Explanipedia

Protein-level batch-effect correction enhances robustness in MS-based proteomics Open

Qiaochu Chen, Zehui Cao, Yaqing Liu, Naixin Zhang, Yan‐Ming Xie , et al. · 2025

Batch effects, defined as unwanted technical variations caused by differences in labs, pipelines, or batches, are notorious in MS-based proteomics data, wherein protein quantities are inferred from precursor- and peptide-level intensities.…

Drug-induced dermatomyositis: a pharmacovigilance study of the FDA adverse event reporting system Open

Jianing Bi, Hua Xie, Yixuan Yang, Qiaochu Chen, Bingnan Cui , et al. · 2025

Background Dermatomyositis (DM) is an autoimmune disease that may be triggered by certain medications. However, most studies have focused on specific drugs, lacking a comprehensive overview. This study uses the FDA’s Adverse Event Reportin…

Q40 sequencing reduces costs and enhances detection of low- frequency somatic variants Open

Shumeng Duan, Yaqing Liu, Xiaorou Guo, Zhiyin An, R.C.W. Ma , et al. · 2025

Background High quality scores (Q-scores) are critical for sequencing accuracy, yet the impact of Q40-achieving sequencing technologies (99.99% accuracy) on detecting subtle biological variations remains unvalidated. Results Using a compre…

Bioinspired photothermal zwitterionic fibrous membrane for high-efficiency solar desalination and electricity generation Open

Yuzhu Wang, Feng Chen, Qiaochu Chen, Wei Liu, Qihang Huang , et al. · 2025

Solar-driven desalination holds great promise for addressing the scarcity of global freshwater. However, salt accumulation remains a significant challenge, particularly for two-dimensional membrane materials. Inspired by aquaporins, we des…

Baseline Plasma GPX3 Level Predicts Efficacy of Insulin-Sensitization Drug Chiglitazar in Type 2 Diabetes Open

Zehui Cao, Haonan Chen, Qiaochu Chen, Chen Ding, Leming Shi , et al. · 2025

CRUST-Bench: A Comprehensive Benchmark for C-to-safe-Rust Transpilation Open

Anirudh Khatry, Robert Zhang, Jia Pan, Ziteng Wang, Qiaochu Chen , et al. · 2025

C-to-Rust transpilation is essential for modernizing legacy C code while enhancing safety and interoperability with modern Rust ecosystems. However, no dataset currently exists for evaluating whether a system can transpile C into safe Rust…

Exploring the role of Chinese herbal medicine in the long-term management of postoperative ovarian endometriotic cysts: a systematic review and meta-analysis Open

Dan‐Ni Ding, Shaoxuan Liu, Fangyuan Liu, Songli Hao, Chunlan Zhang , et al. · 2024

Background Ovarian endometriotic cysts (OEC) represent the primary manifestation of endometriosis, constituting a hormonally dependent inflammatory disorder in gynecology. It significantly affects the quality of life and reproductive healt…

Extend the benchmarking indel set by manual review using the individual cell line sequencing data from the Sequencing Quality Control 2 (SEQC2) project Open

Binsheng Gong, Dan Li, Yifan Zhang, Rebecca Kusko, Samir Lababidi , et al. · 2024

The Price Prediction of Vegetables by Using Machine Learning Open

Qiaochu Chen, Zhihua Yu, Kaixin Zheng · 2024

Vegetable prices are great important in ensuring people's livelihood. With the progress of science and technology, machine learning algorithms have been applied in the field of vegetable price prediction. This paper analyzed the model that…

A comprehensive personal omics clinical interpreter based on genomic and transcriptomic profiles Open

Yaqing Liu, Qingwang Chen, Qiaochu Chen, Leqing Sang, Yunjin Wang , et al. · 2024

Advances in precision medicine rely on the accurate identification and analysis of molecular alterations for personalized diagnostic, prognostic, and therapeutic decision-making. A critical obstacle is the integration of heterogeneous inte…

Multi-omics Quality Assessment in Personalized Medicine through EATRIS Open

Patricia Alonso-Andrés, Davide Baldazzi, Qiaochu Chen, Elisa Conde, Lorena Crespo-Toro , et al. · 2023

Molecular characterization of a biological sample, e.g., with omics approaches, is fundamental for the development and implementation of personalized and precision medicine approaches. In this context, quality assessment is one of the most…

Multi-omics data integration using ratio-based quantitative profiling with Quartet reference materials Open

Yuanting Zheng, Yaqing Liu, Jingcheng Yang, Lianhua Dong, Rui Zhang , et al. · 2023

Data Extraction via Semantic Regular Expression Synthesis Open

Qiaochu Chen, Arko Banerjee, Çağatay Demiralp, Greg Durrett, Işıl Dillig · 2023

Many data extraction tasks of practical relevance require not only syntactic pattern matching but also semantic reasoning about the content of the underlying text. While regular expressions are very well suited for tasks that require only …

SatLM: Satisfiability-Aided Language Models Using Declarative Prompting Open

Xi Ye, Qiaochu Chen, Işıl Dillig, Greg Durrett · 2023

Prior work has combined chain-of-thought prompting in large language models (LLMs) with programmatic representations to perform effective and transparent reasoning. While such an approach works well for tasks that only require forward reas…

PAnno: A pharmacogenomics annotation tool for clinical genomic testing Open

Yaqing Liu, Zipeng Lin, Qingwang Chen, Qiaochu Chen, Leqing Sang , et al. · 2023

Introduction: Next-generation sequencing (NGS) technologies have been widely used in clinical genomic testing for drug response phenotypes. However, the inherent limitations of short reads make accurate inference of diplotypes still challe…

High-Performance Piezoelectric Nanogenerators Based on Cs2ag0.3na0.7incl6 Double Perovskites with High Polarity Induced by Zr/Te Codoping Open

Xiangcong He, Wenna Liu, Deliu Ou, Chris Bowen, Songhan Shi , et al. · 2023

Yb3+/Eu3+/Ho3+ Tridoped Cs2Ag0.3Na0.7InCl6 Double Perovskite with Excitation-Wavelength-Dependent Triple Emission for Anti-Counterfeiting Application Open

Qiaochu Chen, Jialiang Jiang, Hao Zhang, Hui Fu, Wenliang Liu , et al. · 2022

Developing a secure anti-counterfeiting technology with more dimensional encryptions is urgently demanded. The lead-free double perovskite (DP) family represented by A2BIBIIIX6 hold great potential for applications in advanced fluorescence…

Ratio-based quantitative multiomics profiling using universal reference materials empowers data integration Open

Yuanting Zheng, Yaqing Liu, Jingcheng Yang, Lianhua Dong, Rui Zhang , et al. · 2022

Multiomics profiling is a powerful tool to characterize the same samples with complementary features orchestrating the genome, epigenome, transcriptome, proteome, and metabolome. However, the lack of ground truth hampers the objective asse…

Quartet metabolite reference materials for assessing inter-laboratory reliability and data integration of metabolomic profiling Open

Naixin Zhang, Peipei Zhang, Qiaochu Chen, Kejun Zhou, Yaqing Liu , et al. · 2022

Various laboratory-developed metabolomic methods lead to big challenges in inter-laboratory comparability and effective integration of diverse datasets. As part of the Quartet Project, we established a publicly available suite of four meta…

Ratio-based quantitative multiomics profiling using universal reference materials empowers data integration Open

Yuanting Zheng, Yaqing Liu, Jingcheng Yang, Lianhua Dong, Rui Zhang , et al. · 2022

Multiomics profiling is a powerful tool to characterize the same samples with complementary features orchestrating the genome, epigenome, transcriptome, proteome, and metabolome. However, the lack of ground truth hampers the objective asse…

Correcting batch effects in large-scale multiomic studies using a reference-material-based ratio method Open

Ying Yu, Naixin Zhang, Yuanbang Mai, Qiaochu Chen, Zehui Cao , et al. · 2022

Batch effects are notorious technical variations that are common in multiomic data and may result in misleading outcomes. With the era of big data, tackling batch effects in multiomic integration is urgently needed. As part of the Quartet …

The Quartet Data Portal: integration of community-wide resources for multiomics quality control Open

Jingcheng Yang, Yaqing Liu, Jun Shang, Qiaochu Chen, Qingwang Chen , et al. · 2022

The implementation of quality control for multiomic data requires the widespread use of well-characterized reference materials, reference datasets, and related resources. The Quartet Data Portal was built to facilitate community access to …

Type-Directed Synthesis of Visualizations from Natural Language Queries Open

Qiaochu Chen, Shankara Pailoor, Celeste Barnaby, Abby Criswell, Chenglong Wang , et al. · 2022

We propose a new technique based on program synthesis for automatically generating visualizations from natural language queries. Our method parses the natural language query into a refinement type specification using the intents-and-slots …

Web Question Answering with Neurosymbolic Program Synthesis Open

Qiaochu Chen, Aaron Lamoreaux, Xinyu Wang, Greg Durrett, Osbert Bastani , et al. · 2021

In this paper, we propose a new technique based on program synthesis for extracting information from webpages. Given a natural language query and a few labeled webpages, our method synthesizes a program that can be used to extract similar …

Optimal Neural Program Synthesis from Multimodal Specifications Open

Xi Ye, Qiaochu Chen, Işıl Dillig, Greg Durrett · 2021

Multimodal program synthesis, which leverages different types of user input to synthesize a desired program, is an attractive way to scale program synthesis to challenging settings; however, it requires integrating noisy signals from the u…

Sketch-Driven Regular Expression Generation from Natural Language and Examples Open

Xi Ye, Qiaochu Chen, Xinyu Wang, Işıl Dillig, Greg Durrett · 2020

Recent systems for converting natural language descriptions into regular expressions (regexes) have achieved some success, but typically deal with short, formulaic text and can only produce simple regexes. Real-world regexes are complex, h…

Optimal Neural Program Synthesis from Multimodal Specifications Open

Xi Ye, Qiaochu Chen, Işıl Dillig, Greg Durrett · 2020

Multimodal program synthesis, which leverages different types of user input to synthesize a desired program, is an attractive way to scale program synthesis to challenging settings; however, it requires integrating noisy signals from the u…

Benchmarking Multimodal Regex Synthesis with Complex Structures Open

Xi Ye, Qiaochu Chen, Işıl Dillig, Greg Durrett · 2020

Existing datasets for regular expression (regex) generation from natural language are limited in complexity; compared to regex tasks that users post on StackOverflow, the regexes in these datasets are simple, and the language used to descr…

Benchmarking Multimodal Regex Synthesis with Complex Structures Open

Xi Ye, Qiaochu Chen, Işıl Dillig, Greg Durrett · 2020

Existing datasets for regular expression (regex) generation from natural language are limited in complexity; compared to regex tasks that users post on StackOverflow, the regexes in these datasets are simple, and the language used to descr…

Sketch-Driven Regular Expression Generation from Natural Language and Examples Open

Xi Ye, Qiaochu Chen, Xinyu Wang, Işıl Dillig, Greg Durrett · 2019

Recent systems for converting natural language descriptions into regular expressions (regexes) have achieved some success, but typically deal with short, formulaic text and can only produce simple regexes. Realworld regexes are complex, ha…

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