💥 Special Issue extended deadline for submission! 🔗 mdpi.com/journal/bioengineer… 🕑 The new deadline for submissions is 31 May 2026 📌 #biomaterials #clinicalengineering #biomedicaldevices #cardiovascularengineering #biomedicalinstrumentation #biomedicalmodeling

Learning Cell-Aware Hierarchical Multi-Modal Representations for Robust Molecular Modeling 1. A new framework called CHMR is proposed to address limitations in current cell-aware molecular modeling approaches, focusing on modality incompleteness and insufficient hierarchical modeling across molecular, cellular, and genomic levels. 2. CHMR introduces a tree-structured vector quantization module to capture latent biological hierarchies, enabling the model to better understand cross-scale biological mechanisms from molecules to cells and genes. 3. The framework incorporates modality augmentation and semantic consistency alignment to handle missing biological data, significantly improving robustness and generalization in molecular property prediction tasks. 4. Evaluated on nine public benchmarks with 728 tasks, CHMR outperforms state-of-the-art methods, achieving average improvements of 3.6% in classification and 17.2% in regression tasks. 5. CHMR's hierarchical and multi-modal learning approach provides a generalizable framework for integrative biomedical modeling, offering reliable and biologically grounded molecular representations. 📜Paper: arxiv.org/abs/2511.21120v1 #MolecularModeling #HierarchicalLearning #MultiModalRepresentations #BiomedicalModeling

Adapting Biomedical Foundation Models for Predicting Outcomes of Anti Seizure Medications 1. A novel study explores the use of biomedical vision-language foundation models to predict the outcomes of antiseizure medications (ASMs) using only patient MRI scans and reports. This approach could revolutionize epilepsy treatment by reducing the trial-and-error process in ASM selection. 2. The study introduces a novel framework called TREE-TUNE, which integrates expert-built knowledge trees of MRI entities to enhance the performance of foundation models. This contextualized instruction-tuning method significantly improves the accuracy of predicting ASM outcomes compared to traditional methods. 3. A key innovation is the ability to generalize to unseen ASMs. By training on the four most commonly prescribed ASMs, the model can predict outcomes for completely new ASMs not encountered during training. This demonstrates the model's adaptability and potential for broader clinical applications. 4. The study achieved an average AUC of 71.39 for predicting outcomes of four primary ASMs and 63.03 for three completely unseen ASMs. This represents a substantial improvement over standard report-based instruction tuning, with a 5.53 and 3.51 AUC increase for seen and unseen ASMs, respectively. 5. The research leverages large-scale biomedical images and text to train the models, ensuring strong medical context understanding. The integration of MRI scans, reports, and a knowledge tree allows for more nuanced and context-aware predictions. 6. The study's findings highlight the potential of using biomedical foundation models for personalized epilepsy treatment recommendations. The approach not only improves prediction accuracy but also provides a foundation for developing reasoning-based ASM recommendation systems. 📜Paper: medrxiv.org/content/10.1101/… #Epilepsy #MachineLearning #BiomedicalModeling #PersonalizedMedicine

Join us for the CRBM Fall '24 Seminar Series! Kicking off with Dr. Peter Hunter’s talk on using bond graphs to ensure thermodynamic consistency in biophysical models. Register now: forms.gle/PQw3RLA7TPqBzExs9 #BiomedicalModeling #Thermodynamics #ScienceSeminars #multiscalemodeling

You can still register for the 7/12/23 1-day Kinetic Modeling Virtual Course & Hackathon. #Antimony #biochemicalmodeling #biomedicalmodeling #libRoadRunner #metabolicnetworks #parameterfitting #PythonBasics #SBMLDiagrams #systemsbiology #Tellurium reproduciblebiomodels.org/20…

Have you seen the schedule for the 2023 Metabolic Kinetic Modeling Course? reproduciblebiomodels.org/20… #Antimony #biochemicalmodeling #biomodeling #biomedicalmodeling #libRoadRunner #metabolicnetworks #parameterfitting #PythonBasics #SBMLDiagrams #systemsbiology #Tellurium

Just announced: 2023 1-day Kinetic Modeling Virtual Course & Hackathon For more info & to sign-up, please visit: reproduciblebiomodels.org/20… #Antimony #biomedicalmodeling #biomodeling #kineticmodeling #metaboliccontrolanalysis #modelparameters #Tellurium

There's still time to add our upcoming FREE tutorial "Development of signaling models" to your calendar! It's Friday, April 28th from 2-3 PM PDT. #biomedicalmodeling #biomodeling #freetutorials #modeling #reactionnetworks #science #signalingmodels reproduciblebiomodels.org/tu…

TUTORIAL TWEETS: Our next free tutorial - "Developing of signaling models" will be Friday, April 28th. Please join us! reproduciblebiomodels.org/tu… #biomedicalmodeling #biomodeling #modeling #reactionnetworks #signalingmodels

#ICYMI: Part 2 of our most recent tutorial session - "Introduction to parameter fitting using roadrunner and Julia" with Michael Kochen can be found here: youtu.be/qsryU1Fx5sQ #biomedicalmodeling #biomodeling #Julia #modeling #paramaterfitting #roadrunner #science

#ICYMI: Our most recent tutorial - "Introduction to particle-based modeling in Tissue Forge" with T.J. Sego can be found here: youtu.be/IyF-V3ojzA8 #biomedicalmodeling #spatialmodeling #tissueforge #particlebasedmodeling #Python

Reminder: Today last day to register for the 2022 Network Modeling Virtual Summer School & Symposium! #Tellurium #Antimony #libRoadRunner #SBstoat #sbmllint #science #reproducibility #biomedicalmodeling

Join Dr. Weindl and Dr. Hellerstein in this month's series discussion for PETab and SBstoat. Date: May 12th, 2021 Time: 9 AM PDT (12 PM EDT | 6 PM CEST) Zoom registration: washington.zoom.us/meeting/r… #biomedicalmodeling #biomodeling #systemsbiology #ScienceTwitter (4 of 4)

Join us on Wednesday, May 12th at 9 AM PDT to hear from Dr. Joe Hellerstein and Dr. Daniel Weindl about their work developing tools to support parameter estimation #biomedicalmodeling #biomodeling #systemsbio #systemsbiology #parameterestimation #science #simulation (1 of 4)

Don't forget to join us for our seminar with Dr. Jay Bardhan from @PNNLab this Wednesday. You can register for one or all of our monthly seminars at washington.zoom.us/meeting/r… #systemsbiology #bioengineering #biomedicalmodeling #systemsbiology #science

We invite you to participate in our seminar series this Wednesday, April 14th. We will hear from Dr. Jay Bardhan of the Pacific Northwest National Laboratories about methods used to address complexity in biological systems. #systemsbiology #bioengineering #biomedicalmodeling