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EVAdyr: A new dynamic resampling algorithm for auto-tuning noisy High Performance Computing systems

JOUrNAL OF COMPUTATIONAL SCIENCE 2025年 84卷

作者： robert-Hayek, Sophie Zertal, Soraya Couvee, Philippe Eviden BDS R&D Data Management F-38130 Echirolles France UPSaclay UVSQ Li PaRAD F-78297 Guyancourt France

Black-box auto-tuning methods have been proven to be efficient for tuning configurable computer hardware, including those encountered within the High Performance Computing (HPC) ecosystem. However, because of the shared nature of HPC clusters and the complexity of the software and hardware stacks, the measurement of the performance function can be tainted by noise during the tuning process, which can reduce and sometimes prevent the benefit of the tuning approach. A usual choice for performing the tuning in spite of these interference is to add a resampling step at each iteration to reduce uncertainty, but this approach can be timeconsuming and must be done carefully. In this paper, we propose anew resampling and filtering algorithm called EVAdyr (Efficient Value Aware dynamic resampling). Compared to the state of the art, it finds a better exploration versus exploitation trade-off by resampling only promising configuration and increases the level of confidence around the suggested solution as the tuning process advances. This algorithm was able to tune efficiently two I/O accelerators highly sensitive to interference, in two different scenarios. Compared to Standard Error dynamic resampling (SEdr), a state of the art noise reduction strategy, we show that EVAdyr is able to reduce the distance to the optimum by 93.5% and 24.7% for the two I/O accelerators respectively, as well as speed-up the experiment duration by 45.8% and 58.1% because less iterations are needed to reach the found optimum. Our results prove the importance of using noise reduction strategies whenever tuning systems running in production.

关键词： resampling Auto-tuning Noise reduction I/O accelerators HPC

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Group buying with consumer disappointment at failed deals

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TrANSPOrTATION rESEArCH PArT E-LOGISTICS ANd TrANSPOrTATION rEVIEW 2025年 194卷

作者： Wang, Jie Ma, Benedict Jun Yang, Yanyi Cheng, Chun-Hung Kuo, Yong-Hong Southeast Univ Sch Econ & Management Nanjing Peoples R China Univ Hong Kong Dept Data & Syst Engn Hong Kong Peoples R China Chinese Univ Hong Kong Dept Syst Engn & Engn Management Hong Kong Peoples R China Logist & Supply Chain MultiTech R&D Ctr Ltd Hong Kong Peoples R China

In group buying (GB), the retailer launches a deal with a discounted product price and a minimum group size requirement. Strategic consumers then determine whether to sign up for the GB deal or purchase the product at the regular price immediately. If GB fails, disappointed GB participants perceive a negative psychological utility and decide whether or not to buy it again at the regular price. Considering the disappointment caused by a GB failure, in our basic model, we formulate a two-period game to study the retailer's optimal pricing decisions and consumers' purchasing strategies. By deriving the likelihood function of a consumer signing up for the GB deal and utilizing rational expectations theory, we characterize how consumers form their own beliefs about the GB success rate. We find that consumer sentiment toward a failed GB deal serves an important role in a GB deal. Specifically, there exists a threshold of the disappointment factor where the retailer's profit and consumers' purchase decisions may change, and consumer leakage and retention may occur. We prove the existence of the subgame perfect Nash equilibrium and outline how the retailer should design the GB schedule. Our study shows that if properly designed, GB is an effective strategy to enhance consumer interests and improve profit. Moreover, a big discount should be offered when the disappointment factor is significant. When the consumer sentiment toward a failed GB deal is insignificant, the retailer should launch a GB deal;otherwise, he should provide the regular sales channel only. We conduct numerical experiments to study the impacts of different factors in a GB deal. Our key results continue to hold in several extensions from our basic model: retailer competition, observable secured group size, and social interactions between consumers.

关键词： Group buying Strategic consumer behavior disappointment factor

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NTHi killing activity is reduced in COPd patients and is associated with a differential microbiome

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rESPIrATOrY rESEArCH 2025年第1期26卷 1-14页

作者： Gopalakrishnan, Vancheswaran Sparklin, Ben Kim, Jung Hwan Bouquet, Jerome Kehl, Margaret Kenny, Tara Morehouse, Christopher Caceres, Carolina Warrener, Paul Hristova, Ventzislava A. Wilson, Susan Shandilya, Harini Barnes, Arnita ruzin, Alexey Wang, Junmin Oberg, Lisa Angermann, Bastian Mccrae, Christopher Platt, Adam Muthas, daniel Hess, Sonja Tkaczyk, Christine Sellman, Bret r. Ostridge, Kristoffer Belvisi, Maria G. Wilkinson, Tom M. A. Staples, Karl J. digiandomenico, Antonio MICA II Study Grp, Vancheswaran AstraZeneca BioPharmaceut R&D Bioinformat Res & Early Dev Vaccines & Immune Ther Gaithersburg MD USA AstraZeneca BioPharmaceut R&D Bacterial Vaccines Res & Early Dev Vaccines & Immu Gaithersburg MD USA AstraZeneca BioPharmaceut R&D Virol & Vaccine Discovery Res & Early DevVaccines & Immune Therapies Gaithersburg MD USA AstraZeneca BioPharmaceut R&D Res & Early Dev Translat Sci ManagementVaccines & Immune Therapie Gaithersburg MD USA AstraZeneca Ctr Genom Res CGR BioPharmaceut R&D Dynam OmicsDiscovery Sci Gaithersburg MD USA AstraZeneca Oncol R&D Biol Engn Gaithersburg MD USA AstraZeneca BioPharmaceut R&D Quantitat Biol Data Sci & Quantitat BiolDiscovery Sci AstraZeneca Gaithersburg MD USA AstraZeneca Translat Sci & Expt Med Res & Early Dev BioPharmaceut R&DResp & Immunol Gothenburg Sweden AstraZeneca Translat Sci & Expt Med BioPharmaceut R&D Res & Early DevResp & Immunol Gaithersburg MD USA AstraZeneca BioPharmaceut R&D Res & Early Dev Translat Sci & Expt MedResp & Immunol Cambridge England AstraZeneca Res & Early Dev Vaccines & Immune Therapies BioPharmaceut R&DMicrobial Antibodies & Technol Gaithersburg MD 20878 USA Univ Southampton Fac Med Clin & Expt Sci Southampton England AstraZeneca Res & Early Dev Resp & Immunol BioPharmaceut R&D Gothenburg Sweden Univ Hosp Southampton NIHR Southampton Biomed Res Ctr Southampton England

Chronic obstructive pulmonary disease (COPd) is a chronic lung disease characterized by airway obstruction and inflammation. Non-typeable Haemophilus influenzae (NTHi) lung infections are common in COPd, promoting frequent exacerbations and accelerated lung function decline. The relationship with immune responses and NTHi are poorly understood. Herein, we comprehensively characterized the respiratory microbiome and mycobiome of patients while investigating microbial dynamics and host immune changes attributable to NTHi killing activity. Mild-to-moderate COPd patients encompassing frequent and infrequent exacerbators and healthy volunteers (HV) were enrolled. Microbial composition, proteomics and NTHi killing activity was analyzed using bronchoalveolar lavage fluid (BALF). In addition, antigen-antibody titers in sera to COPd pathogens were determined using a multiplex assay. differential abundance analysis revealed an enrichment of Actinobacteria and Bacteroidetes in the BALF of COPd and HV subjects respectively. Significant differences in the IgA titer response were observed against NTHi antigens in COPd vs. HV. Notably, there was also significantly greater killing activity against NTHi in BALF from COPd vs. HV subjects (Or = 5.64;95% CI = 1.75-20.20;p = 0.001). Stratification of COPd patients by NTHi killing activity identified unique microbial and protein signatures wherein Firmicutes, Actinobacteria and haptoglobin were enriched in patients with killing activity. We report that differences in host immune responses and NTHi-killing activity are associated with microbiome changes in mild-to-moderate COPd. This is suggestive of a potential link between the respiratory microbiome and immune activity against NTHi in the context of COPd pathogenesis even at this disease stage.

关键词： COPd Non-typeable Haemophilus influenzae Microbiome Exacerbations

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Co-treatment with Gabapentinoid and Japanese Herbal Medicine Goshajinkigan for CIPN is Associated with Longer duration and Higher dose of Chemotherapy

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AdVANCES IN THErAPY 2025年第6期42卷 2833-2852页

作者： Miyano, Kanako Uezono, Yasuhito Yamaguchi, Takuhiro Hashimoto, Wataru Komoriya, Satoshi Jikei Univ Dept Pain Control Res Sch Med Minato Ku Tokyo Japan Juntendo Univ Fac Pharm Lab Pharmacotherapeut Urayasu Chiba Japan Tohoku Univ Grad Sch Med Div Biostat Sendai Miyagi Japan Daiichi Sankyo Co Ltd Data Intelligence Dept Tokyo Japan Daiichi Sankyo Co Ltd R&D Div R&D Management Dept Tokyo Japan

IntroductionIn Japan, both gabapentinoids and the Japanese traditional herbal medicine goshajinkigan (GJG) are used to manage chemotherapy-induced peripheral neuropathy (CIPN);however, evidence for their effectiveness is inconclusive. Patients with CIPN experience reduced quality of life and often undergo reductions in dose or discontinuation of chemotherapy. Therefore, this retrospective cohort study used a real-world database to examine the efficacy of gabapentinoids and GJG therapy for patients with CIPN by evaluating chemotherapy duration and *** from 145,384 patients diagnosed with CIPN while receiving platinum- or taxane-based chemotherapy between April 1, 2008 and March 31, 2022 were stratified by CIPN treatment: simultaneous gabapentinoid (mirogabalin or pregabalin) plus GJG (prescription dates overlap);non-simultaneous gabapentinoid plus GJG (prescription dates do not overlap);gabapentinoid alone;GJG alone;and neither gabapentinoids nor GJG. duration and dose of chemotherapy were the primary *** with either a gabapentinoid or GJG alone was associated with longer duration and higher doses of chemotherapy versus neither gabapentinoids nor GJG in patients treated with carboplatin, cisplatin, or paclitaxel. Combined gabapentinoid plus GJG treatment elicited further longer duration and higher doses of chemotherapy versus gabapentinoid alone or GJG alone in patients treated with carboplatin, oxaliplatin, cisplatin, paclitaxel, or docetaxel. When stratified by cancer type, similar trends were observed regarding combination gabapentinoid plus GJG treatment among patients with colorectal cancer treated with oxaliplatin and patients with gastric, lung, or breast cancer treated with *** treatment with gabapentinoid plus GJG might prevent reductions in dose or discontinuation of chemotherapy, and might be effective for the treatment of CIPN.

关键词： Chemotherapy-induced peripheral neuropathy Gabapentinoid Goshajinkigan Japanese herbal Kampo medicine Platinum-based chemotherapy Taxane-based chemotherapy

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Computational tools for the prediction of site- and regioselectivity of organic reactions

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CHEMICAL SCIENCE 2025年第13期16卷 5383-5412页

作者： Sigmund, Lukas M. Assante, Michele Johansson, Magnus J. Norrby, Per-Ola Jorner, Kjell Kabeshov, Mikhail AstraZeneca Gothenburg Mol AI Discovery Sci R&D Pepparedsleden 1 S-43183 Molndal Sweden Univ Cambridge Innovat Ctr Digital Mol Technol Dept Chem Lensfield Rd Cambridge CB2 1EW England AstraZeneca Cambridge Discovery Ctr Cpd Synth & Management Cambridge Biomed Campus1 Francis Crick Ave Cambridge CB2 0AA England AstraZeneca Gothenburg Med Chem Res & Early Dev Cardiovasc Renal & Metab BioPharmaceut R&D Pepparedsleden 1 S-43183 Molndal Sweden AstraZeneca Gothenburg R&D Pharmaceut Sci Data Sci & Modelling Pepparedsleden 1 S-43183 Molndal Sweden Swiss Fed Inst Technol Inst Chem & Bioengn Dept Chem & Appl Biosci Vladimir Prelog Weg 1 CH-8093 Zurich Switzerland Swiss Fed Inst Technol Natl Ctr Competence Res NCCR Catalysis Zurich Switzerland

The regio- and site-selectivity of organic reactions is one of the most important aspects when it comes to synthesis planning. due to that, massive research efforts were invested into computational models for regio- and site-selectivity prediction, and the introduction of machine learning to the chemical sciences within the past decade has added a whole new dimension to these endeavors. This review article walks through the currently available predictive tools for regio- and site-selectivity with a particular focus on machine learning models while being organized along the individual reaction classes of organic chemistry. respective featurization techniques and model architectures are described and compared to each other;applications of the tools to critical real-world examples are highlighted. This paper aims to serve as an overview of the field's status quo for both the intended users of the tools, that is synthetic chemists, as well as for developers to find potential new research avenues.

关键词： Prediction models

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Application of model-informed drug development (MIdd) for dose selection in regulatory submissions for drug approval in Japan

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JOUrNAL OF PHArMACOKINETICS ANd PHArMACOdYNAMICS 2025年第1期52卷 1-18页

作者： Sasaki, Tomohiro JPMA MIdd Task Force, Tomohiro Katsube, Takayuki Hayato, Seiichi Yamaguchi, Shingo Tanaka, Jun Yoshimatsu, Hiroki Nakanishi, Yushi Kitamura, Atsushi Watase, Hirotaka Suganami, Hideki Matsuoka, Nobushige Hasegawa, Chihiro Otsuka Pharmaceut Co Ltd Clin Pharmacol Osaka Japan Clin Pharmacol & Pharmacokinet Shionogi & Co Ltd Osaka Japan Eisai & Co Ltd Clin Pharmacol Sci Tokyo Japan GlaxoSmithKine KK Clin Dev Tokyo Japan Bristol Myers Squibb KK Clin Pharmacol & Pharmacometr Tokyo Japan Pfizer R&D Japan GK Biometr & Data Management Tokyo Japan Kowa Co Ltd Clin Data Sci Dept Tokyo Japan Sumitomo Pharm Co Ltd Clin Pharmacol Osaka Japan Sanofi KK Pharmacokinet Dynam & Metab Translat Med & Early D Tokyo Japan MSD KK Clin Pharmacol Dev Area Tokyo Japan

Model-informed drug development (MIdd) is an approach to improve the efficiency of drug development. To promote awareness and application of MIdd in Japan, the data Science Expert Committee of the drug Evaluation Committee in the Japan Pharmaceutical Manufacturers Association established a task force, which surveyed MIdd applications for approved products in Japan. This study aimed to reveal the trends and challenges in the use of MIdd by analyzing the survey results. A total of 322 cases approved in Japan between January 2020 and March 2022 as medical products were included in the survey. Modeling analysis was performed in approximately half of the cases (47.8% [154/322]) and formed a major basis for the selection or justification of dosage and administration in approximately one-fourth of the cases [24.2% (78/322)]. Modeling analysis/model-based dose selection was frequently conducted in cases involving monoclonal antibodies, first indication, orphan drugs, and multi-regional trials. Moreover, the survey results indicated that modeling analyses contributed to dose optimization throughout the developmental phases, including changing dose levels from phase II to phase III and dose adjustment in special populations. Japanese data were included in most cases in which modeling analysis was used for dosage selection. Thus, modelling analysis may also address ethnic factors introduced in the ICH E5 and/or E17 guidelines. In summary, this survey is useful for understanding the current status of MIdd use in Japan and for future drug development.

关键词： MIdd Japan JPMA dose selection Pharmacometrics

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Bus Sub-station Lines Optimization Based on Analysis of Main Passenger Flow in the Same direction

Bus Sub-station Lines Optimization Based on Analysis of Main...

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International Conference on Artificial Intelligence and Autonomous Transportation, AIAT 2024

作者： Wei, Qingbo Xuan, Qipeng Su, Kui Sha, Zhiren Su, Yuejiang Guangzhou Public Transport Data Management Center Co. Ltd. Guangzhou510620 China Guangzhou Municipal Transportation Bureau Guangzhou510620 China Guangzhou Fundway Smart Transportations R&D Co. Ltd. Guangzhou510000 China School of Civil Engineering and Transportation South China University of Technology Guangzhou510641 China

ISBN: (纸本)9789819639601

In traditional design of bus sub-station lines, most are based on experience model, which is easy to distribute the same direction lines at different sub-stations, resulting in a decline in passenger travel experience. To solve this problem, this study proposes an automatic calculation method for the optimal bus sub-station lines. Based on the actual travel Od of bus passengers, stopping lines and their departure frequencies, distribution of downstream bus station, and the stopping capacity of each sub-station, a Genetic Algorithm (GA) model is constructed to solve the optimal scheme. In the GA algorithm, the fitness function is "passengers with the same Od board at the same sub-station as much as possible, and travels of the same direction board at the same sub-station as much as possible", and in the process of selection, crossover and mutation, limitation of each sub-station’s stopping capacity is also fully considered. Finally, some sub-stations in Guangzhou is taken as the test object, with "the total number of passengers boarding at the same sub-station" and other indicators are taken as the test index. results show that after optimization, the stopping sub-station of bus lines in the same direction are more concentrated, and the number of passengers who fully enjoy taking the line at the same station increases by 71%. Overall, this study can provide engineering application solutions for automatic design of bus sub-station lines. © Beijing Paike Culture Commu. Co., Ltd. 2025.

关键词： Genetic algorithms

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Enzyme cycling method using hypoxanthine-guanine phosphoribosyltransferase: a highly sensitive assay for pyrophosphate

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ANALYTICAL METHOdS 2025年第12期17卷 2600-2606页

作者： Ueda, Shigeru Yasutake, Yoshiaki Hirata, Tatsuya Sahara, Takehiko Sakasegawa, Shin-ichi Japanese Comm Clin Lab Stand Tokyo 1010047 Japan Chiba Inst Sci Fac Risk & Crisis Management Dept Hlth & Med Sci Choshi 2880025 Japan Natl Inst Adv Ind Sci & Technol Bioprod Res Inst Sapporo 0628517 Japan AIST Computat Bio Big Data Open Innovat Lab CBBD OIL Tokyo 1698555 Japan Asahi Kasei Pharm Corp Diagnost Dept R&D Grp Izunokuni 4102321 Japan Natl Inst Adv Ind Sci & Technol Bioprod Res Inst Tsukuba 3058561 Japan

We developed a novel enzyme cycling method using hypoxanthine-guanine phosphoribosyltransferase (HGPrT) (EC 2.4.2.8) from Hungateiclostridium thermocellum. This method exploits the reversible nature of the HGPrT reaction, catalyzing both forward and reverse reactions in the presence of excess inosine 5 '-monophosphate (IMP) and guanine (Gua), similar to the established purine nucleoside phosphorylase (PNP)-based method. real-time detection was achieved by coupling the reaction with commercially available xanthine dehydrogenase (XdH) (EC 1.17.1.4) in the presence of nicotinamide adenine dinucleotide (NAd+). The reaction exhibited high efficiency, with a cycling rate constant of approximately 60 min-1 or higher at an HGPrT concentration of 1 U mL-1. Additionally, we demonstrated a preliminary application of this XdH-coupled enzyme cycling reaction for the determination of pyrophosphate (PPi).

关键词： rate constants

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Safety and pharmacokinetics of vepdegestrant in Japanese patients with Er plus advanced breast cancer: a phase 1 study

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INTErNATIONAL JOUrNAL OF CLINICAL ONCOLOGY 2025年第1期30卷 72-82页

作者： Iwata, Hiroji Naito, Yoichi Hattori, Masaya Yoshimura, Akiyo Yonemori, Kan Aizawa, Mana Mori, Yuko Yoshimitsu, Junichiro Umeyama, Yoshiko Mukohara, Toru Aichi Canc Ctr Hosp Dept Breast Oncol 1-1 KanokodenChikusa ku Nagoya Aichi 4648681 Japan Natl Canc Ctr Hosp East Dept Med Oncol 6-5-1 Kashiwanoha Kashiwa Chiba 2778577 Japan Natl Canc Ctr Dept Med Oncol Chuo Ku 5-1-1 TsukijiChuo Ku Tokyo 1040045 Japan Pfizer R&D Japan Dept Biometr & Data Management 3-22-7 YoyShibuya ku Tokyo 1518589 Japan Pfizer R&D Japan Dept Clin Res 3-22-7 YoyShibuya ku Tokyo 1518589 Japan Nagoya City Univ Grad Sch Med Sci Core Lab Dept Med Res & Dev Strategy 1 KawasumiMizuho ku Nagoya 4678601 Japan

BackgroundVepdegestrant (ArV-471) is an oral PrOteolysis TArgeting Chimera (PrOTAC) estrogen receptor (Er) *** phase 1 study (NCT05463952) investigated safety, pharmacokinetics, and antitumor activity of vepdegestrant in Japanese patients with Er-positive (Er+)/human epidermal growth factor receptor 2-negative (HEr2-) advanced breast cancer at the 200-mg once daily (Qd) recommended phase 3 dose. Eligible patients had Er+/HEr2- advanced breast cancer resistant to standard therapy, with no standard therapy available, or had received two or more prior endocrine therapies in any setting. The primary endpoint was dose-limiting toxicities (dLTs) in cycle 1;secondary endpoints included safety, pharmacokinetics, and antitumor *** female patients (median age, 58 [range: 47-62] years) were treated. For advanced disease, three (50.0%) patients received three or more prior regimens and five (83.3%) patients received prior cyclin-dependent kinase 4/6 inhibitors. At data cutoff, median treatment duration was 9.8 (range: 6-28) weeks;two patients remained on treatment. No dLTs were observed. Four (66.7%) patients experienced adverse events;none led to dose reduction or discontinuation. Four (66.7%) patients had treatment-related adverse events;all were grade 1 except anemia (grade 2). Geometric mean maximum plasma concentration and 24-h area under the plasma concentration-time curve of vepdegestrant were 630.9 ng/mL and 10,400 ng center dot hr/mL after a single dose and 1056 ng/mL and 18,310 ng center dot hr/mL after multiple doses. Two (33.3%) patients demonstrated stable disease at week *** 200 mg Qd was well tolerated in Japanese patients with Er+/HEr2- advanced breast cancer with no notable differences in pharmacokinetics from Western *** trial ***: NCT05463952 (date of registration: July 19, 2022).

关键词： Advanced breast cancer Estrogen receptor-positive Human epidermal growth factor receptor 2-negative Vepdegestrant Japanese patients Safety

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Planning and Implementing Master Protocol Trials in Japan: Key Considerations of the Japanese Guideline

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CLINICAL PHArMACOLOGY & THErAPEUTICS 2025年第3期117卷 627-632页

作者： Hirakawa, Akihiro Asakawa, Takashi Tokushige, Kota Ozaki, ryoto Yoshida, Mizuki Okuma, Hitomi Sumiyoshi Saito, Sho Shimizu, Yosuke Kitabayashi, ryo Hanazawa, ryoichi Sato, Hiroyuki Uemura, Yukari Inst Sci Tokyo Grad Sch Med & Dent Sci Dept Clin Biostat Tokyo Japan Chugai Pharmaceut Co Ltd Biometr Dept Tokyo Japan Novartis Pharm KK Adv Quantitat Sci Dev Japan Tokyo Japan Pfizer R&D Japan GK Dept Biometr & Data Management Dev Japan Tokyo Japan Natl Canc Ctr Dept Med Oncol Tokyo Japan Natl Ctr Global Hlth & Med Dis Control & Prevent Ctr Tokyo Japan Natl Ctr Global Hlth & Med Ctr Clin Sci Dept Data Sci Biostat Sect Tokyo Japan

The importance of master protocol trials, which encompass basket, umbrella, and platform trials, has been increasingly recognized worldwide for their efficiency in evaluating multiple drugs or diseases within a single trial. While the US Food and drug Administration and European regulatory bodies have issued guidelines to facilitate such trials, Japan only recently introduced its own set of guidelines to address the unique challenges and opportunities within its regulatory and healthcare landscape. Our study elaborates on these newly issued Japanese guidelines, which were developed through a collaborative effort involving biostatisticians, physicians, clinical trialists, regulatory authorities, and industry representatives. We provide a comprehensive overview of the guidelines, emphasizing their structure, content, and key considerations for effective planning and implementation. By highlighting the specific adaptations and innovations required to conduct master protocol trials in Japan, we aim to contribute to the broader discourse on optimizing clinical trial frameworks and enhancing drug development efficiency.

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