Related papers: An Efficient Algorithm for Exploring RNA Branching…
We propose a simple iterative algorithm to construct the optimal multi-configuration approximation of an $N$-fermion wave function. That is, $M\geq N $ single-particle orbitals are sought iteratively so that the projection of the given wave…
In this paper we relate the partition function to the max-statistics of random variables. In particular, we provide a novel framework for approximating and bounding the partition function using MAP inference on randomly perturbed models. As…
The Random Walks (RW) algorithm is one of the most e - cient and easy-to-use probabilistic segmentation methods. By combining contrast terms with prior terms, it provides accurate segmentations of medical images in a fully automated manner.…
The thesis consists of two projects. In the first project, we present a software that analyses RNA secondary structures and compares them. The goal of this software is to find the differences between two secondary structures (experimental…
The branching algorithm is a fundamental technique for designing fast exponential-time algorithms to solve combinatorial optimization problems exactly. It divides the entire solution space into independent search branches using…
Algorithmic reasoning -- the ability to perform step-by-step logical inference -- has become a core benchmark for evaluating reasoning in graph neural networks (GNNs) and large language models (LLMs). Ideally, one would like to design a…
With the increasing computational demands of deep neural network (DNN) inference on resource-constrained devices, DNN partitioning-based device-edge collaborative inference has emerged as a promising paradigm. However, the transmission of…
Predicting protein 3D structure from amino acid sequence remains as a challenge in the field of computational biology. If protein structure homologues are not found, one has to construct 3D structural conformations from the very beginning…
The parameters of a linear compartment model are usually estimated from experimental input-output data. A problem arises when infinitely many parameter values can yield the same result; such a model is called unidentifiable. In this case,…
The Random Walks (RW) algorithm is one of the most e - cient and easy-to-use probabilistic segmentation methods. By combining contrast terms with prior terms, it provides accurate segmentations of medical images in a fully automated manner.…
Many signal processing problems can be solved by maximizing the fitness of a segmented model over all possible partitions of the data interval. This letter describes a simple but powerful algorithm that searches the exponentially large…
In this article it is shown how optimized and dedicated microarray experiments can be used to study the thermodynamics of DNA hybridization for a large number of different conformations in a highly parallel fashion. In particular, free…
An RNA molecule is structured on several layers. The primary and most obvious structure is its sequence of bases, i.e. a word over the alphabet {A,C,G,U}. The higher structure is a set of one-to-one base-pairings resulting in a…
Safety-critical infrastructures, such as bridges, are periodically inspected to check for existing damage, such as fatigue cracks and corrosion, and to guarantee the safe use of the infrastructure. Visual inspection is the most frequent…
A fundamental step in the development of machine learning models commonly involves the tuning of hyperparameters, often leading to multiple model training runs to work out the best-performing configuration. As machine learning tasks and…
We propose a multi-objective global pattern search algorithm for the task of locating and quantifying damage in flexible mechanical structures. This is achieved by identifying eigenfrequencies and eigenmodes from measurements and matching…
Simulated Moving Bed (SMB) chromatography is a well-known technique for the resolution of several high-value-added compounds. Parameters identification and model topology definition are arduous when one is dealing with complex systems such…
Large RNA molecules often carry multiple functional domains whose spatial arrangement is an important determinant of their function. Pre-mRNA splicing, furthermore, relies on the spatial proximity of the splice junctions that can be…
Deep neural network architectures have traditionally been designed and explored with human expertise in a long-lasting trial-and-error process. This process requires huge amount of time, expertise, and resources. To address this tedious…
The DistFlow model accurately represents power flows in distribution systems, but the model's nonlinearities result in computational challenges for many applications. Accordingly, a linear approximation known as \mbox{LinDistFlow} (and its…