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Toward Total Recall: Enhancing FAIRness through AI-Driven Metadata Standardization

arXiv.org Artificial Intelligence

Scientific metadata often suffer from incompleteness, inconsistency, and formatting errors, which hinder effective discovery and reuse of the associated datasets. We present a method that combines GPT-4 with structured metadata templates from the CEDAR knowledge base to automatically standardize metadata and to ensure compliance with established standards. A CEDAR template specifies the expected fields of a metadata submission and their permissible values. Our standardization process involves using CEDAR templates to guide GPT-4 in accurately correcting and refining metadata entries in bulk, resulting in significant improvements in metadata retrieval performance, especially in recall -- the proportion of relevant datasets retrieved from the total relevant datasets available. Using the BioSample and GEO repositories maintained by the National Center for Biotechnology Information (NCBI), we demonstrate that retrieval of datasets whose metadata are altered by GPT-4 when provided with CEDAR templates (GPT-4+CEDAR) is substantially better than retrieval of datasets whose metadata are in their original state and that of datasets whose metadata are altered using GPT-4 with only data-dictionary guidance (GPT-4+DD). The average recall increases dramatically, from 17.65\% with baseline raw metadata to 62.87\% with GPT-4+CEDAR. Furthermore, we evaluate the robustness of our approach by comparing GPT-4 against other large language models, including LLaMA-3 and MedLLaMA2, demonstrating consistent performance advantages for GPT-4+CEDAR. These results underscore the transformative potential of combining advanced language models with symbolic models of standardized metadata structures for more effective and reliable data retrieval, thus accelerating scientific discoveries and data-driven research.


Auto Review: Second Stage Error Detection for Highly Accurate Information Extraction from Phone Conversations

arXiv.org Artificial Intelligence

Automating benefit verification phone calls saves time in healthcare and helps patients receive treatment faster. It is critical to obtain highly accurate information in these phone calls, as it can affect a patient's healthcare journey. Given the noise in phone call transcripts, we have a two-stage system that involves a post-call review phase for potentially noisy fields, where human reviewers manually verify the extracted data$\unicode{x2013}$a labor-intensive task. To automate this stage, we introduce Auto Review, which significantly reduces manual effort while maintaining a high bar for accuracy. This system, being highly reliant on call transcripts, suffers a performance bottleneck due to automatic speech recognition (ASR) issues. This problem is further exacerbated by the use of domain-specific jargon in the calls. In this work, we propose a second-stage postprocessing pipeline for accurate information extraction. We improve accuracy by using multiple ASR alternatives and a pseudo-labeling approach that does not require manually corrected transcripts. Experiments with general-purpose large language models and feature-based model pipelines demonstrate substantial improvements in the quality of corrected call transcripts, thereby enhancing the efficiency of Auto Review.


An Imbalanced Learning-based Sampling Method for Physics-informed Neural Networks

arXiv.org Machine Learning

This paper introduces Residual-based Smote (RSmote), an innovative local adaptive sampling technique tailored to improve the performance of Physics-Informed Neural Networks (PINNs) through imbalanced learning strategies. Traditional residual-based adaptive sampling methods, while effective in enhancing PINN accuracy, often struggle with efficiency and high memory consumption, particularly in high-dimensional problems. RSmote addresses these challenges by targeting regions with high residuals and employing oversampling techniques from imbalanced learning to refine the sampling process. Our approach is underpinned by a rigorous theoretical analysis that supports the effectiveness of RSmote in managing computational resources more efficiently. Through extensive evaluations, we benchmark RSmote against the state-of-the-art Residual-based Adaptive Distribution (RAD) method across a variety of dimensions and differential equations. The results demonstrate that RSmote not only achieves or exceeds the accuracy of RAD but also significantly reduces memory usage, making it particularly advantageous in high-dimensional scenarios. These contributions position RSmote as a robust and resource-efficient solution for solving complex partial differential equations, especially when computational constraints are a critical consideration.


Use of a Structured Knowledge Base Enhances Metadata Curation by Large Language Models

arXiv.org Artificial Intelligence

Metadata play a crucial role in ensuring the findability, accessibility, interoperability, and reusability of datasets. This paper investigates the potential of large language models (LLMs), specifically GPT-4, to improve adherence to metadata standards. We conducted experiments on 200 random data records describing human samples relating to lung cancer from the NCBI BioSample repository, evaluating GPT-4's ability to suggest edits for adherence to metadata standards. We computed the adherence accuracy of field name-field value pairs through a peer review process, and we observed a marginal average improvement in adherence to the standard data dictionary from 79% to 80% (p<0.5). We then prompted GPT-4 with domain information in the form of the textual descriptions of CEDAR templates and recorded a significant improvement to 97% from 79% (p<0.01). These results indicate that, while LLMs may not be able to correct legacy metadata to ensure satisfactory adherence to standards when unaided, they do show promise for use in automated metadata curation when integrated with a structured knowledge base. Introduction Data sharing, a pivotal requirement for good science that is now required by most funding agencies, continues to be a challenging prospect.


Posterior Probability Matters: Doubly-Adaptive Calibration for Neural Predictions in Online Advertising

arXiv.org Artificial Intelligence

Predicting user response probabilities is vital for ad ranking and bidding. We hope that predictive models can produce accurate probabilistic predictions that reflect true likelihoods. Calibration techniques aim to post-process model predictions to posterior probabilities. Field-level calibration -- which performs calibration w.r.t. to a specific field value -- is fine-grained and more practical. In this paper we propose a doubly-adaptive approach AdaCalib. It learns an isotonic function family to calibrate model predictions with the guidance of posterior statistics, and field-adaptive mechanisms are designed to ensure that the posterior is appropriate for the field value to be calibrated. Experiments verify that AdaCalib achieves significant improvement on calibration performance. It has been deployed online and beats previous approach.


Deep Ensemble Shape Calibration: Multi-Field Post-hoc Calibration in Online Advertising

arXiv.org Artificial Intelligence

In the e-commerce advertising scenario, estimating the true probabilities (known as a calibrated estimate) on CTR and CVR is critical and can directly affect the benefits of the buyer, seller and platform. Previous research has introduced numerous solutions for addressing the calibration problem. These methods typically involve the training of calibrators using a validation set and subsequently applying these calibrators to correct the original estimated values during online inference. However, what sets e-commerce advertising scenarios is the challenge of multi-field calibration. Multi-field calibration can be subdivided into two distinct sub-problems: value calibration and shape calibration. Value calibration is defined as no over- or under-estimation for each value under concerned fields. Shape calibration is defined as no over- or under-estimation for each subset of the pCTR within the specified range under condition of concerned fields. In order to achieve shape calibration and value calibration, it is necessary to have a strong data utilization ability.Because the quantity of pCTR specified range for single field-value sample is relative small, which makes the calibrator more difficult to train. However the existing methods cannot simultaneously fulfill both value calibration and shape calibration. To solve these problems, we propose a new method named Deep Ensemble Shape Calibration (DESC). We introduce innovative basis calibration functions, which enhance both function expression capabilities and data utilization by combining these basis calibration functions. A significant advancement lies in the development of an allocator capable of allocating the most suitable shape calibrators to different estimation error distributions within diverse fields and values.


Don't Say What You Don't Know: Improving the Consistency of Abstractive Summarization by Constraining Beam Search

arXiv.org Artificial Intelligence

Abstractive summarization systems today produce fluent and relevant output, but often "hallucinate" statements not supported by the source text. We analyze the connection between hallucinations and training data, and find evidence that models hallucinate because they train on target summaries that are unsupported by the source. Based on our findings, we present PINOCCHIO, a new decoding method that improves the consistency of a transformer-based abstractive summarizer by constraining beam search to avoid hallucinations. Given the model states and outputs at a given step, PINOCCHIO detects likely model hallucinations based on various measures of attribution to the source text. PINOCCHIO backtracks to find more consistent output, and can opt to produce no summary at all when no consistent generation can be found. In experiments, we find that PINOCCHIO improves the consistency of generation (in terms of F1) by an average of~67% on two abstractive summarization datasets.


One Transformer for All Time Series: Representing and Training with Time-Dependent Heterogeneous Tabular Data

arXiv.org Artificial Intelligence

Despite the success of Deep Learning methods in different areas of Artificial Intelligence (AI), such as, for instance, Natural Language Processing, Computer Vision, Audio Processing, Robotics, etc., the use of deep networks to represent tabular data is so far largely under explored. However, tabular data have a large application interest, since many public institutions or commercial/industrial companies represent their knowledge using datasets of "tables" [1]. For instance, bank data, clinical data, commercial data, etc., are often provided as a list of attributes (field names) and corresponding values (field values) for each represented entity (sample). As reported in [2], over 65% of the datasets in the Google Dataset Search platform contain tabular files in either CSV or XLS formats. Particularly interesting is the case of financial transactions, which, for instance, describe the sequence of (time dependent) transactions of a given bank client on her/his bank account.


Support Generation for Robot-Assisted 3D Printing with Curved Layers

arXiv.org Artificial Intelligence

Robot-assisted 3D printing has drawn a lot of attention by its capability to fabricate curved layers that are optimized according to different objectives. However, the support generation algorithm based on a fixed printing direction for planar layers cannot be directly applied for curved layers as the orientation of material accumulation is dynamically varied. In this paper, we propose a skeleton-based support generation method for robot-assisted 3D printing with curved layers. The support is represented as an implicit solid so that the problems of numerical robustness can be effectively avoided. The effectiveness of our algorithm is verified on a dual-material printing platform that consists of a robotic arm and a newly designed dual-material extruder. Experiments have been successfully conducted on our system to fabricate a variety of freeform models.