Cesar Berrospi Ramis

Christoph Auer, Maksym Lysak, Ahmed Nassar et al.

This technical report introduces Docling, an easy to use, self-contained, MIT-licensed open-source package for PDF document conversion. It is powered by state-of-the-art specialized AI models for layout analysis (DocLayNet) and table structure recognition (TableFormer), and runs efficiently on commodity hardware in a small resource budget. The code interface allows for easy extensibility and addition of new features and models.

Hoang Thanh Lam, Marco Luca Sbodio, Marcos Martínez Galindo et al.

Recent research on predicting the binding affinity between drug molecules and proteins use representations learned, through unsupervised learning techniques, from large databases of molecule SMILES and protein sequences. While these representations have significantly enhanced the predictions, they are usually based on a limited set of modalities, and they do not exploit available knowledge about existing relations among molecules and proteins. In this study, we demonstrate that by incorporating knowledge graphs from diverse sources and modalities into the sequences or SMILES representation, we can further enrich the representation and achieve state-of-the-art results for drug-target binding affinity prediction in the established Therapeutic Data Commons (TDC) benchmarks. We release a set of multimodal knowledge graphs, integrating data from seven public data sources, and containing over 30 million triples. Our intention is to foster additional research to explore how multimodal knowledge enhanced protein/molecule embeddings can improve prediction tasks, including prediction of binding affinity. We also release some pretrained models learned from our multimodal knowledge graphs, along with source code for running standard benchmark tasks for prediction of biding affinity.

Christoph Auer, Michele Dolfi, André Carvalho et al.

Document understanding is a key business process in the data-driven economy since documents are central to knowledge discovery and business insights. Converting documents into a machine-processable format is a particular challenge here due to their huge variability in formats and complex structure. Accordingly, many algorithms and machine-learning methods emerged to solve particular tasks such as Optical Character Recognition (OCR), layout analysis, table-structure recovery, figure understanding, etc. We observe the adoption of such methods in document understanding solutions offered by all major cloud providers. Yet, publications outlining how such services are designed and optimized to scale in the cloud are scarce. In this paper, we focus on the case of document conversion to illustrate the particular challenges of scaling a complex data processing pipeline with a strong reliance on machine-learning methods on cloud infrastructure. Our key objective is to achieve high scalability and responsiveness for different workload profiles in a well-defined resource budget. We outline the requirements, design, and implementation choices of our document conversion service and reflect on the challenges we faced. Evidence for the scaling behavior and resource efficiency is provided for two alternative workload distribution strategies and deployment configurations. Our best-performing method achieves sustained throughput of over one million PDF pages per hour on 3072 CPU cores across 192 nodes.

Nikolaos Livathinos, Christoph Auer, Maksym Lysak et al.

We introduce Docling, an easy-to-use, self-contained, MIT-licensed, open-source toolkit for document conversion, that can parse several types of popular document formats into a unified, richly structured representation. It is powered by state-of-the-art specialized AI models for layout analysis (DocLayNet) and table structure recognition (TableFormer), and runs efficiently on commodity hardware in a small resource budget. Docling is released as a Python package and can be used as a Python API or as a CLI tool. Docling's modular architecture and efficient document representation make it easy to implement extensions, new features, models, and customizations. Docling has been already integrated in other popular open-source frameworks (e.g., LangChain, LlamaIndex, spaCy), making it a natural fit for the processing of documents and the development of high-end applications. The open-source community has fully engaged in using, promoting, and developing for Docling, which gathered 10k stars on GitHub in less than a month and was reported as the No. 1 trending repository in GitHub worldwide in November 2024.

Bishwaranjan Bhattacharjee, Aashka Trivedi, Masayasu Muraoka et al.

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

Lokesh Mishra, Sohayl Dhibi, Yusik Kim et al.

Environment, Social, and Governance (ESG) KPIs assess an organization's performance on issues such as climate change, greenhouse gas emissions, water consumption, waste management, human rights, diversity, and policies. ESG reports convey this valuable quantitative information through tables. Unfortunately, extracting this information is difficult due to high variability in the table structure as well as content. We propose Statements, a novel domain agnostic data structure for extracting quantitative facts and related information. We propose translating tables to statements as a new supervised deep-learning universal information extraction task. We introduce SemTabNet - a dataset of over 100K annotated tables. Investigating a family of T5-based Statement Extraction Models, our best model generates statements which are 82% similar to the ground-truth (compared to baseline of 21%). We demonstrate the advantages of statements by applying our model to over 2700 tables from ESG reports. The homogeneous nature of statements permits exploratory data analysis on expansive information found in large collections of ESG reports.