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Dec 10

A Vulnerability Code Intent Summary Dataset

In the era of Large Language Models (LLMs), the code summarization technique boosts a lot, along with the emergence of many new significant works. However, the potential of code summarization in the Computer Security Area still remains explored. Can we generate a code summary of a code snippet for its security intention? Thus, this work proposes an innovative large-scale multi-perspective Code Intent Summary Dataset named BADS , aiming to increase the understanding of a given code snippet and reduce the risk in the code developing process. The procedure of establishing a dataset can be divided into four steps: First, we collect samples of codes with known vulnerabilities as well as code generated by AI from multiple sources. Second, we do the data clean and format unification, then do the data combination. Third, we utilize the LLM to automatically Annotate the code snippet. Last, We do the human evaluation to double-check. The dataset contains X code examples which cover Y categories of vulnerability. Our data are from Z open-source projects and CVE entries, and compared to existing work, our dataset not only contains original code but also code function summary and security intent summary, providing context information for research in code security analysis. All information is in CSV format. The contributions of this paper are four-fold: the establishment of a high-quality, multi-perspective Code Intent Summary Dataset; an innovative method in data collection and processing; A new multi-perspective code analysis framework that promotes cross-disciplinary research in the fields of software engineering and cybersecurity; improving the practicality and scalability of the research outcomes by considering the code length limitations in real-world applications. Our dataset and related tools have been publicly released on GitHub.

  • 3 authors
·
Apr 10

VisioFirm: Cross-Platform AI-assisted Annotation Tool for Computer Vision

AI models rely on annotated data to learn pattern and perform prediction. Annotation is usually a labor-intensive step that require associating labels ranging from a simple classification label to more complex tasks such as object detection, oriented bounding box estimation, and instance segmentation. Traditional tools often require extensive manual input, limiting scalability for large datasets. To address this, we introduce VisioFirm, an open-source web application designed to streamline image labeling through AI-assisted automation. VisioFirm integrates state-of-the-art foundation models into an interface with a filtering pipeline to reduce human-in-the-loop efforts. This hybrid approach employs CLIP combined with pre-trained detectors like Ultralytics models for common classes and zero-shot models such as Grounding DINO for custom labels, generating initial annotations with low-confidence thresholding to maximize recall. Through this framework, when tested on COCO-type of classes, initial prediction have been proven to be mostly correct though the users can refine these via interactive tools supporting bounding boxes, oriented bounding boxes, and polygons. Additionally, VisioFirm has on-the-fly segmentation powered by Segment Anything accelerated through WebGPU for browser-side efficiency. The tool supports multiple export formats (YOLO, COCO, Pascal VOC, CSV) and operates offline after model caching, enhancing accessibility. VisioFirm demonstrates up to 90\% reduction in manual effort through benchmarks on diverse datasets, while maintaining high annotation accuracy via clustering of connected CLIP-based disambiguate components and IoU-graph for redundant detection suppression. VisioFirm can be accessed from https://github.com/OschAI/VisioFirm{https://github.com/OschAI/VisioFirm}.

  • 2 authors
·
Sep 4

Demo of the Linguistic Field Data Management and Analysis System -- LiFE

In the proposed demo, we will present a new software - Linguistic Field Data Management and Analysis System - LiFE (https://github.com/kmi-linguistics/life) - an open-source, web-based linguistic data management and analysis application that allows for systematic storage, management, sharing and usage of linguistic data collected from the field. The application allows users to store lexical items, sentences, paragraphs, audio-visual content with rich glossing / annotation; generate interactive and print dictionaries; and also train and use natural language processing tools and models for various purposes using this data. Since its a web-based application, it also allows for seamless collaboration among multiple persons and sharing the data, models, etc with each other. The system uses the Python-based Flask framework and MongoDB in the backend and HTML, CSS and Javascript at the frontend. The interface allows creation of multiple projects that could be shared with the other users. At the backend, the application stores the data in RDF format so as to allow its release as Linked Data over the web using semantic web technologies - as of now it makes use of the OntoLex-Lemon for storing the lexical data and Ligt for storing the interlinear glossed text and then internally linking it to the other linked lexicons and databases such as DBpedia and WordNet. Furthermore it provides support for training the NLP systems using scikit-learn and HuggingFace Transformers libraries as well as make use of any model trained using these libraries - while the user interface itself provides limited options for tuning the system, an externally-trained model could be easily incorporated within the application; similarly the dataset itself could be easily exported into a standard machine-readable format like JSON or CSV that could be consumed by other programs and pipelines.

  • 4 authors
·
Mar 21, 2022

Struc-Bench: Are Large Language Models Really Good at Generating Complex Structured Data?

Despite the power of Large Language Models (LLMs) like GPT-4, they still struggle with tasks that require generating complex, structured outputs. In this study, we assess the capability of Current LLMs in generating complex structured data and propose a structure-aware fine-tuning approach as a solution to improve this ability. To perform a comprehensive evaluation, we propose Struc-Bench, include five representative LLMs (i.e., GPT-NeoX 20B, GPT-3.5, GPT-4, and Vicuna) and evaluate them on our carefully constructed datasets spanning raw text, HTML, and LaTeX tables. Based on our analysis of current model performance, we identify specific common formatting errors and areas of potential improvement. To address complex formatting requirements, we utilize FormatCoT (Chain-of-Thought) to generate format instructions from target outputs. Our experiments show that our structure-aware fine-tuning method, when applied to LLaMA-7B, significantly improves adherence to natural language constraints, outperforming other evaluated LLMs. Based on these results, we present an ability map of model capabilities from six dimensions (i.e., coverage, formatting, reasoning, comprehension, pragmatics, and hallucination). This map highlights the weaknesses of LLMs in handling complex structured outputs and suggests promising directions for future work. Our code and models can be found at https://github.com/gersteinlab/Struc-Bench.

  • 5 authors
·
Sep 16, 2023 1

Fine Tuning LLM for Enterprise: Practical Guidelines and Recommendations

There is a compelling necessity from enterprises for fine tuning LLMs (Large Language Models) o get them trained on proprietary domain knowledge. The challenge is to imbibe the LLMs with domain specific knowledge using the most optimial resource and cost and in the best possible time. Many enterprises rely on RAG (Retrieval Augmented Generation) which does not need LLMs to be ine-tuned but they are limited by the quality of vector databases and their retrieval capabilities rather than the intrinsic capabilities of the LLMs themselves. In our current work we focus on fine tuning LLaMA, an open source LLM using proprietary documents and code from an enterprise repository and use the fine tuned models to evaluate the quality of responses. As part of this work, we aim to guide beginners on how to start with fine tuning an LLM for documentation and code by making educated guesses on size of GPU required and options that are available for formatting the data. We also propose pre processing recipes for both documentation and code to prepare dataset in different formats. The proposed methods of data preparation for document datasets are forming paragraph chunks, forming question and answer pairs and forming keyword and paragraph chunk pairs. For code dataset we propose forming summary and function pairs. Further, we qualitatively evaluate the results of the models for domain specific queries. Finally, we also propose practical guidelines and recommendations for fine tuning LLMs.

  • 4 authors
·
Mar 23, 2024

Image-based table recognition: data, model, and evaluation

Important information that relates to a specific topic in a document is often organized in tabular format to assist readers with information retrieval and comparison, which may be difficult to provide in natural language. However, tabular data in unstructured digital documents, e.g., Portable Document Format (PDF) and images, are difficult to parse into structured machine-readable format, due to complexity and diversity in their structure and style. To facilitate image-based table recognition with deep learning, we develop the largest publicly available table recognition dataset PubTabNet (https://github.com/ibm-aur-nlp/PubTabNet), containing 568k table images with corresponding structured HTML representation. PubTabNet is automatically generated by matching the XML and PDF representations of the scientific articles in PubMed Central Open Access Subset (PMCOA). We also propose a novel attention-based encoder-dual-decoder (EDD) architecture that converts images of tables into HTML code. The model has a structure decoder which reconstructs the table structure and helps the cell decoder to recognize cell content. In addition, we propose a new Tree-Edit-Distance-based Similarity (TEDS) metric for table recognition, which more appropriately captures multi-hop cell misalignment and OCR errors than the pre-established metric. The experiments demonstrate that the EDD model can accurately recognize complex tables solely relying on the image representation, outperforming the state-of-the-art by 9.7% absolute TEDS score.

  • 3 authors
·
Nov 24, 2019

A Systematic Literature Review of Software Engineering Research on Jupyter Notebook

Context: Jupyter Notebook has emerged as a versatile tool that transforms how researchers, developers, and data scientists conduct and communicate their work. As the adoption of Jupyter notebooks continues to rise, so does the interest from the software engineering research community in improving the software engineering practices for Jupyter notebooks. Objective: The purpose of this study is to analyze trends, gaps, and methodologies used in software engineering research on Jupyter notebooks. Method: We selected 146 relevant publications from the DBLP Computer Science Bibliography up to the end of 2024, following established systematic literature review guidelines. We explored publication trends, categorized them based on software engineering topics, and reported findings based on those topics. Results: The most popular venues for publishing software engineering research on Jupyter notebooks are related to human-computer interaction instead of traditional software engineering venues. Researchers have addressed a wide range of software engineering topics on notebooks, such as code reuse, readability, and execution environment. Although reusability is one of the research topics for Jupyter notebooks, only 64 of the 146 studies can be reused based on their provided URLs. Additionally, most replication packages are not hosted on permanent repositories for long-term availability and adherence to open science principles. Conclusion: Solutions specific to notebooks for software engineering issues, including testing, refactoring, and documentation, are underexplored. Future research opportunities exist in automatic testing frameworks, refactoring clones between notebooks, and generating group documentation for coherent code cells.

  • 3 authors
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Apr 22

CommonForms: A Large, Diverse Dataset for Form Field Detection

This paper introduces CommonForms, a web-scale dataset for form field detection. It casts the problem of form field detection as object detection: given an image of a page, predict the location and type (Text Input, Choice Button, Signature) of form fields. The dataset is constructed by filtering Common Crawl to find PDFs that have fillable elements. Starting with 8 million documents, the filtering process is used to arrive at a final dataset of roughly 55k documents that have over 450k pages. Analysis shows that the dataset contains a diverse mixture of languages and domains; one third of the pages are non-English, and among the 14 classified domains, no domain makes up more than 25% of the dataset. In addition, this paper presents a family of form field detectors, FFDNet-Small and FFDNet-Large, which attain a very high average precision on the CommonForms test set. Each model cost less than $500 to train. Ablation results show that high-resolution inputs are crucial for high-quality form field detection, and that the cleaning process improves data efficiency over using all PDFs that have fillable fields in Common Crawl. A qualitative analysis shows that they outperform a popular, commercially available PDF reader that can prepare forms. Unlike the most popular commercially available solutions, FFDNet can predict checkboxes in addition to text and signature fields. This is, to our knowledge, the first large scale dataset released for form field detection, as well as the first open source models. The dataset, models, and code will be released at https://github.com/jbarrow/commonforms

  • 1 authors
·
Sep 19 2

Multi-LexSum: Real-World Summaries of Civil Rights Lawsuits at Multiple Granularities

With the advent of large language models, methods for abstractive summarization have made great strides, creating potential for use in applications to aid knowledge workers processing unwieldy document collections. One such setting is the Civil Rights Litigation Clearinghouse (CRLC) (https://clearinghouse.net),which posts information about large-scale civil rights lawsuits, serving lawyers, scholars, and the general public. Today, summarization in the CRLC requires extensive training of lawyers and law students who spend hours per case understanding multiple relevant documents in order to produce high-quality summaries of key events and outcomes. Motivated by this ongoing real-world summarization effort, we introduce Multi-LexSum, a collection of 9,280 expert-authored summaries drawn from ongoing CRLC writing. Multi-LexSum presents a challenging multi-document summarization task given the length of the source documents, often exceeding two hundred pages per case. Furthermore, Multi-LexSum is distinct from other datasets in its multiple target summaries, each at a different granularity (ranging from one-sentence "extreme" summaries to multi-paragraph narrations of over five hundred words). We present extensive analysis demonstrating that despite the high-quality summaries in the training data (adhering to strict content and style guidelines), state-of-the-art summarization models perform poorly on this task. We release Multi-LexSum for further research in summarization methods as well as to facilitate development of applications to assist in the CRLC's mission at https://multilexsum.github.io.

  • 6 authors
·
Jun 22, 2022

Reshaping Free-Text Radiology Notes Into Structured Reports With Generative Transformers

BACKGROUND: Radiology reports are typically written in a free-text format, making clinical information difficult to extract and use. Recently the adoption of structured reporting (SR) has been recommended by various medical societies thanks to the advantages it offers, e.g. standardization, completeness and information retrieval. We propose a pipeline to extract information from free-text radiology reports, that fits with the items of the reference SR registry proposed by a national society of interventional and medical radiology, focusing on CT staging of patients with lymphoma. METHODS: Our work aims to leverage the potential of Natural Language Processing (NLP) and Transformer-based models to deal with automatic SR registry filling. With the availability of 174 radiology reports, we investigate a rule-free generative Question Answering approach based on a domain-specific version of T5 (IT5). Two strategies (batch-truncation and ex-post combination) are implemented to comply with the model's context length limitations. Performance is evaluated in terms of strict accuracy, F1, and format accuracy, and compared with the widely used GPT-3.5 Large Language Model. A 5-point Likert scale questionnaire is used to collect human-expert feedback on the similarity between medical annotations and generated answers. RESULTS: The combination of fine-tuning and batch splitting allows IT5 to achieve notable results; it performs on par with GPT-3.5 albeit its size being a thousand times smaller in terms of parameters. Human-based assessment scores show a high correlation (Spearman's correlation coefficients>0.88, p-values<0.001) with AI performance metrics (F1) and confirm the superior ability of LLMs (i.e., GPT-3.5, 175B of parameters) in generating plausible human-like statements.

  • 8 authors
·
Mar 27, 2024

SynthRAD2023 Grand Challenge dataset: generating synthetic CT for radiotherapy

Purpose: Medical imaging has become increasingly important in diagnosing and treating oncological patients, particularly in radiotherapy. Recent advances in synthetic computed tomography (sCT) generation have increased interest in public challenges to provide data and evaluation metrics for comparing different approaches openly. This paper describes a dataset of brain and pelvis computed tomography (CT) images with rigidly registered CBCT and MRI images to facilitate the development and evaluation of sCT generation for radiotherapy planning. Acquisition and validation methods: The dataset consists of CT, CBCT, and MRI of 540 brains and 540 pelvic radiotherapy patients from three Dutch university medical centers. Subjects' ages ranged from 3 to 93 years, with a mean age of 60. Various scanner models and acquisition settings were used across patients from the three data-providing centers. Details are available in CSV files provided with the datasets. Data format and usage notes: The data is available on Zenodo (https://doi.org/10.5281/zenodo.7260705) under the SynthRAD2023 collection. The images for each subject are available in nifti format. Potential applications: This dataset will enable the evaluation and development of image synthesis algorithms for radiotherapy purposes on a realistic multi-center dataset with varying acquisition protocols. Synthetic CT generation has numerous applications in radiation therapy, including diagnosis, treatment planning, treatment monitoring, and surgical planning.

  • 9 authors
·
Mar 28, 2023

MeetingBank: A Benchmark Dataset for Meeting Summarization

As the number of recorded meetings increases, it becomes increasingly important to utilize summarization technology to create useful summaries of these recordings. However, there is a crucial lack of annotated meeting corpora for developing this technology, as it can be hard to collect meetings, especially when the topics discussed are confidential. Furthermore, meeting summaries written by experienced writers are scarce, making it hard for abstractive summarizers to produce sensible output without a reliable reference. This lack of annotated corpora has hindered the development of meeting summarization technology. In this paper, we present MeetingBank, a new benchmark dataset of city council meetings over the past decade. MeetingBank is unique among other meeting corpora due to its divide-and-conquer approach, which involves dividing professionally written meeting minutes into shorter passages and aligning them with specific segments of the meeting. This breaks down the process of summarizing a lengthy meeting into smaller, more manageable tasks. The dataset provides a new testbed of various meeting summarization systems and also allows the public to gain insight into how council decisions are made. We make the collection, including meeting video links, transcripts, reference summaries, agenda, and other metadata, publicly available to facilitate the development of better meeting summarization techniques. Our dataset can be accessed at: https://meetingbank.github.io

  • 6 authors
·
May 27, 2023

PODTILE: Facilitating Podcast Episode Browsing with Auto-generated Chapters

Listeners of long-form talk-audio content, such as podcast episodes, often find it challenging to understand the overall structure and locate relevant sections. A practical solution is to divide episodes into chapters--semantically coherent segments labeled with titles and timestamps. Since most episodes on our platform at Spotify currently lack creator-provided chapters, automating the creation of chapters is essential. Scaling the chapterization of podcast episodes presents unique challenges. First, episodes tend to be less structured than written texts, featuring spontaneous discussions with nuanced transitions. Second, the transcripts are usually lengthy, averaging about 16,000 tokens, which necessitates efficient processing that can preserve context. To address these challenges, we introduce PODTILE, a fine-tuned encoder-decoder transformer to segment conversational data. The model simultaneously generates chapter transitions and titles for the input transcript. To preserve context, each input text is augmented with global context, including the episode's title, description, and previous chapter titles. In our intrinsic evaluation, PODTILE achieved an 11% improvement in ROUGE score over the strongest baseline. Additionally, we provide insights into the practical benefits of auto-generated chapters for listeners navigating episode content. Our findings indicate that auto-generated chapters serve as a useful tool for engaging with less popular podcasts. Finally, we present empirical evidence that using chapter titles can enhance effectiveness of sparse retrieval in search tasks.

  • 17 authors
·
Oct 21, 2024

Doctors Handwritten Prescription Recognition System In Multi Language Using Deep Learning

Doctors typically write in incomprehensible handwriting, making it difficult for both the general public and some pharmacists to understand the medications they have prescribed. It is not ideal for them to write the prescription quietly and methodically because they will be dealing with dozens of patients every day and will be swamped with work.As a result, their handwriting is illegible. This may result in reports or prescriptions consisting of short forms and cursive writing that a typical person or pharmacist won't be able to read properly, which will cause prescribed medications to be misspelled. However, some individuals are accustomed to writing prescriptions in regional languages because we all live in an area with a diversity of regional languages. It makes analyzing the content much more challenging. So, in this project, we'll use a recognition system to build a tool that can translate the handwriting of physicians in any language. This system will be made into an application which is fully autonomous in functioning. As the user uploads the prescription image the program will pre-process the image by performing image pre-processing, and word segmentations initially before processing the image for training. And it will be done for every language we require the model to detect. And as of the deduction model will be made using deep learning techniques including CNN, RNN, and LSTM, which are utilized to train the model. To match words from various languages that will be written in the system, Unicode will be used. Furthermore, fuzzy search and market basket analysis are employed to offer an end result that will be optimized from the pharmaceutical database and displayed to the user as a structured output.

  • 6 authors
·
Oct 20, 2022

What's In Your Field? Mapping Scientific Research with Knowledge Graphs and Large Language Models

The scientific literature's exponential growth makes it increasingly challenging to navigate and synthesize knowledge across disciplines. Large language models (LLMs) are powerful tools for understanding scientific text, but they fail to capture detailed relationships across large bodies of work. Unstructured approaches, like retrieval augmented generation, can sift through such corpora to recall relevant facts; however, when millions of facts influence the answer, unstructured approaches become cost prohibitive. Structured representations offer a natural complement -- enabling systematic analysis across the whole corpus. Recent work enhances LLMs with unstructured or semistructured representations of scientific concepts; to complement this, we try extracting structured representations using LLMs. By combining LLMs' semantic understanding with a schema of scientific concepts, we prototype a system that answers precise questions about the literature as a whole. Our schema applies across scientific fields and we extract concepts from it using only 20 manually annotated abstracts. To demonstrate the system, we extract concepts from 30,000 papers on arXiv spanning astrophysics, fluid dynamics, and evolutionary biology. The resulting database highlights emerging trends and, by visualizing the knowledge graph, offers new ways to explore the ever-growing landscape of scientific knowledge. Demo: abby101/surveyor-0 on HF Spaces. Code: https://github.com/chiral-carbon/kg-for-science.

  • 4 authors
·
Mar 12

Structural Text Segmentation of Legal Documents

The growing complexity of legal cases has lead to an increasing interest in legal information retrieval systems that can effectively satisfy user-specific information needs. However, such downstream systems typically require documents to be properly formatted and segmented, which is often done with relatively simple pre-processing steps, disregarding topical coherence of segments. Systems generally rely on representations of individual sentences or paragraphs, which may lack crucial context, or document-level representations, which are too long for meaningful search results. To address this issue, we propose a segmentation system that can predict topical coherence of sequential text segments spanning several paragraphs, effectively segmenting a document and providing a more balanced representation for downstream applications. We build our model on top of popular transformer networks and formulate structural text segmentation as topical change detection, by performing a series of independent classifications that allow for efficient fine-tuning on task-specific data. We crawl a novel dataset consisting of roughly 74,000 online Terms-of-Service documents, including hierarchical topic annotations, which we use for training. Results show that our proposed system significantly outperforms baselines, and adapts well to structural peculiarities of legal documents. We release both data and trained models to the research community for future work.https://github.com/dennlinger/TopicalChange

  • 4 authors
·
Dec 7, 2020

Unveiling Document Structures with YOLOv5 Layout Detection

The current digital environment is characterized by the widespread presence of data, particularly unstructured data, which poses many issues in sectors including finance, healthcare, and education. Conventional techniques for data extraction encounter difficulties in dealing with the inherent variety and complexity of unstructured data, hence requiring the adoption of more efficient methodologies. This research investigates the utilization of YOLOv5, a cutting-edge computer vision model, for the purpose of rapidly identifying document layouts and extracting unstructured data. The present study establishes a conceptual framework for delineating the notion of "objects" as they pertain to documents, incorporating various elements such as paragraphs, tables, photos, and other constituent parts. The main objective is to create an autonomous system that can effectively recognize document layouts and extract unstructured data, hence improving the effectiveness of data extraction. In the conducted examination, the YOLOv5 model exhibits notable effectiveness in the task of document layout identification, attaining a high accuracy rate along with a precision value of 0.91, a recall value of 0.971, an F1-score of 0.939, and an area under the receiver operating characteristic curve (AUC-ROC) of 0.975. The remarkable performance of this system optimizes the process of extracting textual and tabular data from document images. Its prospective applications are not limited to document analysis but can encompass unstructured data from diverse sources, such as audio data. This study lays the foundation for future investigations into the wider applicability of YOLOv5 in managing various types of unstructured data, offering potential for novel applications across multiple domains.

  • 3 authors
·
Sep 29, 2023