Related papers: KEGGexpressionMapper allows for analysis of pathwa…

Motivation: Omics data, such as transcriptomics or phosphoproteomics, are broadly used to get a snap-shot of the molecular status of cells. In particular, changes in omics can be used to estimate the activity of pathways, transcription…

Acquiring plausible pathways on high-dimensional structural distributions is beneficial in several domains. For example, in the drug discovery field, a protein conformational pathway, i.e. a highly probable sequence of protein structural…

We present EMISSOR: a platform to capture multimodal interactions as recordings of episodic experiences with explicit referential interpretations that also yield an episodic Knowledge Graph (eKG). The platform stores streams of multiple…

Understanding the dynamics of an environment, such as the movement of humans and vehicles, is crucial for agents to achieve long-term autonomy in urban environments. This requires the development of methods to capture the multi-modal and…

While there exist approaches to integrate heterogeneous data using semantic models, such semantic models can typically not be used by existing software tools. Many software tools - especially in engineering - only have options to import and…

It has been shown that a random-effects framework can be used to test the association between a gene's expression level and the number of DNA copies of a set of genes. This gene-set modelling framework was later applied to find associations…

Multimodal emotion recognition (MER) seeks to integrate various modalities to predict emotional states accurately. However, most current research focuses solely on the fusion of audio and text features, overlooking the valuable information…

My analysis uses methods developed for data mining microarray experiments, adapted for ageing research. Methods bridge knowledge of statistical mechanics with data mining methods developed in statistical mathematics. Analyses can reveal how…

MPAgenomics, standing for multi-patients analysis (MPA) of genomic markers, is an R-package devoted to: (i) efficient segmentation, and (ii) genomic marker selection from multi-patient copy number and SNP data profiles. It provides wrappers…

Spatial Transcriptomics enables mapping of gene expression within its native tissue context, but current platforms measure only a limited set of genes due to experimental constraints and excessive costs. To overcome this, computational…

Motivation: Studies including more than one type of 'omics data sets are becoming more prevalent. Integrating these data sets can be a way to solidify findings and even to make new discoveries. However, integrating multi-omics data sets is…

For the vast majority of genes in sequenced genomes, there is limited understanding of how they are regulated. Without such knowledge, it is not possible to perform a quantitative theory-experiment dialogue on how such genes give rise to…

The R package (R Core Team (2016)) genMOSS is specifically designed for the Bayesian analysis of genome-wide association study data. The package implements the mode oriented stochastic search (MOSS) procedure as well as a simple moving…

Numerous transcription factors self-assemble into different order oligomeric species in a way that is actively regulated by the cell. Until now, no general functional role has been identified for this widespread process. Here we capture the…

While Retrieval Augmented Generation (RAG) is now widely adopted to enhance LLMs, evaluating its true performance benefits in a reproducible and interpretable way remains a major hurdle. Existing methods often fall short: they lack domain…

Protein complexes are macromolecules essential to the functioning and well-being of all living organisms. As the structure of a protein complex, in particular its region of interaction between multiple protein subunits (i.e., chains), has a…

Recent breakthroughs in cancer research have come via the up-and-coming field of pathway analysis. By applying statistical methods to prior known gene and protein regulatory information, pathway analysis provides a meaningful way to…

Background: Identification of the interactions and regulatory relations between biomolecules play pivotal roles in understanding complex biological systems and the mechanisms underlying diverse biological functions. However, the collection…

The reasoning process of Large Language Models (LLMs) is often plagued by hallucinations and missing facts in question-answering tasks. A promising solution is to ground LLMs' answers in verifiable knowledge sources, such as Knowledge…

The vast collection of machine learning records available on the web presents a significant opportunity for meta-learning, where past experiments are leveraged to improve performance. Two crucial meta-learning tasks are pipeline performance…