Analyzing ion distributions around DNA

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Generalization of Scaled Deep ResNets in the Mean-Field Regime

Volkan Cevher, Grigorios Chrysos, Fanghui Liu

Despite the widespread empirical success of ResNet, the generalization properties of deep ResNet are rarely explored beyond the lazy training regime. In this work, we investigate scaled ResNet in the limit of infinitely deep and wide neural networks, of wh ...

2024

Towards improving full-length ribosome density prediction by bridging sequence and graph-based representations

Pierre Vandergheynst, Felix Naef, Cédric Gobet, Francesco Craighero, Mohan Vamsi Nallapareddy

Translation elongation plays an important role in regulating protein concentrations in the cell, and dysregulation of this process has been linked to several human diseases. In this study, we use data from ribo-seq experiments to model ribosome densities, ...

PMLR2024

Regressive Tomography and Direct Regressive Reconstruction: A Research Note

Henri Weisen

Two related methods for inverting line-integrated measurements are presented in this research paper in the context of the recent deuterium-tritium experiments in the JET tokamak. Unlike traditional methods of tomography, these methods rely on making use of ...

2023

Personalized Privacy-Preserving Distributed Learning on Heterogeneous Data

Michael Christoph Gastpar, Aditya Pradeep

One major challenge in distributed learning is to efficiently learn for each client when the data across clients is heterogeneous or non iid (not independent or identically distributed). This provides a significant challenge as the data of the other client ...

2023

Distributionally Robust Linear Quadratic Control

Daniel Kuhn, Bahar Taskesen, Cagil Kocyigit

Linear-Quadratic-Gaussian (LQG) control is a fundamental control paradigm that is studied in various fields such as engineering, computer science, economics, and neuroscience. It involves controlling a system with linear dynamics and imperfect observations ...

2023

Bridging Native and Intrinsic Structures of Microhydrated Biomolecules by Cold Ion Spectroscopy

Andrei Zviagin

Solving native structures of such large molecules, like biomolecules, is often challenging, particularly due to the potentially infinite number of non-covalent interactions with water. In this thesis, we report the use of cold ion gas-phase action spectros ...

EPFL2023

A Geometric Transformer for Structural Biology: Development and Applications of the Protein Structure Transformer

Lucien Fabrice Krapp

Proteins, the central building blocks of life, play pivotal roles in nearly every biological function. To do so, these macromolecular structures interact with their surrounding environment in complex ways, leading to diverse functional behaviors. The predi ...

EPFL2023

cgNA+: A sequence-dependent coarse-grain model of double-stranded nucleic acids

Rahul Sharma

DNA mechanics plays a crucial role in many biological processes, including nucleosome positioning and protein-DNA interactions. It is believed that nature employs epigenetic modifications in DNA to further regulate gene expression. Moreover, double-strande ...

EPFL2023

Secondary structure of the human mitochondrial genome affects formation of deletions

Jacques Fellay, Konstantin Popadin

BackgroundAging in postmitotic tissues is associated with clonal expansion of somatic mitochondrial deletions, the origin of which is not well understood. Such deletions are often flanked by direct nucleotide repeats, but this alone does not fully explain ...

BMC2023

Learning Robust and Adaptive Representations: from Interactions, for Interactions

Yuejiang Liu

Interactions are ubiquitous in our world, spanning from social interactions between human individuals to physical interactions between robots and objects to mechanistic interactions among different components of an intelligent system. Despite their prevale ...

EPFL2023

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