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Oct 16

Comparison of biomedical relationship extraction methods and models for knowledge graph creation

Biomedical research is growing at such an exponential pace that scientists, researchers, and practitioners are no more able to cope with the amount of published literature in the domain. The knowledge presented in the literature needs to be systematized in such a way that claims and hypotheses can be easily found, accessed, and validated. Knowledge graphs can provide such a framework for semantic knowledge representation from literature. However, in order to build a knowledge graph, it is necessary to extract knowledge as relationships between biomedical entities and normalize both entities and relationship types. In this paper, we present and compare few rule-based and machine learning-based (Naive Bayes, Random Forests as examples of traditional machine learning methods and DistilBERT, PubMedBERT, T5 and SciFive-based models as examples of modern deep learning transformers) methods for scalable relationship extraction from biomedical literature, and for the integration into the knowledge graphs. We examine how resilient are these various methods to unbalanced and fairly small datasets. Our experiments show that transformer-based models handle well both small (due to pre-training on a large dataset) and unbalanced datasets. The best performing model was the PubMedBERT-based model fine-tuned on balanced data, with a reported F1-score of 0.92. DistilBERT-based model followed with F1-score of 0.89, performing faster and with lower resource requirements. BERT-based models performed better then T5-based generative models.

  • 2 authors
·
Jan 5, 2022

Beyond Efficiency: A Systematic Survey of Resource-Efficient Large Language Models

The burgeoning field of Large Language Models (LLMs), exemplified by sophisticated models like OpenAI's ChatGPT, represents a significant advancement in artificial intelligence. These models, however, bring forth substantial challenges in the high consumption of computational, memory, energy, and financial resources, especially in environments with limited resource capabilities. This survey aims to systematically address these challenges by reviewing a broad spectrum of techniques designed to enhance the resource efficiency of LLMs. We categorize methods based on their optimization focus: computational, memory, energy, financial, and network resources and their applicability across various stages of an LLM's lifecycle, including architecture design, pretraining, finetuning, and system design. Additionally, the survey introduces a nuanced categorization of resource efficiency techniques by their specific resource types, which uncovers the intricate relationships and mappings between various resources and corresponding optimization techniques. A standardized set of evaluation metrics and datasets is also presented to facilitate consistent and fair comparisons across different models and techniques. By offering a comprehensive overview of the current sota and identifying open research avenues, this survey serves as a foundational reference for researchers and practitioners, aiding them in developing more sustainable and efficient LLMs in a rapidly evolving landscape.

  • 13 authors
·
Dec 31, 2023

Malaysian English News Decoded: A Linguistic Resource for Named Entity and Relation Extraction

Standard English and Malaysian English exhibit notable differences, posing challenges for natural language processing (NLP) tasks on Malaysian English. Unfortunately, most of the existing datasets are mainly based on standard English and therefore inadequate for improving NLP tasks in Malaysian English. An experiment using state-of-the-art Named Entity Recognition (NER) solutions on Malaysian English news articles highlights that they cannot handle morphosyntactic variations in Malaysian English. To the best of our knowledge, there is no annotated dataset available to improvise the model. To address these issues, we constructed a Malaysian English News (MEN) dataset, which contains 200 news articles that are manually annotated with entities and relations. We then fine-tuned the spaCy NER tool and validated that having a dataset tailor-made for Malaysian English could improve the performance of NER in Malaysian English significantly. This paper presents our effort in the data acquisition, annotation methodology, and thorough analysis of the annotated dataset. To validate the quality of the annotation, inter-annotator agreement was used, followed by adjudication of disagreements by a subject matter expert. Upon completion of these tasks, we managed to develop a dataset with 6,061 entities and 3,268 relation instances. Finally, we discuss on spaCy fine-tuning setup and analysis on the NER performance. This unique dataset will contribute significantly to the advancement of NLP research in Malaysian English, allowing researchers to accelerate their progress, particularly in NER and relation extraction. The dataset and annotation guideline has been published on Github.

  • 4 authors
·
Feb 22, 2024

VLURes: Benchmarking VLM Visual and Linguistic Understanding in Low-Resource Languages

Vision Language Models (VLMs) are pivotal for advancing perception in intelligent agents. Yet, evaluation of VLMs remains limited to predominantly English-centric benchmarks in which the image-text pairs comprise short texts. To evaluate VLM fine-grained abilities, in four languages under long-text settings, we introduce a novel multilingual benchmark VLURes featuring eight vision-and-language tasks, and a pioneering unrelatedness task, to probe the fine-grained Visual and Linguistic Understanding capabilities of VLMs across English, Japanese, and low-resource languages, Swahili, and Urdu. Our datasets, curated from web resources in the target language, encompass ten diverse image categories and rich textual context, introducing valuable vision-language resources for Swahili and Urdu. By prompting VLMs to generate responses and rationales, evaluated automatically and by native speakers, we uncover performance disparities across languages and tasks critical to intelligent agents, such as object recognition, scene understanding, and relationship understanding. We conducted evaluations of ten VLMs with VLURes. The best performing model, GPT-4o, achieves an overall accuracy of 90.8% and lags human performance by 6.7%, though the gap is larger for open-source models. The gap highlights VLURes' critical role in developing intelligent agents to tackle multi-modal visual reasoning.

  • 5 authors
·
Oct 13, 2025

KH-FUNSD: A Hierarchical and Fine-Grained Layout Analysis Dataset for Low-Resource Khmer Business Document

Automated document layout analysis remains a major challenge for low-resource, non-Latin scripts. Khmer is a language spoken daily by over 17 million people in Cambodia, receiving little attention in the development of document AI tools. The lack of dedicated resources is particularly acute for business documents, which are critical for both public administration and private enterprise. To address this gap, we present KH-FUNSD, the first publicly available, hierarchically annotated dataset for Khmer form document understanding, including receipts, invoices, and quotations. Our annotation framework features a three-level design: (1) region detection that divides each document into core zones such as header, form field, and footer; (2) FUNSD-style annotation that distinguishes questions, answers, headers, and other key entities, together with their relationships; and (3) fine-grained classification that assigns specific semantic roles, such as field labels, values, headers, footers, and symbols. This multi-level approach supports both comprehensive layout analysis and precise information extraction. We benchmark several leading models, providing the first set of baseline results for Khmer business documents, and discuss the distinct challenges posed by non-Latin, low-resource scripts. The KH-FUNSD dataset and documentation will be available at URL.

  • 2 authors
·
Dec 3, 2025

SraVaani 1.0: Scaling Inclusive Speech Recognition for Indic Languages

India's linguistic landscape spans over 700 languages and thousands of dialects, yet the vast majority of automatic speech recognition (ASR) systems support only a small fraction of this diversity. We present SraVaani-1.0, a multilingual ASR model covering 65 Indian languages and dialects, many of which currently have no publicly available or competing ASR system. SraVaani-1.0 is built on a FastConformer architecture and trained from scratch through a three-stage pipeline.In the first stage, we perform self-supervised pretraining on 31,255 hours of unlabelled speech from the VAANI corpus using a contrastive learning objective. In the second stage, we introduce an audio-image representation alignment stage that leverages the paired images and speech available in the VAANI corpus. This multimodal alignment encourages the speech encoder to learn semantically richer representations by exploiting the relationship between visual context and spoken content, thereby improving downstream recognition, particularly for low-resource languages.In the final stage, the aligned encoder is fine-tuned end-to-end using a Hybrid Token-and-Duration Transducer (TDT)-CTC decoder on 31,263 hours of labelled multilingual Indian speech compiled from 24 public datasets spanning 65 languages and dialects. We evaluate SraVaani-1.0 against three state-of-the-art multilingual ASR systems across eight benchmarks. SraVaani-1.0 achieves the lowest word error rate (WER) on a large number of language-dataset pairs while remaining competitive with the best-performing systems on high-resource languages.Most importantly, it is the only open-source evaluated model that provides transcription capability for multiple low-resource and tribal Indian languages, which are assessed exclusively on the VAANI benchmark.

  • 7 authors
·
Aug 7

HODDI: A Dataset of High-Order Drug-Drug Interactions for Computational Pharmacovigilance

Drug-side effect research is vital for understanding adverse reactions arising in complex multi-drug therapies. However, the scarcity of higher-order datasets that capture the combinatorial effects of multiple drugs severely limits progress in this field. Existing resources such as TWOSIDES primarily focus on pairwise interactions. To fill this critical gap, we introduce HODDI, the first Higher-Order Drug-Drug Interaction Dataset, constructed from U.S. Food and Drug Administration (FDA) Adverse Event Reporting System (FAERS) records spanning the past decade, to advance computational pharmacovigilance. HODDI contains 109,744 records involving 2,506 unique drugs and 4,569 unique side effects, specifically curated to capture multi-drug interactions and their collective impact on adverse effects. Comprehensive statistical analyses demonstrate HODDI's extensive coverage and robust analytical metrics, making it a valuable resource for studying higher-order drug relationships. Evaluating HODDI with multiple models, we found that simple Multi-Layer Perceptron (MLP) can outperform graph models, while hypergraph models demonstrate superior performance in capturing complex multi-drug interactions, further validating HODDI's effectiveness. Our findings highlight the inherent value of higher-order information in drug-side effect prediction and position HODDI as a benchmark dataset for advancing research in pharmacovigilance, drug safety, and personalized medicine. The dataset and codes are available at https://github.com/TIML-Group/HODDI.

  • 6 authors
·
Feb 10, 2025

Detecting LLM Fact-conflicting Hallucinations Enhanced by Temporal-logic-based Reasoning

Large language models (LLMs) face the challenge of hallucinations -- outputs that seem coherent but are actually incorrect. A particularly damaging type is fact-conflicting hallucination (FCH), where generated content contradicts established facts. Addressing FCH presents three main challenges: 1) Automatically constructing and maintaining large-scale benchmark datasets is difficult and resource-intensive; 2) Generating complex and efficient test cases that the LLM has not been trained on -- especially those involving intricate temporal features -- is challenging, yet crucial for eliciting hallucinations; and 3) Validating the reasoning behind LLM outputs is inherently difficult, particularly with complex logical relationships, as it requires transparency in the model's decision-making process. This paper presents Drowzee, an innovative end-to-end metamorphic testing framework that utilizes temporal logic to identify fact-conflicting hallucinations (FCH) in large language models (LLMs). Drowzee builds a comprehensive factual knowledge base by crawling sources like Wikipedia and uses automated temporal-logic reasoning to convert this knowledge into a large, extensible set of test cases with ground truth answers. LLMs are tested using these cases through template-based prompts, which require them to generate both answers and reasoning steps. To validate the reasoning, we propose two semantic-aware oracles that compare the semantic structure of LLM outputs to the ground truths. Across nine LLMs in nine different knowledge domains, experimental results show that Drowzee effectively identifies rates of non-temporal-related hallucinations ranging from 24.7% to 59.8%, and rates of temporal-related hallucinations ranging from 16.7% to 39.2%.

  • 7 authors
·
Feb 18, 2025

ShareGPT4V: Improving Large Multi-Modal Models with Better Captions

In the realm of large multi-modal models (LMMs), efficient modality alignment is crucial yet often constrained by the scarcity of high-quality image-text data. To address this bottleneck, we introduce the ShareGPT4V dataset, a pioneering large-scale resource featuring 1.2 million highly descriptive captions, which surpasses existing datasets in diversity and information content, covering world knowledge, object properties, spatial relationships, and aesthetic evaluations. Specifically, ShareGPT4V originates from a curated 100K high-quality captions collected from advanced GPT4-Vision and has been expanded to 1.2M with a superb caption model trained on this subset. ShareGPT4V first demonstrates its effectiveness for the Supervised Fine-Tuning (SFT) phase, by substituting an equivalent quantity of detailed captions in existing SFT datasets with a subset of our high-quality captions, significantly enhancing the LMMs like LLaVA-7B, LLaVA-1.5-13B, and Qwen-VL-Chat-7B on the MME and MMBench benchmarks, with respective gains of 222.8/22.0/22.3 and 2.7/1.3/1.5. We further incorporate ShareGPT4V data into both the pre-training and SFT phases, obtaining ShareGPT4V-7B, a superior LMM based on a simple architecture that has remarkable performance across a majority of the multi-modal benchmarks. This project is available at https://ShareGPT4V.github.io to serve as a pivotal resource for advancing the LMMs community.

  • 8 authors
·
Nov 21, 2023 2

Serverless Cold Starts and Where to Find Them

This paper releases and analyzes a month-long trace of 85 billion user requests and 11.9 million cold starts from Huawei's serverless cloud platform. Our analysis spans workloads from five data centers. We focus on cold starts and provide a comprehensive examination of the underlying factors influencing the number and duration of cold starts. These factors include trigger types, request synchronicity, runtime languages, and function resource allocations. We investigate components of cold starts, including pod allocation time, code and dependency deployment time, and scheduling delays, and examine their relationships with runtime languages, trigger types, and resource allocation. We introduce pod utility ratio to measure the pod's useful lifetime relative to its cold start time, giving a more complete picture of cold starts, and see that some pods with long cold start times have longer useful lifetimes. Our findings reveal the complexity and multifaceted origins of the number, duration, and characteristics of cold starts, driven by differences in trigger types, runtime languages, and function resource allocations. For example, cold starts in Region 1 take up to 7 seconds, dominated by dependency deployment time and scheduling. In Region 2, cold starts take up to 3 seconds and are dominated by pod allocation time. Based on this, we identify opportunities to reduce the number and duration of cold starts using strategies for multi-region scheduling. Finally, we suggest directions for future research to address these challenges and enhance the performance of serverless cloud platforms. Our datasets and code are available here https://github.com/sir-lab/data-release

  • 8 authors
·
Oct 8, 2024

Benefits of Resource Strategy for Sustainable Materials Research and Development

Material and product life cycles are based on complex value chains of technology-specific elements. Resource strategy aspects of essential and strategic raw materials have a direct impact on applications of new functionalized materials or the development of novel products. Thus, an urgent challenge of modern materials science is to obtain information about the supply risk and environmental aspects of resource utilization, especially at an early stage of basic research. Combining the fields of materials science, industrial engineering and resource strategy enables a multidisciplinary research approach to identify specific risks within the value chain, aggregated as the so-called resource criticality. Here, we demonstrate a step-by-step criticality assessment in the sector of basic materials research for multifunctional hexagonal manganite YMnO3, which can be a candidate for future electronic systems. Raw material restrictions can be quantitatively identified, even at such an early stage of materials research, from eleven long-term indicators including our new developed Sector Competition Index. This approach for resource strategy for modern material science integrates two objective targets: reduced supply risk and enhanced environmental sustainability of new functionalized materials, showing drawbacks but also benefits towards a sustainable materials research and development.

  • 7 authors
·
Mar 6, 2017

Resource supply dynamics control stability and chaos in complex ecosystems

Ecological interactions are often mediated by feedbacks between organisms and their resource environments. Yet, how resource supply dynamics dictate collective dynamical phases of an ecosystem remains unclear. Here, we analyse a generalised consumer--resource model with non-reciprocal interactions to demonstrate that self-renewing versus externally-supplied resources yield fundamentally different dynamical phase diagrams. As interactions become increasingly non-reciprocal, ecosystems relying on self-renewing resources transition from stable dynamics to chaos and ultimately to infeasibility. By contrast, ecosystems with externally-supplied resources remain stable over a broader parameter range and transition to infeasibility without experiencing an intervening chaotic phase. Using the cavity method, we derive a unified stability condition applicable to a broad class of resource supply functions, explaining why externally-supplied resources can expand the stable region. We show that stability hinges crucially on the susceptibility of resources to perturbations, which depends strongly on their supply. Further, we show that external resource supply suppresses chaos in the unstable region by drastically reducing the susceptibility of resources closest to extinction. Our findings demonstrate that resource dynamics fundamentally reshape the accessible dynamical behaviours of an ecosystem, with implications for interpreting microbial community experiments.

  • 3 authors
·
Aug 30

A game-theoretic analysis of networked system control for common-pool resource management using multi-agent reinforcement learning

Multi-agent reinforcement learning has recently shown great promise as an approach to networked system control. Arguably, one of the most difficult and important tasks for which large scale networked system control is applicable is common-pool resource management. Crucial common-pool resources include arable land, fresh water, wetlands, wildlife, fish stock, forests and the atmosphere, of which proper management is related to some of society's greatest challenges such as food security, inequality and climate change. Here we take inspiration from a recent research program investigating the game-theoretic incentives of humans in social dilemma situations such as the well-known tragedy of the commons. However, instead of focusing on biologically evolved human-like agents, our concern is rather to better understand the learning and operating behaviour of engineered networked systems comprising general-purpose reinforcement learning agents, subject only to nonbiological constraints such as memory, computation and communication bandwidth. Harnessing tools from empirical game-theoretic analysis, we analyse the differences in resulting solution concepts that stem from employing different information structures in the design of networked multi-agent systems. These information structures pertain to the type of information shared between agents as well as the employed communication protocol and network topology. Our analysis contributes new insights into the consequences associated with certain design choices and provides an additional dimension of comparison between systems beyond efficiency, robustness, scalability and mean control performance.

  • 9 authors
·
Oct 15, 2020