combined the contributions of the follow-up works into MultiWOZ 2.1. Hence, our dataset also includes user dialogue acts as well as multiple slot descriptions per dialogue state slot. We then benchmark a number of state-of-the-art dialogue state tracking models on the MultiWOZ 2.1 dataset and show the joint state tracking performance on the corrected state annotations. We are publicly releasing MultiWOZ 2.1 to the community, hoping that this dataset resource will allow for more effective models across various dialogue subproblems to be built in the future.

Goal oriented dialogue systems were originally designed as a natural language interface to a fixed data-set of entities that users might inquire about, further described by domain, slots, and values. As we move towards adaptable dialogue systems where knowledge about domains, slots, and values may change, there is an increasing need to automatically extract these terms from raw dialogues or related non-dialogue data on a large scale. In this paper, we take an important step in this direction by exploring different features that can enable systems to discover realizations of domains, slots, and values in dialogues in a purely data-driven fashion. The features that we examine stem from word embeddings, language modelling features, as well as topological features of the word embedding space. To examine the utility of each feature set, we train a seed model based on the widely used MultiWOZ data-set. Then, we apply this model to a different corpus, the Schema-Guided Dialogue data-set. Our method outperforms the previously proposed approach that relies solely on word embeddings. We also demonstrate that each of the features is responsible for discovering different kinds of content. We believe our results warrant further research towards ontology induction, and continued harnessing of topological data analysis for dialogue and natural language processing research.

Large Language Models (LLMs), like LLaMA, have exhibited remarkable performance across various tasks. Nevertheless, when deployed to specific domains such as law or medicine, the models still confront the challenge of a deficiency in domain-specific knowledge and an inadequate capability to leverage that knowledge to resolve domain-related problems. In this paper, we propose a new framework to adapt LLMs to specific domains and build Lawyer LLaMA, a legal domain LLM, based on this framework. Specifically, we inject domain knowledge during the continual training stage and teach the model to learn professional skills using properly designed supervised fine-tuning tasks. Moreover, to alleviate the hallucination problem during the model's generation, we add a retrieval module and extract relevant legal articles before the model answers any queries. When learning domain-specific skills, we find that experts' experience is much more useful than experiences distilled from ChatGPT, where hundreds of expert-written data outperform tens of thousands of ChatGPT-generated ones. We will release our model and data.

In this paper, we present our approaches for the FinSim-3 Shared Task 2021: Learning Semantic Similarities for the Financial Domain. The aim of this shared task is to correctly classify a list of given terms from the financial domain into the most relevant hypernym (or top-level) concept in an external ontology. For our system submission, we evaluate two methods: a Sentence-RoBERTa (SRoBERTa) embeddings model pre-trained on a custom corpus, and a dual word-sentence embeddings model that builds on the first method by improving the proposed baseline word embeddings construction using the FastText model to boost the classification performance. Our system ranks 2nd overall on both metrics, scoring 0.917 on Average Accuracy and 1.141 on Mean Rank.

Retrieval-Augmented Generation (RAG) systems combine Large Language Models (LLMs) with external knowledge, and their performance depends heavily on how that knowledge is represented. This study investigates how different Knowledge Graph (KG) construction strategies influence RAG performance. We compare a variety of approaches: standard vector-based RAG, GraphRAG, and retrieval over KGs built from ontologies derived either from relational databases or textual corpora. Results show that ontology-guided KGs incorporating chunk information achieve competitive performance with state-of-the-art frameworks, substantially outperforming vector retrieval baselines. Moreover, the findings reveal that ontology-guided KGs built from relational databases perform competitively to ones built with ontologies extracted from text, with the benefit of offering a dual advantage: they require a one-time-only ontology learning process, substantially reducing LLM usage costs; and avoid the complexity of ontology merging inherent to text-based approaches.

Knowledge graphs (KGs) have been successfully applied to the analysis of complex scientific and technological domains, with automatic KG generation methods typically building upon relation extraction models capturing fine-grained relations between domain entities in text. While these relations are fully applicable across scientific areas, existing models are trained on few domain-specific datasets such as SciERC and do not perform well on new target domains. In this paper, we experiment with leveraging in-context learning capabilities of Large Language Models to perform schema-constrained data annotation, collecting in-domain training instances for a Transformer-based relation extraction model deployed on titles and abstracts of research papers in the Architecture, Construction, Engineering and Operations (AECO) domain. By assessing the performance gain with respect to a baseline Deep Learning architecture trained on off-domain data, we show that by using a few-shot learning strategy with structured prompts and only minimal expert annotation the presented approach can potentially support domain adaptation of a science KG generation model.

With the rapid development of large language models in recent years, there has been an increasing demand for domain-specific Agents that can cater to the unique needs of enterprises and organizations. Unlike general models, which strive for broad coverage, these specialized Agents rely on focused datasets tailored to their intended applications. This research proposes a pipeline that leverages the power of LLMs and the Retrieval-Augmented Generation related framework to construct high-quality instruction datasets for fine-tuning on specific domains using custom document collections. By ingesting domain-specific documents, the pipeline generates relevant and contextually appropriate instructions, thus effectively creating a comprehensive dataset for fine-tuning LLMs on the target domain. This approach overcomes the limitations of traditional dataset creation methods, which often rely on manual curation or web-scraping techniques that may introduce noise and irrelevant data. Notably, our pipeline offers a dynamic solution that can quickly adapt to updates or modifications in the domain-specific document collection, eliminating the need for complete retraining. Additionally, it addresses the challenge of data scarcity by enabling the generation of instruction datasets from a limited set of initial documents, rendering it suitable for unpopular or specialized domains where comprehensive datasets are scarce. As a case study, we apply this approach to the domain of psychiatry, a field requiring specialized knowledge and sensitive handling of patient information. The resulting fine-tuned LLM demonstrates showcases the viability of the proposed approach and underscores its potential for widespread adoption across various industries and domains where tailored, accurate, and contextually relevant language models are indispensable.

There is a growing interest in applying pre-trained large language models (LLMs) to planning problems. However, methods that use LLMs directly as planners are currently impractical due to several factors, including limited correctness of plans, strong reliance on feedback from interactions with simulators or even the actual environment, and the inefficiency in utilizing human feedback. In this work, we introduce a novel alternative paradigm that constructs an explicit world (domain) model in planning domain definition language (PDDL) and then uses it to plan with sound domain-independent planners. To address the fact that LLMs may not generate a fully functional PDDL model initially, we employ LLMs as an interface between PDDL and sources of corrective feedback, such as PDDL validators and humans. For users who lack a background in PDDL, we show that LLMs can translate PDDL into natural language and effectively encode corrective feedback back to the underlying domain model. Our framework not only enjoys the correctness guarantee offered by the external planners but also reduces human involvement by allowing users to correct domain models at the beginning, rather than inspecting and correcting (through interactive prompting) every generated plan as in previous work. On two IPC domains and a Household domain that is more complicated than commonly used benchmarks such as ALFWorld, we demonstrate that GPT-4 can be leveraged to produce high-quality PDDL models for over 40 actions, and the corrected PDDL models are then used to successfully solve 48 challenging planning tasks. Resources including the source code will be released at: https://guansuns.github.io/pages/llm-dm.

A research division plays an important role of driving innovation in an organization. Drawing insights, following trends, keeping abreast of new research, and formulating strategies are increasingly becoming more challenging for both researchers and executives as the amount of information grows in both velocity and volume. In this paper we present a use case of how a corporate research community, IBM Research, utilizes Semantic Web technologies to induce a unified Knowledge Graph from both structured and textual data obtained by integrating various applications used by the community related to research projects, academic papers, datasets, achievements and recognition. In order to make the Knowledge Graph more accessible to application developers, we identified a set of common patterns for exploiting the induced knowledge and exposed them as APIs. Those patterns were born out of user research which identified the most valuable use cases or user pain points to be alleviated. We outline two distinct scenarios: recommendation and analytics for business use. We will discuss these scenarios in detail and provide an empirical evaluation on entity recommendation specifically. The methodology used and the lessons learned from this work can be applied to other organizations facing similar challenges.

In this work we study various Retrieval Augmented Regeneration (RAG) approaches to gain an understanding of the strengths and weaknesses of each approach in a question-answering analysis. To gain this understanding we use a case-study subset of the Global Database of Events, Language, and Tone (GDELT) dataset as well as a corpus of raw text scraped from the online news articles. To retrieve information from the text corpus we implement a traditional vector store RAG as well as state-of-the-art large language model (LLM) based approaches for automatically constructing KGs and retrieving the relevant subgraphs. In addition to these corpus approaches, we develop a novel ontology-based framework for constructing knowledge graphs (KGs) from GDELT directly which leverages the underlying schema of GDELT to create structured representations of global events. For retrieving relevant information from the ontology-based KGs we implement both direct graph queries and state-of-the-art graph retrieval approaches. We compare the performance of each method in a question-answering task. We find that while our ontology-based KGs are valuable for question-answering, automated extraction of the relevant subgraphs is challenging. Conversely, LLM-generated KGs, while capturing event summaries, often lack consistency and interpretability. Our findings suggest benefits of a synergistic approach between ontology and LLM-based KG construction, with proposed avenues toward that end.

Modern language models are trained on large, unstructured datasets consisting of trillions of tokens and obtained by crawling the web. The unstructured nature makes it difficult to reason about their contents and develop systematic approaches to data curation. In this paper, we unpack monolithic web corpora by developing taxonomies of their contents and organizing them into domains. We introduce WebOrganizer, a framework for organizing web pages in terms of both their topic and format. Using these two complementary notions of domains, we automatically annotate pre-training data by distilling annotations from a large language model into efficient classifiers. This allows us to study how data from different domains should be mixed to improve models on downstream tasks, and we show that we can combine insights about effective topics and formats to further boost performance. We demonstrate that our domain mixing also improves existing methods that select data based on quality. Furthermore, we study and compare how quality-based methods will implicitly change the domain mixture. Overall, our work demonstrates that constructing and mixing domains provides a valuable complement to quality-based data curation methods, opening new avenues for effective and insightful pre-training data curation.

System design is often taught through domain-specific solutions specific to particular domains, such as databases, operating systems, or computer architecture, each with its own methods and vocabulary. While this diversity is a strength, it can obscure cross-cutting principles that recur across domains. This paper proposes a preliminary "periodic table" of system design principles distilled from several domains in computer systems. The goal is a shared, concise vocabulary that helps students, researchers, and practitioners reason about structure and trade-offs, compare designs across domains, and communicate choices more clearly. For supporting materials and updates, please refer to the repository at: https://github.com/jarulraj/periodic-table.

Large Language Models (LLMs) have demonstrated remarkable proficiency in understanding and generating natural language. However, their capabilities wane in highly specialized domains underrepresented in the pretraining corpus, such as physical and biomedical sciences. This work explores how to repurpose general LLMs into effective task solvers for specialized domains. We introduce a novel, model-agnostic framework for learning custom input tags, which are parameterized as continuous vectors appended to the LLM's embedding layer, to condition the LLM. We design two types of input tags: domain tags are used to delimit specialized representations (e.g., chemical formulas) and provide domain-relevant context; function tags are used to represent specific functions (e.g., predicting molecular properties) and compress function-solving instructions. We develop a three-stage protocol to learn these tags using auxiliary data and domain knowledge. By explicitly disentangling task domains from task functions, our method enables zero-shot generalization to unseen problems through diverse combinations of the input tags. It also boosts LLM's performance in various specialized domains, such as predicting protein or chemical properties and modeling drug-target interactions, outperforming expert models tailored to these tasks.

The growing popularity of data mining catalyses the researchers to explore various exciting aspects of education. Early prediction of student performance is an emerging area among them. The researchers have used various predictors in performance modelling studies. Although prior cognition can affect student performance, establishing their relationship is still an open research challenge. Quantifying the knowledge from readily available data is the major challenge here. We have proposed a semantic approach for this purpose. Association mining on nearly 0.35 million observations establishes that prior cognition impacts the student performance. The proposed approach of measuring domain knowledge can help the early performance modelling studies to use it as a predictor.

When experiencing an information need, users want to engage with a domain expert, but often turn to an information retrieval system, such as a search engine, instead. Classical information retrieval systems do not answer information needs directly, but instead provide references to (hopefully authoritative) answers. Successful question answering systems offer a limited corpus created on-demand by human experts, which is neither timely nor scalable. Pre-trained language models, by contrast, are capable of directly generating prose that may be responsive to an information need, but at present they are dilettantes rather than domain experts -- they do not have a true understanding of the world, they are prone to hallucinating, and crucially they are incapable of justifying their utterances by referring to supporting documents in the corpus they were trained over. This paper examines how ideas from classical information retrieval and pre-trained language models can be synthesized and evolved into systems that truly deliver on the promise of domain expert advice.

Word embeddings are an essential instrument in many NLP tasks. Most available resources are trained on general language from Web corpora or Wikipedia dumps. However, word embeddings for domain-specific language are rare, in particular for the social science domain. Therefore, in this work, we describe the creation and evaluation of word embedding models based on 37,604 open-access social science research papers. In the evaluation, we compare domain-specific and general language models for (i) language coverage, (ii) diversity, and (iii) semantic relationships. We found that the created domain-specific model, even with a relatively small vocabulary size, covers a large part of social science concepts, their neighborhoods are diverse in comparison to more general models. Across all relation types, we found a more extensive coverage of semantic relationships.

Knowledge Bases (KBs) find applications in many knowledge-intensive tasks and, most notably, in information retrieval. Wikidata is one of the largest public general-purpose KBs. Yet, its collaborative nature has led to a convoluted schema and taxonomy. The YAGO 4 KB cleaned up the taxonomy by incorporating the ontology of Schema.org, resulting in a cleaner structure amenable to automated reasoning. However, it also cut away large parts of the Wikidata taxonomy, which is essential for information retrieval. In this paper, we extend YAGO 4 with a large part of the Wikidata taxonomy - while respecting logical constraints and the distinction between classes and instances. This yields YAGO 4.5, a new, logically consistent version of YAGO that adds a rich layer of informative classes. An intrinsic and an extrinsic evaluation show the value of the new resource.

Domain-specific named entity recognition (NER) on Computer Science (CS) scholarly articles is an information extraction task that is arguably more challenging for the various annotation aims that can beset the task and has been less studied than NER in the general domain. Given that significant progress has been made on NER, we believe that scholarly domain-specific NER will receive increasing attention in the years to come. Currently, progress on CS NER -- the focus of this work -- is hampered in part by its recency and the lack of a standardized annotation aim for scientific entities/terms. This work proposes a standardized task by defining a set of seven contribution-centric scholarly entities for CS NER viz., research problem, solution, resource, language, tool, method, and dataset. Following which, its main contributions are: combines existing CS NER resources that maintain their annotation focus on the set or subset of contribution-centric scholarly entities we consider; further, noting the need for big data to train neural NER models, this work additionally supplies thousands of contribution-centric entity annotations from article titles and abstracts, thus releasing a cumulative large novel resource for CS NER; and, finally, trains a sequence labeling CS NER model inspired after state-of-the-art neural architectures from the general domain NER task. Throughout the work, several practical considerations are made which can be useful to information technology designers of the digital libraries.

Large language models (LLMs) have significantly advanced the field of natural language processing, with GPT models at the forefront. While their remarkable performance spans a range of tasks, adapting LLMs for real-world business scenarios still poses challenges warranting further investigation. This paper presents an empirical analysis aimed at bridging the gap in adapting LLMs to practical use cases. To do that, we select the question answering (QA) task of insurance as a case study due to its challenge of reasoning. Based on the task we design a new model relied on LLMs which are empowered by additional knowledge extracted from insurance policy rulebooks and DBpedia. The additional knowledge helps LLMs to understand new concepts of insurance for domain adaptation. Preliminary results on two QA datasets show that knowledge enhancement significantly improves the reasoning ability of GPT-3.5 (55.80% and 57.83% in terms of accuracy). The analysis also indicates that existing public knowledge bases, e.g., DBPedia is beneficial for knowledge enhancement. Our findings reveal that the inherent complexity of business scenarios often necessitates the incorporation of domain-specific knowledge and external resources for effective problem-solving.

The synergy between symbolic knowledge, often represented by Knowledge Graphs (KGs), and the generative capabilities of neural networks is central to advancing neurosymbolic AI. A primary bottleneck in realizing this potential is the difficulty of automating KG construction, which faces challenges related to output reliability, consistency, and verifiability. These issues can manifest as structural inconsistencies within the generated graphs, such as the formation of disconnected isolated islands of data or the inaccurate conflation of abstract classes with specific instances. To address these challenges, we propose HyDRA, a Hybrid-Driven Reasoning Architecture designed for verifiable KG automation. Given a domain or an initial set of documents, HyDRA first constructs an ontology via a panel of collaborative neurosymbolic agents. These agents collaboratively agree on a set of competency questions (CQs) that define the scope and requirements the ontology must be able to answer. Given these CQs, we build an ontology graph that subsequently guides the automated extraction of triplets for KG generation from arbitrary documents. Inspired by design-by-contracts (DbC) principles, our method leverages verifiable contracts as the primary control mechanism to steer the generative process of Large Language Models (LLMs). To verify the output of our approach, we extend beyond standard benchmarks and propose an evaluation framework that assesses the functional correctness of the resulting KG by leveraging symbolic verifications as described by the neurosymbolic AI framework, SymbolicAI. This work contributes a hybrid-driven architecture for improving the reliability of automated KG construction and the exploration of evaluation methods for measuring the functional integrity of its output. The code is publicly available.

Recent breakthroughs in large language models (LLMs) exemplified by the impressive mathematical and scientific reasoning capabilities of the o1 model have spotlighted the critical importance of high-quality training data in advancing LLM performance across STEM disciplines. While the mathematics community has benefited from a growing body of curated datasets, the scientific domain at the higher education level has long suffered from a scarcity of comparable resources. To address this gap, we present SCP-116K, a new large-scale dataset of 116,756 high-quality problem-solution pairs, automatically extracted from heterogeneous sources using a streamlined and highly generalizable pipeline. Our approach involves stringent filtering to ensure the scientific rigor and educational level of the extracted materials, while maintaining adaptability for future expansions or domain transfers. By openly releasing both the dataset and the extraction pipeline, we seek to foster research on scientific reasoning, enable comprehensive performance evaluations of new LLMs, and lower the barrier to replicating the successes of advanced models like o1 in the broader science community. We believe SCP-116K will serve as a critical resource, catalyzing progress in high-level scientific reasoning tasks and promoting further innovations in LLM development. The dataset and code are publicly available at https://github.com/AQA6666/SCP-116K-open.

Of primary importance in formulating a response to the increasing prevalence and power of artificial intelligence (AI) applications in society are questions of ontology. Questions such as: What "are" these systems? How are they to be regarded? How does an algorithm come to be regarded as an agent? We discuss three factors which hinder discussion and obscure attempts to form a clear ontology of AI: (1) the various and evolving definitions of AI, (2) the tendency for pre-existing technologies to be assimilated and regarded as "normal," and (3) the tendency of human beings to anthropomorphize. This list is not intended as exhaustive, nor is it seen to preclude entirely a clear ontology, however, these challenges are a necessary set of topics for consideration. Each of these factors is seen to present a 'moving target' for discussion, which poses a challenge for both technical specialists and non-practitioners of AI systems development (e.g., philosophers and theologians) to speak meaningfully given that the corpus of AI structures and capabilities evolves at a rapid pace. Finally, we present avenues for moving forward, including opportunities for collaborative synthesis for scholars in philosophy and science.

Graphs are able to model interconnected entities in many online services, supporting a wide range of applications on the Web. This raises an important question: How can we train a graph foundational model on multiple source domains and adapt to an unseen target domain? A major obstacle is that graphs from different domains often exhibit divergent characteristics. Some studies leverage large language models to align multiple domains based on textual descriptions associated with the graphs, limiting their applicability to text-attributed graphs. For text-free graphs, a few recent works attempt to align different feature distributions across domains, while generally neglecting structural differences. In this work, we propose a novel Structure Alignment framework for text-free Multi-domain Graph Pre-Training and cross-domain adaptation (SAMGPT). It is designed to learn multi-domain knowledge from graphs originating in multiple source domains, which can then be adapted to address applications in an unseen target domain. Specifically, we introduce a set of structure tokens to harmonize structure-based aggregation across source domains during the pre-training phase. Next, for cross-domain adaptation, we design dual prompts, namely, holistic prompts and specific prompts, which adapt unified multi-domain structural knowledge and fine-grained, domain-specific information, respectively, to a target domain. Finally, we conduct comprehensive experiments on seven public datasets to evaluate and analyze the effectiveness of SAMGPT.

In adapting LLMs to specific domains, achieving both domain expertise and reasoning ability remains an urgent challenge. This study proposes a general method for constructing high-quality synthetic instruction data for any domain, starting from domain-specific vocabulary. As a demonstration, we applied this method to the financial domain and constructed a large-scale instruction dataset totaling approximately 9.5 billion tokens with Chain-of-Thought reasoning traces. Evaluation results confirmed performance improvements over baseline models on financial benchmarks, demonstrating the effectiveness of our approach. We also report findings on the impact of reasoning trace length on performance and its limitations. Lastly, we open-source our models and datasets on https://huggingface.co/nri-ai .

This survey examines the rapidly evolving field of Deep Research systems -- AI-powered applications that automate complex research workflows through the integration of large language models, advanced information retrieval, and autonomous reasoning capabilities. We analyze more than 80 commercial and non-commercial implementations that have emerged since 2023, including OpenAI/Deep Research, Gemini/Deep Research, Perplexity/Deep Research, and numerous open-source alternatives. Through comprehensive examination, we propose a novel hierarchical taxonomy that categorizes systems according to four fundamental technical dimensions: foundation models and reasoning engines, tool utilization and environmental interaction, task planning and execution control, and knowledge synthesis and output generation. We explore the architectural patterns, implementation approaches, and domain-specific adaptations that characterize these systems across academic, scientific, business, and educational applications. Our analysis reveals both the significant capabilities of current implementations and the technical and ethical challenges they present regarding information accuracy, privacy, intellectual property, and accessibility. The survey concludes by identifying promising research directions in advanced reasoning architectures, multimodal integration, domain specialization, human-AI collaboration, and ecosystem standardization that will likely shape the future evolution of this transformative technology. By providing a comprehensive framework for understanding Deep Research systems, this survey contributes to both the theoretical understanding of AI-augmented knowledge work and the practical development of more capable, responsible, and accessible research technologies. The paper resources can be viewed at https://github.com/scienceaix/deepresearch.

Large language models (LLMs) have been increasingly applied to various domains, which triggers increasing concerns about LLMs' safety on specialized domains, e.g. medicine. However, testing the domain-specific safety of LLMs is challenging due to the lack of domain knowledge-driven attacks in existing benchmarks. To bridge this gap, we propose a new task, knowledge-to-jailbreak, which aims to generate jailbreaks from domain knowledge to evaluate the safety of LLMs when applied to those domains. We collect a large-scale dataset with 12,974 knowledge-jailbreak pairs and fine-tune a large language model as jailbreak-generator, to produce domain knowledge-specific jailbreaks. Experiments on 13 domains and 8 target LLMs demonstrate the effectiveness of jailbreak-generator in generating jailbreaks that are both relevant to the given knowledge and harmful to the target LLMs. We also apply our method to an out-of-domain knowledge base, showing that jailbreak-generator can generate jailbreaks that are comparable in harmfulness to those crafted by human experts. Data and code: https://github.com/THU-KEG/Knowledge-to-Jailbreak/.

Large language models (LLMs) trained on general domain corpora showed remarkable results on natural language processing (NLP) tasks. However, previous research demonstrated LLMs trained using domain-focused corpora perform better on specialized tasks. Inspired by this pivotal insight, we developed INDUS, a comprehensive suite of LLMs tailored for the Earth science, biology, physics, heliophysics, planetary sciences and astrophysics domains and trained using curated scientific corpora drawn from diverse data sources. The suite of models include: (1) an encoder model trained using domain-specific vocabulary and corpora to address natural language understanding tasks, (2) a contrastive-learning-based general text embedding model trained using a diverse set of datasets drawn from multiple sources to address information retrieval tasks and (3) smaller versions of these models created using knowledge distillation techniques to address applications which have latency or resource constraints. We also created three new scientific benchmark datasets namely, CLIMATE-CHANGE-NER (entity-recognition), NASA-QA (extractive QA) and NASA-IR (IR) to accelerate research in these multi-disciplinary fields. Finally, we show that our models outperform both general-purpose encoders (RoBERTa) and existing domain-specific encoders (SciBERT) on these new tasks as well as existing benchmark tasks in the domains of interest.

Keyphrase generation has primarily been explored within the context of academic research articles, with a particular focus on scientific domains and the English language. In this work, we present EUROPA, a dataset for multilingual keyphrase generation in the legal domain. It is derived from legal judgments from the Court of Justice of the European Union (EU), and contains instances in all 24 EU official languages. We run multilingual models on our corpus and analyze the results, showing room for improvement on a domain-specific multilingual corpus such as the one we present.

We propose a novel approach to enhancing the performance and efficiency of large language models (LLMs) by combining domain prompt routing with domain-specialized models. We introduce a system that utilizes a BERT-based router to direct incoming prompts to the most appropriate domain expert model. These expert models are specifically tuned for domains such as health, mathematics and science. Our research demonstrates that this approach can significantly outperform general-purpose models of comparable size, leading to a superior performance-to-cost ratio across various benchmarks. The implications of this study suggest a potential paradigm shift in LLM development and deployment. Rather than focusing solely on creating increasingly large, general-purpose models, the future of AI may lie in developing ecosystems of smaller, highly specialized models coupled with sophisticated routing systems. This approach could lead to more efficient resource utilization, reduced computational costs, and superior overall performance.

Large language models (LLMs) are widely used as general-purpose knowledge sources, but they rely on parametric knowledge, limiting explainability and trustworthiness. In task-oriented dialogue (TOD) systems, this separation is explicit, using an external database structured by an explicit ontology to ensure explainability and controllability. However, building such ontologies requires manual labels or supervised training. We introduce TeQoDO: a Text-to-SQL task-oriented Dialogue Ontology construction method. Here, an LLM autonomously builds a TOD ontology from scratch without supervision using its inherent SQL programming capabilities combined with dialogue theory provided in the prompt. We show that TeQoDO outperforms transfer learning approaches, and its constructed ontology is competitive on a downstream dialogue state tracking task. Ablation studies demonstrate the key role of dialogue theory. TeQoDO also scales to allow construction of much larger ontologies, which we investigate on a Wikipedia and ArXiv dataset. We view this as a step towards broader application of ontologies to increase LLM explainability.

Pre-trained language models (PLMs) have been the de facto paradigm for most natural language processing (NLP) tasks. This also benefits biomedical domain: researchers from informatics, medicine, and computer science (CS) communities propose various PLMs trained on biomedical datasets, e.g., biomedical text, electronic health records, protein, and DNA sequences for various biomedical tasks. However, the cross-discipline characteristics of biomedical PLMs hinder their spreading among communities; some existing works are isolated from each other without comprehensive comparison and discussions. It expects a survey that not only systematically reviews recent advances of biomedical PLMs and their applications but also standardizes terminology and benchmarks. In this paper, we summarize the recent progress of pre-trained language models in the biomedical domain and their applications in biomedical downstream tasks. Particularly, we discuss the motivations and propose a taxonomy of existing biomedical PLMs. Their applications in biomedical downstream tasks are exhaustively discussed. At last, we illustrate various limitations and future trends, which we hope can provide inspiration for the future research of the research community.

In this paper we present a system that exploits different pre-trained Language Models for assigning domain labels to WordNet synsets without any kind of supervision. Furthermore, the system is not restricted to use a particular set of domain labels. We exploit the knowledge encoded within different off-the-shelf pre-trained Language Models and task formulations to infer the domain label of a particular WordNet definition. The proposed zero-shot system achieves a new state-of-the-art on the English dataset used in the evaluation.

Scientific Large Language Models (Sci-LLMs) are transforming how knowledge is represented, integrated, and applied in scientific research, yet their progress is shaped by the complex nature of scientific data. This survey presents a comprehensive, data-centric synthesis that reframes the development of Sci-LLMs as a co-evolution between models and their underlying data substrate. We formulate a unified taxonomy of scientific data and a hierarchical model of scientific knowledge, emphasizing the multimodal, cross-scale, and domain-specific challenges that differentiate scientific corpora from general natural language processing datasets. We systematically review recent Sci-LLMs, from general-purpose foundations to specialized models across diverse scientific disciplines, alongside an extensive analysis of over 270 pre-/post-training datasets, showing why Sci-LLMs pose distinct demands -- heterogeneous, multi-scale, uncertainty-laden corpora that require representations preserving domain invariance and enabling cross-modal reasoning. On evaluation, we examine over 190 benchmark datasets and trace a shift from static exams toward process- and discovery-oriented assessments with advanced evaluation protocols. These data-centric analyses highlight persistent issues in scientific data development and discuss emerging solutions involving semi-automated annotation pipelines and expert validation. Finally, we outline a paradigm shift toward closed-loop systems where autonomous agents based on Sci-LLMs actively experiment, validate, and contribute to a living, evolving knowledge base. Collectively, this work provides a roadmap for building trustworthy, continually evolving artificial intelligence (AI) systems that function as a true partner in accelerating scientific discovery.

Domain generalization (DG) aims to tackle the distribution shift between training domains and unknown target domains. Generating new domains is one of the most effective approaches, yet its performance gain depends on the distribution discrepancy between the generated and target domains. Distributionally robust optimization is promising to tackle distribution discrepancy by exploring domains in an uncertainty set. However, the uncertainty set may be overwhelmingly large, leading to low-confidence prediction in DG. It is because a large uncertainty set could introduce domains containing semantically different factors from training domains. To address this issue, we propose to perform a moderately distributional exploration (MODE) for domain generalization. Specifically, MODE performs distribution exploration in an uncertainty subset that shares the same semantic factors with the training domains. We show that MODE can endow models with provable generalization performance on unknown target domains. The experimental results show that MODE achieves competitive performance compared to state-of-the-art baselines.

Artefact descriptions are the primary carriers of engineering design knowledge that is both an outcome and a driver of the design process. While an artefact could be described in different connotations, the design process requires a description to embody engineering design knowledge, which is expressed in the text through intricate placement of entities and relationships. As large-language models learn from all kinds of text merely as a sequence of characters/tokens, these are yet to generate text that embodies explicit engineering design facts. Existing ontological design theories are less likely to guide the large-language models whose applications are currently limited to ideation and learning purposes. In this article, we explicate engineering design knowledge as knowledge graphs from a large sample of 33,881 patent documents. We examine the constituents of these knowledge graphs to understand the linguistic and structural basis of engineering design knowledge. In terms of linguistic basis, we observe that entities and relationships could be generalised to 64 and 24 linguistic syntaxes. While relationships mainly capture attributes ('of'), structure ('in', 'with'), purpose ('to', 'for'), hierarchy ('include'), exemplification ('such as'), and behaviour ('to', 'from'), the hierarchical relationships could specifically be identified using 75 unique syntaxes. To understand the structural basis, we draw inspiration from various studies on biological/ecological networks and discover motifs from patent knowledge graphs. We identify four 3-node and four 4-node patterns that could further be converged and simplified into sequence [->...->], aggregation [->...<-], and hierarchy [<-...->]. Expected to guide large-language model based design tools, we propose few regulatory precepts for concretising abstract entities and relationships within subgraphs, while explicating hierarchical structures.

Recent works in Event Argument Extraction (EAE) have focused on improving model generalizability to cater to new events and domains. However, standard benchmarking datasets like ACE and ERE cover less than 40 event types and 25 entity-centric argument roles. Limited diversity and coverage hinder these datasets from adequately evaluating the generalizability of EAE models. In this paper, we first contribute by creating a large and diverse EAE ontology. This ontology is created by transforming FrameNet, a comprehensive semantic role labeling (SRL) dataset for EAE, by exploiting the similarity between these two tasks. Then, exhaustive human expert annotations are collected to build the ontology, concluding with 115 events and 220 argument roles, with a significant portion of roles not being entities. We utilize this ontology to further introduce GENEVA, a diverse generalizability benchmarking dataset comprising four test suites, aimed at evaluating models' ability to handle limited data and unseen event type generalization. We benchmark six EAE models from various families. The results show that owing to non-entity argument roles, even the best-performing model can only achieve 39% F1 score, indicating how GENEVA provides new challenges for generalization in EAE. Overall, our large and diverse EAE ontology can aid in creating more comprehensive future resources, while GENEVA is a challenging benchmarking dataset encouraging further research for improving generalizability in EAE. The code and data can be found at https://github.com/PlusLabNLP/GENEVA.

For monitoring crises, political events are extracted from the news. The large amount of unstructured full-text event descriptions makes a case-by-case analysis unmanageable, particularly for low-resource humanitarian aid organizations. This creates a demand to classify events into event types, a task referred to as event coding. Typically, domain experts craft an event type ontology, annotators label a large dataset and technical experts develop a supervised coding system. In this work, we propose PR-ENT, a new event coding approach that is more flexible and resource-efficient, while maintaining competitive accuracy: first, we extend an event description such as "Military injured two civilians'' by a template, e.g. "People were [Z]" and prompt a pre-trained (cloze) language model to fill the slot Z. Second, we select answer candidates Z* = {"injured'', "hurt"...} by treating the event description as premise and the filled templates as hypothesis in a textual entailment task. This allows domain experts to draft the codebook directly as labeled prompts and interpretable answer candidates. This human-in-the-loop process is guided by our interactive codebook design tool. We evaluate PR-ENT in several robustness checks: perturbing the event description and prompt template, restricting the vocabulary and removing contextual information.