Leander Schietgat
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View article: Automated detection of toxicophores and prediction of mutagenicity using PMCSFG algorithm
Automated detection of toxicophores and prediction of mutagenicity using PMCSFG algorithm Open
Maximum common substructures (MCS) have received a lot of attention in the chemoinformatics community. They are typically used as a similarity measure between molecules, showing high predictive performance when used in classification tasks…
View article: Sales Volume Prediction and Application to Materials Trading
Sales Volume Prediction and Application to Materials Trading Open
International audience
View article: A Q-Learning algorithm for flexible job shop scheduling in a real-world manufacturing scenario
A Q-Learning algorithm for flexible job shop scheduling in a real-world manufacturing scenario Open
In this work we propose a Reinforcement Learning approach for a real-world flexible job shop scheduling scenario, where a two-armed robot and a human operator share two workstations in order to assemble light switches. The approach returns…
View article: Beyond global and local multi-target learning
Beyond global and local multi-target learning Open
View article: On the complexity of haplotyping a microbial community
On the complexity of haplotyping a microbial community Open
Motivation Population-level genetic variation enables competitiveness and niche specialization in microbial communities. Despite the difficulty in culturing many microbes from an environment, we can still study these communities by isolati…
View article: On the complexity of haplotyping a microbial community
On the complexity of haplotyping a microbial community Open
Motivation Population-level genetic variation enables competitiveness and niche specialization in microbial communities. Despite the difficulty in culturing many microbes from an environment, we can still study these communities by isolati…
View article: A machine learning based framework to identify and classify long terminal repeat retrotransposons
A machine learning based framework to identify and classify long terminal repeat retrotransposons Open
Transposable elements (TEs) are repetitive nucleotide sequences that make up a large portion of eukaryotic genomes. They can move and duplicate within a genome, increasing genome size and contributing to genetic diversity within and across…
View article: Computational haplotype recovery and long-read validation identifies novel isoforms of industrially relevant enzymes from natural microbial communities
Computational haplotype recovery and long-read validation identifies novel isoforms of industrially relevant enzymes from natural microbial communities Open
Population-level diversity of natural microbiomes represent a biotechnological resource for biomining, biorefining and synthetic biology but requires the recovery of the exact DNA sequence (or "haplotype") of the genes and genomes of every…
View article: Recovery of gene haplotypes from a metagenome
Recovery of gene haplotypes from a metagenome Open
Elucidation of population-level diversity of microbiomes is a significant step towards a complete understanding of the evolutionary, ecological and functional importance of microbial communities. Characterizing this diversity requires the …
View article: Probabilistic recovery of cryptic haplotypes from metagenomic data
Probabilistic recovery of cryptic haplotypes from metagenomic data Open
The cryptic diversity of microbial communities represent an untapped biotechnological resource for biomining, biorefining and synthetic biology. Revealing this information requires the recovery of the exact sequence of DNA bases (or “haplo…
View article: Predicting human olfactory perception from chemical features of odor molecules
Predicting human olfactory perception from chemical features of odor molecules Open
How will this molecule smell? We still do not understand what a given substance will smell like. Keller et al. launched an international crowd-sourced competition in which many teams tried to solve how the smell of a molecule will be perce…
View article: Reverse-engineering human olfactory perception from chemical features of odor molecules
Reverse-engineering human olfactory perception from chemical features of odor molecules Open
Despite 25 years of progress in understanding the molecular mechanisms of olfaction, it is still not possible to predict whether a given molecule will have a perceived odor, or what olfactory percept it will produce. To address this stimul…
View article: Partitioning the target space in multi-output learning
Partitioning the target space in multi-output learning Open
View article: Towards an algorithm for extracting exciting enzymes from metagenomic data
Towards an algorithm for extracting exciting enzymes from metagenomic data Open
High-throughput sequencing has allowed us to look beyond consensus sequences to the variation observed within organisms; their haplotypes. However, existing approaches for recovery of haplotypes make assumptions that are violated when inve…
View article: A data structure and algorithm for recovering haplotypes from metagenomes (with Hansel and Gretel)
A data structure and algorithm for recovering haplotypes from metagenomes (with Hansel and Gretel) Open
High-throughput sequencing has allowed us to look beyond consensus sequences to the variation observed within organisms; their haplotypes. However, existing approaches for recovery of haplotypes make assumptions that are violated when inve…
View article: Predicting HIV resistance with the 3D neighborhood kernel
Predicting HIV resistance with the 3D neighborhood kernel Open
Recently, we developed the 3D Neighborhood Kernel (3DNK), which acts on 3D structures of small molecules and proteins. We showed its state-of-the-art performance on several biological datasets. However, 3D data are in many cases difficult …
View article: Advances in the recovery of haplotypes from the metagenome
Advances in the recovery of haplotypes from the metagenome Open
High-throughput DNA sequencing has enabled us to look beyond consensus reference sequences to the variation observed in sequences within organisms; their haplotypes. Recovery, or assembly of haplotypes has proved computationally difficult …
View article: Predicting Protein Function and Protein-Ligand Interaction with the 3D Neighborhood Kernel (Extended Abstract) 1
Predicting Protein Function and Protein-Ligand Interaction with the 3D Neighborhood Kernel (Extended Abstract) 1 Open
Introduction Kernels for structured data have gained a lot of attention in a world where increasingly complex data are continuously generated. For example, biological databases contain thousands of 3D structures of proteins, sometimes with…
View article: Learning HMMs for nucleotide sequences from amino acid alignments
Learning HMMs for nucleotide sequences from amino acid alignments Open
Profile hidden Markov models (profile HMMs) are known to efficiently predict whether an amino acid (AA) sequence belongs to a specific protein family. Profile HMMs can also be used to search for protein domains in genome sequences. In this…