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Apr 14

Author Once, Publish Everywhere: Portable Metadata Authoring with the CEDAR Embeddable Editor

High-quality, "rich" metadata are essential for making research data findable, interoperable, and reusable. The Center for Expanded Data Annotation and Retrieval (CEDAR) has long addressed this need by providing tools to design machine-actionable metadata templates that encode community standards in a computable form. To make these capabilities more accessible within real-world research workflows, we have developed the CEDAR Embeddable Editor (CEE)-a lightweight, interoperable Web Component that brings structured, standards-based metadata authoring directly into third-party platforms. The CEE dynamically renders metadata forms from machine-actionable templates and produces semantically rich metadata in JSON-LD format. It supports ontology-based value selection via the BioPortal ontology repository, and it includes external authority resolution for persistent identifiers such as ORCIDs for individuals and RORs for research organizations. Crucially, the CEE requires no custom user-interface development, allowing deployment across diverse platforms. The CEE has been successfully integrated into generalist scientific data repositories such as Dryad and the Open Science Framework, demonstrating its ability to support discipline-specific metadata creation. By supporting the embedding of metadata authoring within existing research environments, the CEE can facilitate the adoption of community standards and help improve metadata quality across scientific disciplines.

  • 6 authors
·
Jul 16, 2025

Meta Prompting for AGI Systems

This paper presents an in-depth exploration of Meta Prompting, a novel technique that revolutionizes the way large language models (LLMs), multi-modal foundation models, and AI systems approach problem-solving and data interpretation. Meta Prompting, rooted in type theory and category theory, prioritizes the structure and syntax of information, providing a unique framework that transcends traditional content-focused methods. We delve into the formal definitions of Meta Prompting, contrasting it with Few-Shot Prompting, and highlight its applicability and superiority in various AI applications. Key to this exploration is the expansion of Meta Prompting into the realm of complex reasoning. Here, we demonstrate how this technique adeptly breaks down intricate problems into manageable sub-problems, facilitating a step-by-step, detailed approach to problem-solving. This method proves especially advantageous in terms of token efficiency and offering a fair comparison in problem-solving scenarios, standing out against few-shot example approaches. Furthermore, the paper breaks new ground by extending Meta Prompting into multi-modal foundation model settings. This extension addresses the integration of diverse data types, such as images, audio, and video, within the structured framework of Meta Prompting, highlighting both the challenges and the vast potential of this approach in handling complex, multi-faceted data (The code is available at https://github.com/meta-prompting/meta-prompting).

  • 1 authors
·
Nov 19, 2023 1

Metasql: A Generate-then-Rank Framework for Natural Language to SQL Translation

The Natural Language Interface to Databases (NLIDB) empowers non-technical users with database access through intuitive natural language (NL) interactions. Advanced approaches, utilizing neural sequence-to-sequence models or large-scale language models, typically employ auto-regressive decoding to generate unique SQL queries sequentially. While these translation models have greatly improved the overall translation accuracy, surpassing 70% on NLIDB benchmarks, the use of auto-regressive decoding to generate single SQL queries may result in sub-optimal outputs, potentially leading to erroneous translations. In this paper, we propose Metasql, a unified generate-then-rank framework that can be flexibly incorporated with existing NLIDBs to consistently improve their translation accuracy. Metasql introduces query metadata to control the generation of better SQL query candidates and uses learning-to-rank algorithms to retrieve globally optimized queries. Specifically, Metasql first breaks down the meaning of the given NL query into a set of possible query metadata, representing the basic concepts of the semantics. These metadata are then used as language constraints to steer the underlying translation model toward generating a set of candidate SQL queries. Finally, Metasql ranks the candidates to identify the best matching one for the given NL query. Extensive experiments are performed to study Metasql on two public NLIDB benchmarks. The results show that the performance of the translation models can be effectively improved using Metasql.

  • 7 authors
·
Feb 26, 2024

Science Hierarchography: Hierarchical Organization of Science Literature

Scientific knowledge is growing rapidly, making it challenging to track progress and high-level conceptual links across broad disciplines. While existing tools like citation networks and search engines make it easy to access a few related papers, they fundamentally lack the flexible abstraction needed to represent the density of activity in various scientific subfields. We motivate SCIENCE HIERARCHOGRAPHY, the goal of organizing scientific literature into a high-quality hierarchical structure that allows for the categorization of scientific work across varying levels of abstraction, from very broad fields to very specific studies. Such a representation can provide insights into which fields are well-explored and which are under-explored. To achieve the goals of SCIENCE HIERARCHOGRAPHY, we develop a range of algorithms. Our primary approach combines fast embedding-based clustering with LLM-based prompting to balance the computational efficiency of embedding methods with the semantic precision offered by LLM prompting. We demonstrate that this approach offers the best trade-off between quality and speed compared to methods that heavily rely on LLM prompting, such as iterative tree construction with LLMs. To better reflect the interdisciplinary and multifaceted nature of research papers, our hierarchy captures multiple dimensions of categorization beyond simple topic labels. We evaluate the utility of our framework by assessing how effectively an LLM-based agent can locate target papers using the hierarchy. Results show that this structured approach enhances interpretability, supports trend discovery, and offers an alternative pathway for exploring scientific literature beyond traditional search methods. Code, data and demo: https://github.com/JHU-CLSP/science-hierarchography{https://github.com/JHU-CLSP/science-hierarchography}

  • 4 authors
·
Apr 18, 2025

Ragnarök: A Reusable RAG Framework and Baselines for TREC 2024 Retrieval-Augmented Generation Track

Did you try out the new Bing Search? Or maybe you fiddled around with Google AI~Overviews? These might sound familiar because the modern-day search stack has recently evolved to include retrieval-augmented generation (RAG) systems. They allow searching and incorporating real-time data into large language models (LLMs) to provide a well-informed, attributed, concise summary in contrast to the traditional search paradigm that relies on displaying a ranked list of documents. Therefore, given these recent advancements, it is crucial to have an arena to build, test, visualize, and systematically evaluate RAG-based search systems. With this in mind, we propose the TREC 2024 RAG Track to foster innovation in evaluating RAG systems. In our work, we lay out the steps we've made towards making this track a reality -- we describe the details of our reusable framework, Ragnar\"ok, explain the curation of the new MS MARCO V2.1 collection choice, release the development topics for the track, and standardize the I/O definitions which assist the end user. Next, using Ragnar\"ok, we identify and provide key industrial baselines such as OpenAI's GPT-4o or Cohere's Command R+. Further, we introduce a web-based user interface for an interactive arena allowing benchmarking pairwise RAG systems by crowdsourcing. We open-source our Ragnar\"ok framework and baselines to achieve a unified standard for future RAG systems.

  • 8 authors
·
Jun 24, 2024

HoneyBee: Progressive Instruction Finetuning of Large Language Models for Materials Science

We propose an instruction-based process for trustworthy data curation in materials science (MatSci-Instruct), which we then apply to finetune a LLaMa-based language model targeted for materials science (HoneyBee). MatSci-Instruct helps alleviate the scarcity of relevant, high-quality materials science textual data available in the open literature, and HoneyBee is the first billion-parameter language model specialized to materials science. In MatSci-Instruct we improve the trustworthiness of generated data by prompting multiple commercially available large language models for generation with an Instructor module (e.g. Chat-GPT) and verification from an independent Verifier module (e.g. Claude). Using MatSci-Instruct, we construct a dataset of multiple tasks and measure the quality of our dataset along multiple dimensions, including accuracy against known facts, relevance to materials science, as well as completeness and reasonableness of the data. Moreover, we iteratively generate more targeted instructions and instruction-data in a finetuning-evaluation-feedback loop leading to progressively better performance for our finetuned HoneyBee models. Our evaluation on the MatSci-NLP benchmark shows HoneyBee's outperformance of existing language models on materials science tasks and iterative improvement in successive stages of instruction-data refinement. We study the quality of HoneyBee's language modeling through automatic evaluation and analyze case studies to further understand the model's capabilities and limitations. Our code and relevant datasets are publicly available at https://github.com/BangLab-UdeM-Mila/NLP4MatSci-HoneyBee.

  • 4 authors
·
Oct 12, 2023

Retrieval-Augmented Meta Learning for Low-Resource Text Classification

Meta learning have achieved promising performance in low-resource text classification which aims to identify target classes with knowledge transferred from source classes with sets of small tasks named episodes. However, due to the limited training data in the meta-learning scenario and the inherent properties of parameterized neural networks, poor generalization performance has become a pressing problem that needs to be addressed. To deal with this issue, we propose a meta-learning based method called Retrieval-Augmented Meta Learning(RAML). It not only uses parameterization for inference but also retrieves non-parametric knowledge from an external corpus to make inferences, which greatly alleviates the problem of poor generalization performance caused by the lack of diverse training data in meta-learning. This method differs from previous models that solely rely on parameters, as it explicitly emphasizes the importance of non-parametric knowledge, aiming to strike a balance between parameterized neural networks and non-parametric knowledge. The model is required to determine which knowledge to access and utilize during inference. Additionally, our multi-view passages fusion network module can effectively and efficiently integrate the retrieved information into low-resource classification task. The extensive experiments demonstrate that RAML significantly outperforms current SOTA low-resource text classification models.

  • 7 authors
·
Sep 10, 2023

New Methods for Metadata Extraction from Scientific Literature

Within the past few decades we have witnessed digital revolution, which moved scholarly communication to electronic media and also resulted in a substantial increase in its volume. Nowadays keeping track with the latest scientific achievements poses a major challenge for the researchers. Scientific information overload is a severe problem that slows down scholarly communication and knowledge propagation across the academia. Modern research infrastructures facilitate studying scientific literature by providing intelligent search tools, proposing similar and related documents, visualizing citation and author networks, assessing the quality and impact of the articles, and so on. In order to provide such high quality services the system requires the access not only to the text content of stored documents, but also to their machine-readable metadata. Since in practice good quality metadata is not always available, there is a strong demand for a reliable automatic method of extracting machine-readable metadata directly from source documents. This research addresses these problems by proposing an automatic, accurate and flexible algorithm for extracting wide range of metadata directly from scientific articles in born-digital form. Extracted information includes basic document metadata, structured full text and bibliography section. Designed as a universal solution, proposed algorithm is able to handle a vast variety of publication layouts with high precision and thus is well-suited for analyzing heterogeneous document collections. This was achieved by employing supervised and unsupervised machine-learning algorithms trained on large, diverse datasets. The evaluation we conducted showed good performance of proposed metadata extraction algorithm. The comparison with other similar solutions also proved our algorithm performs better than competition for most metadata types.

  • 1 authors
·
Oct 27, 2017

An Automatic Approach for Generating Rich, Linked Geo-Metadata from Historical Map Images

Historical maps contain detailed geographic information difficult to find elsewhere covering long-periods of time (e.g., 125 years for the historical topographic maps in the US). However, these maps typically exist as scanned images without searchable metadata. Existing approaches making historical maps searchable rely on tedious manual work (including crowd-sourcing) to generate the metadata (e.g., geolocations and keywords). Optical character recognition (OCR) software could alleviate the required manual work, but the recognition results are individual words instead of location phrases (e.g., "Black" and "Mountain" vs. "Black Mountain"). This paper presents an end-to-end approach to address the real-world problem of finding and indexing historical map images. This approach automatically processes historical map images to extract their text content and generates a set of metadata that is linked to large external geospatial knowledge bases. The linked metadata in the RDF (Resource Description Framework) format support complex queries for finding and indexing historical maps, such as retrieving all historical maps covering mountain peaks higher than 1,000 meters in California. We have implemented the approach in a system called mapKurator. We have evaluated mapKurator using historical maps from several sources with various map styles, scales, and coverage. Our results show significant improvement over the state-of-the-art methods. The code has been made publicly available as modules of the Kartta Labs project at https://github.com/kartta-labs/Project.

  • 7 authors
·
Dec 2, 2021

Meta-Transformer: A Unified Framework for Multimodal Learning

Multimodal learning aims to build models that can process and relate information from multiple modalities. Despite years of development in this field, it still remains challenging to design a unified network for processing various modalities (e.g. natural language, 2D images, 3D point clouds, audio, video, time series, tabular data) due to the inherent gaps among them. In this work, we propose a framework, named Meta-Transformer, that leverages a frozen encoder to perform multimodal perception without any paired multimodal training data. In Meta-Transformer, the raw input data from various modalities are mapped into a shared token space, allowing a subsequent encoder with frozen parameters to extract high-level semantic features of the input data. Composed of three main components: a unified data tokenizer, a modality-shared encoder, and task-specific heads for downstream tasks, Meta-Transformer is the first framework to perform unified learning across 12 modalities with unpaired data. Experiments on different benchmarks reveal that Meta-Transformer can handle a wide range of tasks including fundamental perception (text, image, point cloud, audio, video), practical application (X-Ray, infrared, hyperspectral, and IMU), and data mining (graph, tabular, and time-series). Meta-Transformer indicates a promising future for developing unified multimodal intelligence with transformers. Code will be available at https://github.com/invictus717/MetaTransformer

  • 7 authors
·
Jul 20, 2023 3

MetaSynth: Meta-Prompting-Driven Agentic Scaffolds for Diverse Synthetic Data Generation

Recent smaller language models such Phi-3.5 and Phi-4 rely on synthetic data generated using larger Language models. Questions remain about leveraging synthetic data for other use cases, such as adapting LLMs to specific domains. A key limitation of synthetic data is low diversity, which negatively impacts its downstream applicability for improving other models. To address this, we propose MetaSynth, a method for generating synthetic data that enhances diversity through meta-prompting, where a language model orchestrates multiple "expert" LLM agents to collaboratively generate data. Using only 25 million tokens of synthetic data generated with MetaSynth, we successfully adapt a well-trained LLM (Mistral-7B-v0.3) to two specialized domains-Finance and Biomedicine-without compromising the capabilities of the resulting model in general tasks. In addition, we evaluate the diversity of our synthetic data using seven automated metrics, and find that it approaches the diversity of LLM pre-training corpora. Continually pre-training Mistral-7B-v0.3 with MetaSynth notably outperforms the base LLM, showing improvements of up to 4.08% in Finance and 13.75% in Biomedicine. The same model shows degraded performance when trained on data generated using a template prompt, even when the template includes prior generations and varying In-Context exemplars of real data. Our findings suggest that a few million tokens of diverse synthetic data without mixing any real data, is sufficient for effective domain adaptation when using MetaSynth.

  • 5 authors
·
Apr 16, 2025 2

Meta-rater: A Multi-dimensional Data Selection Method for Pre-training Language Models

The composition of pre-training datasets for large language models (LLMs) remains largely undisclosed, hindering transparency and efforts to optimize data quality, a critical driver of model performance. Current data selection methods, such as natural language quality assessments, diversity-based filters, and classifier-based approaches, are limited by single-dimensional evaluation or redundancy-focused strategies. To address these gaps, we propose four dimensions to evaluate data quality: professionalism, readability, reasoning, and cleanliness. We further introduce Meta-rater,a multi-dimensional data selection method that integrates these dimensions with existing quality metrics through learned optimal weightings. Meta-rater employs proxy models to train a regression model that predicts validation loss, enabling the identification of optimal combinations of quality scores. Experiments demonstrate that Meta-rater doubles convergence speed for 1.3B parameter models and improves downstream task performance by 3.23, with advantages that scale to models as large as 7.2B parameters. Our work establishes that holistic, multi-dimensional quality integration significantly outperforms conventional single-dimension approaches, offering a scalable paradigm for enhancing pre-training efficiency and model capability. To advance future research, we release scripts, data, and models at https://github.com/opendatalab/Meta-rater.

  • 10 authors
·
Apr 19, 2025

MetaAgent: Toward Self-Evolving Agent via Tool Meta-Learning

In this work, we propose MetaAgent, an agentic paradigm inspired by the principle of learning-by-doing, where expertise is developed through hands-on practice and continual self-improvement. MetaAgent starts with a minimal workflow, equipped only with basic reasoning and adaptive help-seeking abilities. When a knowledge gap is encountered, MetaAgent generates natural language help requests, which are routed to the most suitable external tool by a dedicated tool router. As MetaAgent solves tasks, it continually conducts self-reflection and answer verification, distilling actionable experience into concise texts that are dynamically incorporated into future task contexts. Besides, MetaAgent autonomously builds in-house tools and a persistent knowledge base by organizing its tool-use history, further enhancing its ability to retrieve and integrate relevant information We term this continual, data-driven process as meta tool learning, through which MetaAgent incrementally refines its reasoning and tool-use strategies, without changing model parameters or requiring further post-training. Evaluated on challenging knowledge discovery benchmarks, including GAIA, WebWalkerQA, and BrowseCamp, MetaAgent consistently outperforms workflow-based baselines and matches or exceeds end-to-end trained agents, demonstrating the promise of self-evolving agentic systems for robust, general-purpose knowledge discovery. We provide our source codes in https://github.com/qhjqhj00/MetaAgent.

  • 2 authors
·
Jul 31, 2025

Meta-ticket: Finding optimal subnetworks for few-shot learning within randomly initialized neural networks

Few-shot learning for neural networks (NNs) is an important problem that aims to train NNs with a few data. The main challenge is how to avoid overfitting since over-parameterized NNs can easily overfit to such small dataset. Previous work (e.g. MAML by Finn et al. 2017) tackles this challenge by meta-learning, which learns how to learn from a few data by using various tasks. On the other hand, one conventional approach to avoid overfitting is restricting hypothesis spaces by endowing sparse NN structures like convolution layers in computer vision. However, although such manually-designed sparse structures are sample-efficient for sufficiently large datasets, they are still insufficient for few-shot learning. Then the following questions naturally arise: (1) Can we find sparse structures effective for few-shot learning by meta-learning? (2) What benefits will it bring in terms of meta-generalization? In this work, we propose a novel meta-learning approach, called Meta-ticket, to find optimal sparse subnetworks for few-shot learning within randomly initialized NNs. We empirically validated that Meta-ticket successfully discover sparse subnetworks that can learn specialized features for each given task. Due to this task-wise adaptation ability, Meta-ticket achieves superior meta-generalization compared to MAML-based methods especially with large NNs. The code is available at: https://github.com/dchiji-ntt/meta-ticket

  • 4 authors
·
May 31, 2022

MetamatBench: Integrating Heterogeneous Data, Computational Tools, and Visual Interface for Metamaterial Discovery

Metamaterials, engineered materials with architected structures across multiple length scales, offer unprecedented and tunable mechanical properties that surpass those of conventional materials. However, leveraging advanced machine learning (ML) for metamaterial discovery is hindered by three fundamental challenges: (C1) Data Heterogeneity Challenge arises from heterogeneous data sources, heterogeneous composition scales, and heterogeneous structure categories; (C2) Model Complexity Challenge stems from the intricate geometric constraints of ML models, which complicate their adaptation to metamaterial structures; and (C3) Human-AI Collaboration Challenge comes from the "dual black-box'' nature of sophisticated ML models and the need for intuitive user interfaces. To tackle these challenges, we introduce a unified framework, named MetamatBench, that operates on three levels. (1) At the data level, we integrate and standardize 5 heterogeneous, multi-modal metamaterial datasets. (2) The ML level provides a comprehensive toolkit that adapts 17 state-of-the-art ML methods for metamaterial discovery. It also includes a comprehensive evaluation suite with 12 novel performance metrics with finite element-based assessments to ensure accurate and reliable model validation. (3) The user level features a visual-interactive interface that bridges the gap between complex ML techniques and non-ML researchers, advancing property prediction and inverse design of metamaterials for research and applications. MetamatBench offers a unified platform deployed at http://zhoulab-1.cs.vt.edu:5550 that enables machine learning researchers and practitioners to develop and evaluate new methodologies in metamaterial discovery. For accessibility and reproducibility, we open-source our benchmark and the codebase at https://github.com/cjpcool/Metamaterial-Benchmark.

  • 13 authors
·
May 8, 2025

A Hierarchical Bayesian Model for Deep Few-Shot Meta Learning

We propose a novel hierarchical Bayesian model for learning with a large (possibly infinite) number of tasks/episodes, which suits well the few-shot meta learning problem. We consider episode-wise random variables to model episode-specific target generative processes, where these local random variables are governed by a higher-level global random variate. The global variable helps memorize the important information from historic episodes while controlling how much the model needs to be adapted to new episodes in a principled Bayesian manner. Within our model framework, the prediction on a novel episode/task can be seen as a Bayesian inference problem. However, a main obstacle in learning with a large/infinite number of local random variables in online nature, is that one is not allowed to store the posterior distribution of the current local random variable for frequent future updates, typical in conventional variational inference. We need to be able to treat each local variable as a one-time iterate in the optimization. We propose a Normal-Inverse-Wishart model, for which we show that this one-time iterate optimization becomes feasible due to the approximate closed-form solutions for the local posterior distributions. The resulting algorithm is more attractive than the MAML in that it is not required to maintain computational graphs for the whole gradient optimization steps per episode. Our approach is also different from existing Bayesian meta learning methods in that unlike dealing with a single random variable for the whole episodes, our approach has a hierarchical structure that allows one-time episodic optimization, desirable for principled Bayesian learning with many/infinite tasks. The code is available at https://github.com/minyoungkim21/niwmeta.

  • 2 authors
·
Jun 16, 2023

Meta-training with Demonstration Retrieval for Efficient Few-shot Learning

Large language models show impressive results on few-shot NLP tasks. However, these models are memory and computation-intensive. Meta-training allows one to leverage smaller models for few-shot generalization in a domain-general and task-agnostic manner; however, these methods alone results in models that may not have sufficient parameterization or knowledge to adapt quickly to a large variety of tasks. To overcome this issue, we propose meta-training with demonstration retrieval, where we use a dense passage retriever to retrieve semantically similar labeled demonstrations to each example for more varied supervision. By separating external knowledge from model parameters, we can use meta-training to train parameter-efficient models that generalize well on a larger variety of tasks. We construct a meta-training set from UnifiedQA and CrossFit, and propose a demonstration bank based on UnifiedQA tasks. To our knowledge, our work is the first to combine retrieval with meta-training, to use DPR models to retrieve demonstrations, and to leverage demonstrations from many tasks simultaneously, rather than randomly sampling demonstrations from the training set of the target task. Our approach outperforms a variety of targeted parameter-efficient and retrieval-augmented few-shot methods on QA, NLI, and text classification tasks (including SQuAD, QNLI, and TREC). Our approach can be meta-trained and fine-tuned quickly on a single GPU.

  • 5 authors
·
Jun 30, 2023

MetaShift: A Dataset of Datasets for Evaluating Contextual Distribution Shifts and Training Conflicts

Understanding the performance of machine learning models across diverse data distributions is critically important for reliable applications. Motivated by this, there is a growing focus on curating benchmark datasets that capture distribution shifts. While valuable, the existing benchmarks are limited in that many of them only contain a small number of shifts and they lack systematic annotation about what is different across different shifts. We present MetaShift--a collection of 12,868 sets of natural images across 410 classes--to address this challenge. We leverage the natural heterogeneity of Visual Genome and its annotations to construct MetaShift. The key construction idea is to cluster images using its metadata, which provides context for each image (e.g. "cats with cars" or "cats in bathroom") that represent distinct data distributions. MetaShift has two important benefits: first, it contains orders of magnitude more natural data shifts than previously available. Second, it provides explicit explanations of what is unique about each of its data sets and a distance score that measures the amount of distribution shift between any two of its data sets. We demonstrate the utility of MetaShift in benchmarking several recent proposals for training models to be robust to data shifts. We find that the simple empirical risk minimization performs the best when shifts are moderate and no method had a systematic advantage for large shifts. We also show how MetaShift can help to visualize conflicts between data subsets during model training.

  • 2 authors
·
Feb 14, 2022

MetaFormer: A Unified Meta Framework for Fine-Grained Recognition

Fine-Grained Visual Classification(FGVC) is the task that requires recognizing the objects belonging to multiple subordinate categories of a super-category. Recent state-of-the-art methods usually design sophisticated learning pipelines to tackle this task. However, visual information alone is often not sufficient to accurately differentiate between fine-grained visual categories. Nowadays, the meta-information (e.g., spatio-temporal prior, attribute, and text description) usually appears along with the images. This inspires us to ask the question: Is it possible to use a unified and simple framework to utilize various meta-information to assist in fine-grained identification? To answer this problem, we explore a unified and strong meta-framework(MetaFormer) for fine-grained visual classification. In practice, MetaFormer provides a simple yet effective approach to address the joint learning of vision and various meta-information. Moreover, MetaFormer also provides a strong baseline for FGVC without bells and whistles. Extensive experiments demonstrate that MetaFormer can effectively use various meta-information to improve the performance of fine-grained recognition. In a fair comparison, MetaFormer can outperform the current SotA approaches with only vision information on the iNaturalist2017 and iNaturalist2018 datasets. Adding meta-information, MetaFormer can exceed the current SotA approaches by 5.9% and 5.3%, respectively. Moreover, MetaFormer can achieve 92.3% and 92.7% on CUB-200-2011 and NABirds, which significantly outperforms the SotA approaches. The source code and pre-trained models are released athttps://github.com/dqshuai/MetaFormer.

  • 5 authors
·
Mar 5, 2022

METAGENE-1: Metagenomic Foundation Model for Pandemic Monitoring

We pretrain METAGENE-1, a 7-billion-parameter autoregressive transformer model, which we refer to as a metagenomic foundation model, on a novel corpus of diverse metagenomic DNA and RNA sequences comprising over 1.5 trillion base pairs. This dataset is sourced from a large collection of human wastewater samples, processed and sequenced using deep metagenomic (next-generation) sequencing methods. Unlike genomic models that focus on individual genomes or curated sets of specific species, the aim of METAGENE-1 is to capture the full distribution of genomic information present within this wastewater, to aid in tasks relevant to pandemic monitoring and pathogen detection. We carry out byte-pair encoding (BPE) tokenization on our dataset, tailored for metagenomic sequences, and then pretrain our model. In this paper, we first detail the pretraining dataset, tokenization strategy, and model architecture, highlighting the considerations and design choices that enable the effective modeling of metagenomic data. We then show results of pretraining this model on our metagenomic dataset, providing details about our losses, system metrics, and training stability over the course of pretraining. Finally, we demonstrate the performance of METAGENE-1, which achieves state-of-the-art results on a set of genomic benchmarks and new evaluations focused on human-pathogen detection and genomic sequence embedding, showcasing its potential for public health applications in pandemic monitoring, biosurveillance, and early detection of emerging health threats.

  • 7 authors
·
Jan 3, 2025 2

A large collection of bioinformatics question-query pairs over federated knowledge graphs: methodology and applications

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.

  • 17 authors
·
Oct 8, 2024

Matching Table Metadata with Business Glossaries Using Large Language Models

Enterprises often own large collections of structured data in the form of large databases or an enterprise data lake. Such data collections come with limited metadata and strict access policies that could limit access to the data contents and, therefore, limit the application of classic retrieval and analysis solutions. As a result, there is a need for solutions that can effectively utilize the available metadata. In this paper, we study the problem of matching table metadata to a business glossary containing data labels and descriptions. The resulting matching enables the use of an available or curated business glossary for retrieval and analysis without or before requesting access to the data contents. One solution to this problem is to use manually-defined rules or similarity measures on column names and glossary descriptions (or their vector embeddings) to find the closest match. However, such approaches need to be tuned through manual labeling and cannot handle many business glossaries that contain a combination of simple as well as complex and long descriptions. In this work, we leverage the power of large language models (LLMs) to design generic matching methods that do not require manual tuning and can identify complex relations between column names and glossaries. We propose methods that utilize LLMs in two ways: a) by generating additional context for column names that can aid with matching b) by using LLMs to directly infer if there is a relation between column names and glossary descriptions. Our preliminary experimental results show the effectiveness of our proposed methods.

  • 6 authors
·
Sep 7, 2023 2

GUIDE: Graphical User Interface Data for Execution

In this paper, we introduce GUIDE, a novel dataset tailored for the advancement of Multimodal Large Language Model (MLLM) applications, particularly focusing on Robotic Process Automation (RPA) use cases. Our dataset encompasses diverse data from various websites including Apollo(62.67\%), Gmail(3.43\%), Calendar(10.98\%) and Canva(22.92\%). Each data entry includes an image, a task description, the last action taken, CoT and the next action to be performed along with grounding information of where the action needs to be executed. The data is collected using our in-house advanced annotation tool NEXTAG (Next Action Grounding and Annotation Tool). The data is adapted for multiple OS, browsers and display types. It is collected by multiple annotators to capture the variation of design and the way person uses a website. Through this dataset, we aim to facilitate research and development in the realm of LLMs for graphical user interfaces, particularly in tasks related to RPA. The dataset's multi-platform nature and coverage of diverse websites enable the exploration of cross-interface capabilities in automation tasks. We believe that our dataset will serve as a valuable resource for advancing the capabilities of multi-platform LLMs in practical applications, fostering innovation in the field of automation and natural language understanding. Using GUIDE, we build V-Zen, the first RPA model to automate multiple websites using our in-House Automation tool AUTONODE

  • 5 authors
·
Apr 9, 2024

A Literature Review of Literature Reviews in Pattern Analysis and Machine Intelligence

By consolidating scattered knowledge, the literature review provides a comprehensive understanding of the investigated topic. However, reading, conducting, or peer-reviewing review papers generally demands a significant investment of time and effort from researchers. To improve efficiency, this paper aims to provide a thorough review of reviews in the PAMI field from diverse perspectives. First, this paper proposes several article-level, field-normalized, and large language model-empowered bibliometric indicators to evaluate reviews. To facilitate this, a meta-data database dubbed RiPAMI, and a topic dataset are constructed. Second, based on these indicators, the study presents comparative analyses of representative reviews, unveiling the characteristics of publications across various fields, periods, and journals. The newly emerging AI-generated literature reviews are also appraised, and the observed differences suggest that most AI-generated reviews still lag behind human-authored reviews in multiple aspects. Third, we briefly provide a subjective evaluation of representative PAMI reviews and introduce a paper structure-based typology of literature reviews. This typology may improve the clarity and effectiveness for scholars in reading and writing reviews, while also serving as a guide for AI systems in generating well-organized reviews. Finally, this work offers insights into the current challenges of literature reviews and envisions future directions for their development.

  • 5 authors
·
Feb 20, 2024

Automated Design of Agentic Systems

Researchers are investing substantial effort in developing powerful general-purpose agents, wherein Foundation Models are used as modules within agentic systems (e.g. Chain-of-Thought, Self-Reflection, Toolformer). However, the history of machine learning teaches us that hand-designed solutions are eventually replaced by learned solutions. We formulate a new research area, Automated Design of Agentic Systems (ADAS), which aims to automatically create powerful agentic system designs, including inventing novel building blocks and/or combining them in new ways. We further demonstrate that there is an unexplored yet promising approach within ADAS where agents can be defined in code and new agents can be automatically discovered by a meta agent programming ever better ones in code. Given that programming languages are Turing Complete, this approach theoretically enables the learning of any possible agentic system: including novel prompts, tool use, control flows, and combinations thereof. We present a simple yet effective algorithm named Meta Agent Search to demonstrate this idea, where a meta agent iteratively programs interesting new agents based on an ever-growing archive of previous discoveries. Through extensive experiments across multiple domains including coding, science, and math, we show that our algorithm can progressively invent agents with novel designs that greatly outperform state-of-the-art hand-designed agents. Importantly, we consistently observe the surprising result that agents invented by Meta Agent Search maintain superior performance even when transferred across domains and models, demonstrating their robustness and generality. Provided we develop it safely, our work illustrates the potential of an exciting new research direction toward automatically designing ever-more powerful agentic systems to benefit humanity.

  • 3 authors
·
Aug 15, 2024 3

Toward a traceable, explainable, and fairJD/Resume recommendation system

In the last few decades, companies are interested to adopt an online automated recruitment process in an international recruitment environment. The problem is that the recruitment of employees through the manual procedure is a time and money consuming process. As a result, processing a significant number of applications through conventional methods can lead to the recruitment of clumsy individuals. Different JD/Resume matching model architectures have been proposed and reveal a high accuracy level in selecting relevant candidatesfor the required job positions. However, the development of an automatic recruitment system is still one of the main challenges. The reason is that the development of a fully automated recruitment system is a difficult task and poses different challenges. For example, providing a detailed matching explanation for the targeted stakeholders is needed to ensure a transparent recommendation. There are several knowledge bases that represent skills and competencies (e.g, ESCO, O*NET) that are used to identify the candidate and the required job skills for a matching purpose. Besides, modernpre-trained language models are fine-tuned for this context such as identifying lines where a specific feature was introduced. Typically, pre-trained language models use transfer-based machine learning models to be fine-tuned for a specific field. In this proposal, our aim is to explore how modern language models (based on transformers) can be combined with knowledge bases and ontologies to enhance the JD/Resume matching process. Our system aims at using knowledge bases and features to support the explainability of the JD/Resume matching. Finally, given that multiple software components, datasets, ontology, andmachine learning models will be explored, we aim at proposing a fair, ex-plainable, and traceable architecture for a Resume/JD matching purpose.

  • 3 authors
·
Feb 2, 2022

VitaLITy: Promoting Serendipitous Discovery of Academic Literature with Transformers & Visual Analytics

There are a few prominent practices for conducting reviews of academic literature, including searching for specific keywords on Google Scholar or checking citations from some initial seed paper(s). These approaches serve a critical purpose for academic literature reviews, yet there remain challenges in identifying relevant literature when similar work may utilize different terminology (e.g., mixed-initiative visual analytics papers may not use the same terminology as papers on model-steering, yet the two topics are relevant to one another). In this paper, we introduce a system, VitaLITy, intended to complement existing practices. In particular, VitaLITy promotes serendipitous discovery of relevant literature using transformer language models, allowing users to find semantically similar papers in a word embedding space given (1) a list of input paper(s) or (2) a working abstract. VitaLITy visualizes this document-level embedding space in an interactive 2-D scatterplot using dimension reduction. VitaLITy also summarizes meta information about the document corpus or search query, including keywords and co-authors, and allows users to save and export papers for use in a literature review. We present qualitative findings from an evaluation of VitaLITy, suggesting it can be a promising complementary technique for conducting academic literature reviews. Furthermore, we contribute data from 38 popular data visualization publication venues in VitaLITy, and we provide scrapers for the open-source community to continue to grow the list of supported venues.

  • 4 authors
·
Aug 7, 2021

Code Summarization Beyond Function Level

Code summarization is a critical task in natural language processing and software engineering, which aims to generate concise descriptions of source code. Recent advancements have improved the quality of these summaries, enhancing code readability and maintainability. However, the content of a repository or a class has not been considered in function code summarization. This study investigated the effectiveness of code summarization models beyond the function level, exploring the impact of class and repository contexts on the summary quality. The study involved revising benchmarks for evaluating models at class and repository levels, assessing baseline models, and evaluating LLMs with in-context learning to determine the enhancement of summary quality with additional context. The findings revealed that the fine-tuned state-of-the-art CodeT5+ base model excelled in code summarization, while incorporating few-shot learning and retrieved code chunks from RAG significantly enhanced the performance of LLMs in this task. Notably, the Deepseek Coder 1.3B and Starcoder2 15B models demonstrated substantial improvements in metrics such as BLEURT, METEOR, and BLEU-4 at both class and repository levels. Repository-level summarization exhibited promising potential but necessitates significant computational resources and gains from the inclusion of structured context. Lastly, we employed the recent SIDE code summarization metric in our evaluation. This study contributes to refining strategies for prompt engineering, few-shot learning, and RAG, addressing gaps in benchmarks for code summarization at various levels. Finally, we publish all study details, code, datasets, and results of evaluation in the GitHub repository available at https://github.com/kilimanj4r0/code-summarization-beyond-function-level.

  • 2 authors
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Feb 23, 2025

MetaAID 2.5: A Secure Framework for Developing Metaverse Applications via Large Language Models

Large language models (LLMs) are increasingly being used in Metaverse environments to generate dynamic and realistic content and to control the behavior of non-player characters (NPCs). However, the cybersecurity concerns associated with LLMs have become increasingly prominent. Previous research has primarily focused on patching system vulnerabilities to enhance cybersecurity, but these approaches are not well-suited to the Metaverse, where the virtual space is more complex, LLMs are vulnerable, and ethical user interaction is critical. Moreover, the scope of cybersecurity in the Metaverse is expected to expand significantly. This paper proposes a method for enhancing cybersecurity through the simulation of user interaction with LLMs. Our goal is to educate users and strengthen their defense capabilities through exposure to a comprehensive simulation system. This system includes extensive Metaverse cybersecurity Q&A and attack simulation scenarios. By engaging with these, users will improve their ability to recognize and withstand risks. Additionally, to address the ethical implications of user input, we propose using LLMs as evaluators to assess user content across five dimensions. We further adapt the models through vocabulary expansion training to better understand personalized inputs and emoticons. We conduct experiments on multiple LLMs and find that our approach is effective.

  • 1 authors
·
Dec 22, 2023

Meta-World: A Benchmark and Evaluation for Multi-Task and Meta Reinforcement Learning

Meta-reinforcement learning algorithms can enable robots to acquire new skills much more quickly, by leveraging prior experience to learn how to learn. However, much of the current research on meta-reinforcement learning focuses on task distributions that are very narrow. For example, a commonly used meta-reinforcement learning benchmark uses different running velocities for a simulated robot as different tasks. When policies are meta-trained on such narrow task distributions, they cannot possibly generalize to more quickly acquire entirely new tasks. Therefore, if the aim of these methods is to enable faster acquisition of entirely new behaviors, we must evaluate them on task distributions that are sufficiently broad to enable generalization to new behaviors. In this paper, we propose an open-source simulated benchmark for meta-reinforcement learning and multi-task learning consisting of 50 distinct robotic manipulation tasks. Our aim is to make it possible to develop algorithms that generalize to accelerate the acquisition of entirely new, held-out tasks. We evaluate 7 state-of-the-art meta-reinforcement learning and multi-task learning algorithms on these tasks. Surprisingly, while each task and its variations (e.g., with different object positions) can be learned with reasonable success, these algorithms struggle to learn with multiple tasks at the same time, even with as few as ten distinct training tasks. Our analysis and open-source environments pave the way for future research in multi-task learning and meta-learning that can enable meaningful generalization, thereby unlocking the full potential of these methods.

  • 10 authors
·
Oct 23, 2019

Using clarification questions to improve software developers' Web search

Context: Recent research indicates that Web queries written by software developers are not very successful in retrieving relevant results, performing measurably worse compared to general purpose Web queries. Most approaches up to this point have addressed this problem with software engineering-specific automated query reformulation techniques, which work without developer involvement but are limited by the content of the original query. In other words, these techniques automatically improve the existing query but can not contribute new, previously unmentioned, concepts. Objective: In this paper, we propose a technique to guide software developers in manually improving their own Web search queries. We examine a conversational approach that follows unsuccessful queries with a clarification question aimed at eliciting additional query terms, thus providing to the developer a clear dimension along which the query could be improved. Methods: We describe a set of clarification questions derived from a corpus of software developer queries and a neural approach to recommending them for a newly issued query. Results: Our evaluation indicates that the recommendation technique is accurate, predicting a valid clarification question 80% of the time and outperforms simple baselines, as well as, state-of-the-art Learning To Rank (LTR) baselines. Conclusion: As shown in the experimental results, the described approach is capable at recommending appropriate clarification questions to software developers and considered useful by a sample of developers ranging from novices to experienced professionals.

  • 2 authors
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Jul 26, 2022

MixtureVitae: Open Web-Scale Pretraining Dataset With High Quality Instruction and Reasoning Data Built from Permissive-First Text Sources

We present MixtureVitae, an open-access pretraining corpus built to minimize legal risk while providing strong model performance. MixtureVitae follows a risk-mitigated sourcing strategy that combines public-domain and permissively licensed text (e.g., CC-BY/Apache) with carefully justified low-risk additions (e.g., government works and EU TDM-eligible sources), alongside targeted instruction, reasoning and synthetic data with documented provenance. We detail a transparent, multi-stage pipeline for license-aware filtering, safety and quality screening, and domain-aware mixing, and we release the dataset and curation recipes to support reproducible research. In controlled experiments using the open-sci-ref training protocol (fixed architectures at 130M/400M/1.3B/1.7B parameters; training budgets of 50B and 300B tokens), models trained on MixtureVitae consistently outperform other permissive datasets across a suite of standard benchmarks, and at the 1.7B/300B setting they surpass FineWeb-Edu and approach DCLM in the later stages of training. Performance is particularly strong on math/code and competitive on QA tasks. These results demonstrate that permissive-first, risk-mitigated data provides a practical and legally mitigated foundation for training capable LLMs, reducing reliance on indiscriminate web scraping without sacrificing competitiveness. Code: https://github.com/ontocord/mixturevitae

ontocord Ontocord.AI
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Sep 29, 2025 3