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Proteins adopt multiple structural conformations to perform their diverse biological functions, and understanding these conformations is crucial for advancing drug discovery. Traditional physics-based simulation methods often struggle with…

Biomolecules · Quantitative Biology 2025-03-14 Jiarui Lu , Xiaoyin Chen , Stephen Zhewen Lu , Chence Shi , Hongyu Guo , Yoshua Bengio , Jian Tang

Although large language models (LLMs) have demonstrated impressive ability in code generation, they are still struggling to address the complicated intent provided by humans. It is widely acknowledged that humans typically employ planning…

Software Engineering · Computer Science 2025-10-21 Xue Jiang , Yihong Dong , Lecheng Wang , Zheng Fang , Qiwei Shang , Ge Li , Zhi Jin , Wenpin Jiao

We propose multiple techniques for automatic document order generation for (1) curriculum development and for (2) creation of optimal reading order for use in learning, training, and other content-sequencing applications. Such techniques…

Computation and Language · Computer Science 2023-12-18 Arturo N. Villanueva , Steven J. Simske

In this paper, we introduce a data-driven approach for Formality-Sensitive Machine Translation (FSMT) that caters to the unique linguistic properties of four target languages. Our methodology centers on two core strategies: 1)…

Computation and Language · Computer Science 2023-06-28 Seugnjun Lee , Hyeonseok Moon , Chanjun Park , Heuiseok Lim

Proteins are essential macromolecules defined by their amino acid sequences, which determine their three-dimensional structures and, consequently, their functions in all living organisms. Therefore, generative protein modeling necessitates…

Machine Learning · Computer Science 2024-10-18 Xinyou Wang , Zaixiang Zheng , Fei Ye , Dongyu Xue , Shujian Huang , Quanquan Gu

The advancement of data-driven materials science is currently constrained by a fundamental bottleneck: the vast majority of historical experimental data remains locked within the unstructured text and rasterized figures of legacy scientific…

Databases · Computer Science 2026-02-04 Yue Wu , Tianhao Su , Shunbo Hu , Deng Pan

We consider the task of data-to-text generation, which aims to create textual output from non-linguistic input. We focus on generating long-form text, i.e., documents with multiple paragraphs, and propose a neural model enhanced with a…

Computation and Language · Computer Science 2022-03-01 Ratish Puduppully , Yao Fu , Mirella Lapata

Information in industry, research, and the public sector is widely stored as rendered documents (e.g., PDF files, scans). Hence, to enable downstream tasks, systems are needed that map rendered documents onto a structured hierarchical…

Machine Learning · Computer Science 2023-10-16 Johannes Rausch , Gentiana Rashiti , Maxim Gusev , Ce Zhang , Stefan Feuerriegel

A program is characterized by its input model, and a formal input model can be of use in diverse areas including vulnerability analysis, reverse engineering, fuzzing and software testing, clone detection and refactoring. Unfortunately,…

Software Engineering · Computer Science 2019-12-13 Rahul Gopinath , Björn Mathis , Andreas Zeller

Traditional benchmarks for large language models (LLMs) typically rely on static evaluations through storytelling or opinion expression, which fail to capture the dynamic requirements of real-time information processing in contemporary…

Machine Learning · Computer Science 2025-06-27 Jingyao Li , Hao Sun , Zile Qiao , Yong Jiang , Pengjun Xie , Fei Huang , Hong Xu , Jiaya Jia

File systems are critical OS components that require constant evolution to support new hardware and emerging application needs. However, the traditional paradigm of developing features, fixing bugs, and maintaining the system incurs…

Operating Systems · Computer Science 2026-02-11 Qingyuan Liu , Mo Zou , Hengbin Zhang , Dong Du , Yubin Xia , Haibo Chen

In the task of automatic program synthesis, one obtains pairs of matching inputs and outputs and generates a computer program, in a particular domain-specific language (DSL), which given each sample input returns the matching output. A key…

Machine Learning · Computer Science 2023-03-14 Aran Carmon , Lior Wolf

Containerization allows developers to define the execution environment in which their software needs to be installed. Docker is the leading platform in this field, and developers that use it are required to write a Dockerfile for their…

Software Engineering · Computer Science 2023-03-29 Giovanni Rosa , Antonio Mastropaolo , Simone Scalabrino , Gabriele Bavota , Rocco Oliveto

Understanding and extracting of information from large documents, such as business opportunities, academic articles, medical documents and technical reports, poses challenges not present in short documents. Such large documents may be…

Computation and Language · Computer Science 2019-10-10 Muhammad Mahbubur Rahman , Tim Finin

Recent developments show that Large Language Models (LLMs) produce state-of-the-art performance on natural language (NL) to code generation for resource-rich general-purpose languages like C++, Java, and Python. However, their practical…

A new approach is presented to obtain candidate structures from atomic pair distribution function (PDF) data in a highly automated way. It fetches, from web-based structural databases, all the structures meeting the experimenter's search…

Materials Science · Physics 2020-05-07 Long Yang , Pavol Juhás , Maxwell W. Terban , Matthew G. Tucker , Simon J. L. Billinge

Composing Web services is a convenient means of dealing with complex requests. However, the number of Web services on the Internet is increasing. This explains the growing interest in composing Web services automatically. Nevertheless, the…

Networking and Internet Architecture · Computer Science 2010-04-20 Fatima-Zahra Belouadha , Hajar Omrana , Ounsa Roudies

Automatic code generation has recently attracted large attention and is becoming more significant to the software development process. Solutions based on Machine Learning and Artificial Intelligence are being used to increase human and…

Software Engineering · Computer Science 2023-05-22 Leon Chemnitz , David Reichenbach , Hani Aldebes , Mariam Naveed , Krishna Narasimhan , Mira Mezini

The generation of large, high-quality datasets for code understanding and generation remains a significant challenge, particularly when aligning decompiled binaries with their original source code. To address this, we present CodableLLM, a…

Software Engineering · Computer Science 2025-07-31 Dylan Manuel , Paul Rad

The exponential growth of scientific literature in PDF format necessitates advanced tools for efficient and accurate document understanding, summarization, and content optimization. Traditional methods fall short in handling complex layouts…

Computer Vision and Pattern Recognition · Computer Science 2025-08-12 Kun Qian , Wenjie Li , Tianyu Sun , Wenhong Wang , Wenhan Luo