20 papers · ranked by Valyu relevance
Zenghui Zhou, Yuechen Li, Yi Cai, Wen + 5 more
Quantum computing is gaining attention from academia and industry. With the quantum Software Development Kits (SDKs), programmers can develop quantum software to explore the power of quantum computing. However, programmers may face challenges in understanding quantum software due to the non-intuitive quantum mechanics.…
M. Siepel, G.T.N. Burger, Q.J.M. Voorham, R. Cornet + 2 more
Palga Foundation is responsible for indexing Dutch pathology data across the Netherlands, which relies on annotations of pathology reports. These annotations, derived from the conclusion text, consist of codes from the Palga thesaurus, serving patient care and scientific research. However, manual annotation by…
Zhipeng Xue, Zhipeng Gao, Xing Hu, Jingyuan Chen + 2 more
Type annotations are more and more popular in Python projects to avoid type errors caused by Python's dynamic typing feature. However, when developers change source code, these type annotations are often neglected or overlooked, resulting in outdated and inconsistent type annotations. Such obsolete type annotations can…
Maria Camporese, Fabio Massacci, Yuanjun Gong
[Background:] Thematic analysis of free-text justifications in human experiments provides significant qualitative insights. Yet, it is costly because reliable annotations require multiple domain experts. Large language models (LLMs) seem ideal candidates to replace human annotators. [Problem:] Coding security-specific…
Zhenghan Chen, Zekai Shao, Lidan Tan, Xin Lin + 9 more
Multimodal large language models (MLLMs) have made significant progress in chart understanding, generation, and editing, but their ability to annotate existing charts remains underexplored. Annotating charts is a common yet challenging communicative task, requiring models to infer intended messages, interpret chart…
Zhihao Lin, Mingyi Zhou, Yizhuo Yang, Li Li
LLM-based code agents navigate repositories through keyword search but miss the structural relationships, such as call graphs, inheritance hierarchies, and configuration dependencies, that define how software actually works. This makes agent navigation stochastic and difficult to reproduce across runs. We investigate…
Hanyu Zhang, Tomoji Kishi
Code smell is a great challenge in software refactoring, which indicates latent design or implementation flaws that may degrade the software maintainability and evolution. Over the past decades, a variety of refactoring approaches have been proposed, which can be broadly classified into metrics-based, rule-based, and…
Eik Niederlohmann
Computational psychiatry has advanced formal accounts of individual prediction, affect regulation, and maladaptive rigidity, but it still has fewer clinically interpretable tools for representing social and institutional processes under collective stress. This Hypothesis and Theory article proposes a theory-driven…
Yiwen Zhang, Wei Liu, Fazhong Jiang, Jiquan Ma + 4 more
Large Language Models of the Transformer architecture display great promise in automated code error detection based on their strength in processing sequential data. Nevertheless, their efficacy could be further improved by addressing the inherent weakness in handling structural code dependencies. In response to this…
Lei Shi, Min Dai, Yongbo Zhang, Song Wu + 2 more
Single-cell omics and spatial omics technologies are nowadays widely used in biological and medical research. In both single-cell and spatial omics data analysis, accurate cell type annotation is a key step for downstream analysis and scientific discoveries. However, high-quality cell annotation usually requires…
Alex R. Van Dam, Francisco Hita Garcia
The accelerating biodiversity crisis demands new approaches to taxonomic description that can scale beyond the capacity of professional taxonomists alone. We present the Descriptron-GBIF Annotator, a zero-installation, browser-based tool for morphological annotation of biodiversity specimen images retrieved directly…
Md Dilshadur Rahman, Devin Lange, Ghulam Jilani Quadri, Paul Rosen
Annotation is a central mechanism in visualization design that enables people to communicate key insights. Prior research has provided essential accounts of the visual forms annotations take, but less attention has been paid to the decisions behind them. This paper examines how annotations are designed in practice and…
Hung Q. Vo, Huy Q. Vo, Son T. Ly, Zhihao Wan + 5 more
Conventional tissue image analysis software provides foundational capabilities for cellular analysis, including segmentation, basic morphological feature extraction, and spatial organization analysis. However, these tools often require manual intervention and are not well integrated with code-driven automation…
Helen Lumbard, Lauren Cadwallader, Devin Soper
PLOS Medicine has always championed open science and data transparency. Now, recognizing that code is as essential a research artifact as the data it analyzes, we are strengthening our code sharing policy to further ensure reproducibility and trust in the scientific record.
M. Shahbaz Ismail, Sara Shahzad, Fahmi H. Quradaa, Sajid Anwar
Semantic code clone detection plays an essential role in software maintenance and quality assurance, as it helps uncover fragments of code that express the same logic even when their syntax has been altered or deliberately obfuscated. In this study, we propose a framework that combines hybrid representation learning…
Yanshuo Chen, Yuming Zhang, Joshua Li, Boxue Tian + 1 more
Codon optimization involves selecting synonymous codons to match host-specific preferences. It is critical for heterologous expression but remains challenging due to the combinatorial design space. Under long-term evolutionary selection, natural coding sequences are near-optimal compromises between translational…
Tomasz Przygodzki
Quantitative analysis of microscopic images has become a standard in basic biological and biomedical research. Deep machine learning provided a powerful tool facilitating this process. However, practical adoption of deep machine learning to image analysis may be difficult for a researcher who lacks basic coding skills.…
Authors not listed
Bayesian optimization (BO) has become increasingly important for experimental optimization across scientific domains, yet implementing BO pipelines requires significant programming expertise and familiarity with specialized frameworks. This creates a barrier for domain experts who could benefit from BO but lack the…
Authors not listed
This comprehensive review examines the evolution of autonomous materials synthesis laboratories that integrate artificial intelligence with advanced robotics to accelerate discovery. Traditional materials development pipelines typically require 10-20 years, but self-driving laboratories (SDLs) and Materials…
Khizra Maqsood, Duarte Polvora Brandao, Jareth Wolfe, Bhavana Kayyar + 9 more
Enhancers are non-coding regions of DNA that regulate gene transcription, yet the mechanisms underlying enhancer activity remain incompletely understood. Despite extensive experimental and computational efforts, we still lack accurate enhancer maps in many human cells, tissues and disease contexts. Here, we developed…