Simone Bianco

Multiscale Modeling Primer: Focus on Chromatin and Epigenetics

Achal Mahajan, Erik J. Navarro, William Poole, Hana El-Samad et autres

A central challenge in modern biology is to understand how molecular interactions produce cellular and organismal functions across vast spatiotemporal scales. Nowhere is this challenge more apparent than in the study of chromatin, where meters of DNA compact into a micron-sized nucleus. …

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Deep learning of dynamic signatures resolves mechanistic ambiguity in complex signaling networks

Mustafa Ozen, Chaitra Agrahar, Francesca Zappa, Simone Bianco et autres

Abstract Sparse experimental data often yields vast mechanistic hypothesis spaces with numerous equally probable models. Traditional model selection metrics like the Akaike Information Criterion fall short because they reduce models’ nonlinear dynamics to a scalar score that masks crucial mechanistic details. Here, …

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The projection basis determines the information ceiling for perturbation prediction

Simone Bianco

Abstract Recent benchmarks show that deep-learning models for perturbation prediction do not outperform simple baselines operating in principal-component (PCA) space. We explain this with an information-theoretic ceiling: for any orthonormal projection basis Φ , the squared correlation between prediction and truth is …

Beyond distortions: a benchmark for subjective evaluation of image rendering quality

Vsevolod Plokhotnyuk, Artyom Panshin, Nikola Banić, Simone Bianco et autres

Traditional Image Quality Assessment (IQA) has primarily aimed to quantify perceptual quality in terms of technical degradations such as noise, blur, or compression artifacts. However, in image rendering, the key factor influencing perceived quality is not the presence of degradations but the …

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A Physics-based Model Reveals Mechanisms of Epigenetic Memory

Erik J. Navarro, William Poole, Ariane Lismer, Jieqiong Qu et autres

In multi-cellular eukaryotic organisms, cell type and specific functional identity are defined by the epigenetic patterning of chemical modifications to DNA and chromatin that modulate the expression and silencing of specific genes. When a cell divides, histones containing important epigenetic marks are …

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Federated Learning for Cross-Dataset Generalization in Litter Detection

Luciano Baresi, Simone Bianco, Livia Lestingi, Iyad Wehbe

The accumulation of litter in natural environments poses significant ecological and social challenges, motivating the development of automated solutions for litter detection. However, collecting and centrally aggregating large-scale annotated datasets for training object detectors often raises privacy and ownership concerns. In this …

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scGeneScope: A Treatment-Matched Single Cell Imaging and Transcriptomics Dataset and Benchmark for Treatment Response Modeling

Joel Dapello, Marcel Nassar, Ridvan Eksi, Ban Wang et autres

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Author Correction: ML-enhanced peroxisome capacity enables compartmentalization of multienzyme pathway

Jordan J. Baker, Jie Shi, Shangying Wang, Elena M. Mujica et autres

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ML-enhanced peroxisome capacity enables compartmentalization of multienzyme pathway

Jordan J. Baker, Jie Shi, Shangying Wang, Elena M. Mujica et autres

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Dismantling Silos: Academia, Industry, and a Science Museum Working Together

Thomas Zimmerman, Kristina Yu, Dana Carrison-Stone, Jonathan Erwin et autres

ABSTRACT A partnership between four universities, an industrial research lab, and a public science museum, created as a National Science Foundation Science and Technology Center, offers diverse collaboration and learning opportunities in cellular engineering. Each institution plays a vital role: universities advance …

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Statistical mechanics and thermodynamics of viral evolution

Simone Bianco, J. H. Kaufman, Barbara Jones, Justin Lessler

This paper uses methods drawn from physics to study the life cycle of viruses. The paper analyzes a model of viral infection and evolution using the "grand canonical ensemble" and formalisms from statistical mechanics and thermodynamics. Using this approach we enumerate all …

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Breaking Barriers: The Power of Artificial Intelligence in Advancing Health Equity

Arash Shaban‐Nejad, Martin Michalowski, Simone Bianco

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