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Foundation models in genomics have shown mixed success compared to their counterparts in natural language processing. Yet, the reasons for their limited effectiveness remain poorly understood. In this work, we investigate the role of…
Life finds a way. For sessile organisms like plants, the need to adapt to changes in the environment is even more poignant. For humanity, the need to develop crops that can grow in diverse environments and feed our growing population is an…
Genetic Programming (GP) has found various applications. Understanding this type of algorithm from a theoretical point of view is a challenging task. The first results on the computational complexity of GP have been obtained for problems…
Today's sequencing technology allows sequencing an individual genome within a few weeks for a fraction of the costs of the original Human Genome project. Genomics labs are faced with dozens of TB of data per week that have to be…
We explore the AI2050 "hard problems" that block the promise of AI and cause AI risks: (1) developing general capabilities of the systems; (2) assuring the performance of AI systems and their training processes; (3) aligning system goals…
As in many other scientific domains, we face a fundamental problem when using machine learning to identify proteins from mass spectrometry data: large ground truth datasets mapping inputs to correct outputs are extremely difficult to…
Recent advancements in deep learning have brought significant improvements to plant disease recognition. However, achieving satisfactory performance often requires high-quality training datasets, which are challenging and expensive to…
The automatic generation of computer programs is one of the main applications with practical relevance in the field of evolutionary computation. With program synthesis techniques not only software developers could be supported in their…
The BIOSCAN project, led by the International Barcode of Life Consortium, seeks to study changes in biodiversity on a global scale. One component of the project is focused on studying the species interaction and dynamics of all insects. In…
Background: Selecting feature genes to predict phenotypes is one of the typical tasks in analyzing genomics data. Though many general-purpose algorithms were developed for prediction, dealing with highly correlated genes in the prediction…
Accurately fitting the term structure of interest rates is critical to central banks and other market participants. The Nelson-Siegel and Nelson-Siegel-Svensson models are probably the best-known models for this purpose due to their…
Over a quarter of century after the invention of genetic algorithms and miriads of their modifications, as well as successful implementations, we are still lacking many essential details of thorough analysis of it's inner working. One of…
In DNA computing, it is impossible to decide whether a specific hybridization among complex DNA molecules is effective or not within acceptable time. In order to address this common problem, we introduce a new method based on the machine…
The 0-1 knapsack problem is a well-known combinatorial optimisation problem. Approximation algorithms have been designed for solving it and they return provably good solutions within polynomial time. On the other hand, genetic algorithms…
Genetic Programming is an evolutionary algorithm that generates computer programs, or mathematical expressions, to solve complex problems. In this Guide, we demonstrate how to use Genetic Programming to develop surrogate models to mitigate…
RNA-Seq and gene expression microarrays provide comprehensive profiles of gene activity, but lack of reproducibility has hindered their application. A key challenge in the data analysis is the normalization of gene expression levels, which…
We demonstrate how a genetic algorithm solves the problem of minimizing the resources used for network coding, subject to a throughput constraint, in a multicast scenario. A genetic algorithm avoids the computational complexity that makes…
Poultry farms are an important contributor to the human food chain. Worldwide, humankind keeps an enormous number of domesticated birds (e.g. chickens) for their eggs and their meat, providing rich sources of low-fat protein. However,…
Given two graphs, the graph matching problem is to align the two vertex sets so as to minimize the number of adjacency disagreements between the two graphs. The seeded graph matching problem is the graph matching problem when we are first…
It is important to study on genes affecting to growing environment of main crops. Especially the recognition problem of promoter region, which is the problem to predict whether DNA sequences contain promoter regions or not, is prior to find…