Reconciling Utility with Privacy in Genomics

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Pulse-Echo Ultrasound Imaging suffers from several sources of image degradation. In clinical conditions, superficial layers made of different tissues (e.g. skin, fat or muscles) create aberrations that can severely deteriorate image quality. To correct suc ...

Distributed learning is the key for enabling training of modern large-scale machine learning models, through parallelising the learning process. Collaborative learning is essential for learning from privacy-sensitive data that is distributed across various ...

How chronic mutational processes and punctuated bursts of DNA damage drive evolution of the cancer genome is poorly understood. Here, we demonstrate a strategy to disentangle and quantify distinct mechanisms underlying genome evolution in single cells, dur ...

Vibrio cholerae has caused seven cholera pandemics in the past two centuries. The seventh and ongoing pandemic has been particularly severe on the African continent. Here, we report long read-based genome sequences of six V. cholerae strains isolated in th ...

Growing evidence indicates that transposable elements (TEs) play important roles in evolution by providing genomes with coding and non-coding sequences. Identification of TE-derived functional elements, however, has relied on TE annotations in individual s ...

Distributed constraint optimization (DCOP) is a framework in which multiple agents with private constraints (or preferences) cooperate to achieve a common goal optimally. DCOPs are applicable in several multi-agent coordination/allocation problems, such as ...

Global change exposes ecosystems to changes in the frequency, magnitude, and concomitancy of disturbances, which impact the composition and functioning of these systems. Here, we experimentally evaluate the effects of salinity disturbances and eutrophicati ...

Glacier-fed streams are the cold, ultra-oligotrophic, and unstable streams that are fed by glacial meltwater. Despite these extreme conditions, they harbour a diverse and abundant microbial diversity that develops into biofilms, covering the boulders and s ...

Viral metagenomics is a useful tool for detecting multiple human viruses in urban sewage. However, more refined protocols are required for its effective use in disease surveillance. In this study, we investigated the performance of three different preampli ...

Sample efficiency is a fundamental challenge in de novo molecular design. Ideally, molecular generative models should learn to satisfy a desired objective under minimal calls to oracles (computational property predictors). This problem becomes more apparen ...

This paper offers a new algorithm to efficiently optimize scheduling decisions for dial-a-ride problems (DARPs), including problem variants considering electric and autonomous vehicles (e-ADARPs). The scheduling heuristic, based on linear programming theor ...

Decentralized learning is appealing as it enables the scalable usage of large amounts of distributed data and resources (without resorting to any central entity), while promoting privacy since every user minimizes the direct exposure of their data. Yet, wi ...

Electric vehicles (EVs) are becoming more popular due to environmental consciousness. The limited availability of charging stations (CSs), compared to the number of EVs on the road, has led to increased range anxiety and a higher frequency of CS queries du ...

We develop new tools to study landscapes in nonconvex optimization. Given one optimization problem, we pair it with another by smoothly parametrizing the domain. This is either for practical purposes (e.g., to use smooth optimization algorithms with good g ...

Modern optimization is tasked with handling applications of increasingly large scale, chiefly due to the massive amounts of widely available data and the ever-growing reach of Machine Learning. Consequently, this area of research is under steady pressure t ...

Microorganisms are a key component in the chain of life. They are essential for agriculture, produce a large proportion of oxygen, and play a central role in the cycle of elements. Microorganisms are widely used in the production of food and alcoholic beve ...

Orthogonal group synchronization is the problem of estimating n elements Z(1),& mldr;,Z(n) from the rxr orthogonal group given some relative measurements R-ij approximate to Z(i)Z(j)(-1). The least-squares formulation is nonconvex. To avoid its local minim ...

Cis-genetic effects are key determinants of transcriptional divergence in discrete tissues and cell types. However, how cis- and trans-effects act across continuous trajectories of cellular differentiation in vivo is poorly understood. Here, we quantify al ...

DNA-binding proteins physically interact with the DNA and directly affect genomic functions. The eukaryotic genome is compacted into chromatin, limiting the DNA access to nuclear factors. In this Ph.D. thesis, I explored the dynamic mechanisms, that allow ...

We present the Breakpoint Exact Algorithm (BEA) together with a Spatial Branch and Bound (B&B), and Spatial Branch and Benders Decomposition (B&BD) approach to tackle the uncapacitated choice-based pricing problem (CPP) where demand is captured by a disc ...

Reconciling Utility with Privacy in Genomics

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A Path-Based Model for Aberration Correction in Ultrasound Imaging

Optimization Algorithms for Decentralized, Distributed and Collaborative Machine Learning

Single-mitosis dissection of acute and chronic DNA mutagenesis and repair

Genome sequences of Vibrio cholerae strains isolated in the DRC between 2009 and 2012

Ancestral genome reconstruction enhances transposable element annotation by identifying degenerate integrants

Differentially private multi-agent constraint optimization

The cost of adaptability: resource availability constrains functional stability under pulsed disturbances

The microbial genomics of glacier-fed streams: adaptations to an extreme ecosystem

Comparison of Three Viral Nucleic Acid Preamplification Pipelines for Sewage Viral Metagenomics

Augmented Memory: Sample-Efficient Generative Molecular Design with Reinforcement Learning

A ride time-oriented scheduling algorithm for dial-a-ride problems

The Privacy Power of Correlated Noise in Decentralized Learning

A Privacy-Preserving Querying Mechanism with High Utility for Electric Vehicles

The effect of smooth parametrizations on nonconvex optimization landscapes

Scalable constrained optimization

Reconstruction and analysis of genome-scale metabolic networks in single organisms and microbial communities

BENIGN LANDSCAPES OF LOW-DIMENSIONAL RELAXATIONS FOR ORTHOGONAL SYNCHRONIZATION ON GENERAL GRAPHS

The dynamic genetic determinants of increased transcriptional divergence in spermatids

Development of multiplexed single-molecule imaging techniques to study chromatin invasion dynamics of chromatin effector proteins

Exact Algorithms for Continuous Pricing with Advanced Discrete Choice Demand Models