OUT NOW Handbook of Digital and Computational #ResearchMethods In the Social Sciences and Humanities Eds @Anderskoed1 and @AndersKMunk ℹ️ tinyurl.com/y8fnpmy4 👓 Read a sample doi.org/10.4337/978180220899… #ComputationalMethods #DigitalMethods #Methodology #Toolmaking #Algorithms

New in the February 15 issue from the Cancer Research special series: CanSig Benchmarks Methods for Reproducible Cancer Cell State Discovery from Single-Cell Transcriptomic Data doi.org/10.1158/0008-5472.CA… @JoYatesResearch @KraftAgnieszka @val_boeva #ComputationalMethods #OpenAccess

New in the February 15 issue from the Cancer Research special series: Deep-Learning Tool ScVital Enables Species-Agnostic Integration of Cancer Cell States doi.org/10.1158/0008-5472.CA… @TuomasTammela @MSKCancerCenter #ComputationalMethods #OpenAccess

📢 Call for Reading: "Exploring Tonal Variation Using Dialect Tonometry" 🔗Full Text: mdpi.com/2226-471X/9/12/378 📚Special Issue: mdpi.com/journal/languages/s… #tonalvariation #dialecttonometry #dialectometry #computationalmethods #OpenAccess #AcademicPublishing

TusOAI: Agentic Optimization for Scientific Methods 1. TusOAI is an innovative AI system that autonomously develops and optimizes computational methods for scientific tasks. It integrates domain knowledge into a knowledge tree representation and performs iterative, domain-specific optimization and model diagnosis, significantly improving performance over existing methods. 2. The system outperformed state-of-the-art expert methods, MLE agents, and scientific AI agents across diverse tasks such as single-cell RNA-seq data denoising and satellite-based earth monitoring. This demonstrates its versatility and potential to accelerate scientific discovery. 3. TusOAI achieved a 40% power improvement to scDRS in associating cells to disease in simulations and a 10.5% enrichment improvement to pgBoost for identifying ground-truth variant-gene pairs. These enhancements highlight its ability to uncover novel biology. 4. The system also revealed 9 new associations between autoimmune diseases and T cell subtypes, as well as 7 previously unreported links between disease variants and their target genes. This showcases its potential to provide new biological insights. 5. TusOAI features a novel framework with a knowledge tree for structured representation of domain knowledge, hierarchical planning with Bayesian updates to balance solution quality and diversity, and fine-grained generation that integrates model optimization with diagnostic feedback. 6. The system was benchmarked on 6 single-cell analysis tasks and 5 scientific deep learning tasks, consistently outperforming baseline methods with an average 16% improvement in single-cell tasks. This highlights its robustness and effectiveness. 7. The code for TusOAI is publicly available, allowing researchers to explore and utilize this powerful tool for their own scientific endeavors. 📜Paper: arxiv.org/abs/2509.23986 #AI #ScientificDiscovery #ComputationalMethods #Genetics #SingleCell #DeepLearning

New in the October 1 issue from the Cancer Research special series: Challenges and Opportunities in Analyzing Cancer-Associated #Microbiomes doi.org/10.1158/0008-5472.CA… @stevensalzberg1 @niranjantw @JHUBME @JHUCompSci @astar_gis @NUSMedicine #ComputationalMethods

New publication alert! 🚨 A team at @UHN’s @pmcancercentre explored #computationalmethods for analyzing CUT&RUN #genomic data, offering insights to improve this new, powerful technique for studying protein-DNA interactions. 🔗 doi.org/10.1093/bioinformati…

Hybrid threats—from #cyberattacks to #misinformation—undermine trust & fuel social unrest. Can we predict & counter them? This study models how threat agents adapt & spread chaos. A game-changer for security research! Read #OpenAccess on #JASSS: jasss.org/28/1/1.html #Hybridwarfare #Security #AgentbasedModelling #ReinforcementLearning #computationalsociology #computationalmethods

Next up at #CAAUK2024: Exploring shipwrecks with AI! Cal T. Pols reveals how Machine Learning can be used for shipwrecks detection and analysis in big datasets. 🚢 #MaritimeArchaeology #MachineLearning #ComputationalMethods

Virtual seminar alert 📣📣 Tomorrow at 2 p.m. ET Sean Johnson (@NEBiolabs) joins us for an #IPISeminar on how to use #computationalmethods to explore the natural and non-natural #protein space. Find the link on our events calendar ➡️ calendar.google.com/calendar…

How many of the PDB models that were solved using experimental phasing could have been solved by molecular replacement using models obtained from AlphaFold? @ActaCrystD @IUCr #MolecularReplacement #AlphaFold2 #ComputationalMethods doi.org/10.1107/S20597983240…

I'm serving as a Guest Editor for BMC Psychiatry collection on Computational Psychiatry. For more info, please check the collection website: lnkd.in/gfsyBzsV #ComputationalPsychiatry #DigitalMentalHealth #MentalHealthInnovation #ComputationalMethods #PrecisionPsychiatry

Advances in designing functional protein fragments and peptides are summarized, addressing challenges and future directions in the field. #ProteinDesign #PeptideBinding #ComputationalMethods Details:spj.science.org/doi/10.34133…

❓Did you know? In ECCOMAS, there are 23 member associations🫂 🔸Some of them are supranational: ERCOFTAC, CEACM and NOACM 🔸Some countries have multiple member associations. 👉 Discover more about #ECCOMAS members: eccomas.org/about/member-ass… #computationalMethods #appliedScience

📯 #Mathematics New Special Issue Book! #NumericalSimulation and #ComputationalMethods in Engineering and Sciences Edited by Prof. Dr. Zhuojia Fu, Prof. Dr. Yiqian He and Prof. Dr. Hui Zheng. 🔗 buff.ly/3xTNDzo #MDPIOpenAccess @ComSciMath_Mdpi @BooksMDPI

💨 First Paper published in the Special Issue " Advances in #Computational Statistics, Design of Experiments, and Its Applications"! #experimentaldesigns #statisticalmodelling #computationalmethods 🔗 buff.ly/4ca8Zrd #MDPIOpenAccess @ComSciMath_Mdpi

The SI "Generative #AI and Advanced #ComputationalMethods for #IntelligentSystems" aims to advance the capabilities of intelligent systems, spanning from #smartmanufacturing, #supplychainmanagement, #autonomousvehicles. buff.ly/4bOgnZr #MDPIOpenAccess @ComSciMath_Mdpi

Excited to launch our Computational Multi-Modal Communication Lab website: sites.google.com/view/cmmcla…! With @cuihua, @pengyilang & our excellent students, we're dedicated to understanding visual and multimodal information using #computationalmethods. Visit our website to learn more!

🧬💻 The mitochondrial genome assessing the functional impact of #variants through #computationalmethods 🎤Proud to present at @Cnr_Ibbc with our talk on Computational Research on #Mitochondria

🔍 #PhDStudent Wanted! Passionate about #computationalmethods in #structuralvirology & #cryoET? Join Beata Turoňová’s project group @Beck_Laboratory! Start April 2024! 🚀Master's in CS, biophysics, math, or biochem? #Apply: biophys.mpg.de/molecular-soc… #PhDposition #StructuralBiology