Related papers: Finding New Order in Biological Functions from the…
Ontologies enable knowledge sharing and interdisciplinary collaboration by providing standardized, structured vocabularies for diverse communities. While logical axioms are a cornerstone of ontology design, natural language elements such as…
Dendrograms are a way to represent evolutionary relationships between organisms. Nowadays, these are inferred based on the comparison of genes or protein sequences by taking into account their differences and similarities. The genetic…
Many ontologies have been developed in biology and these ontologies increasingly contain large volumes of formalized knowledge commonly expressed in the Web Ontology Language (OWL). Computational access to the knowledge contained within…
Complex dynamical systems are often modeled as networks, with nodes representing dynamical units which interact through the network's links. Gene regulatory networks, responsible for the production of proteins inside a cell, are an example…
In language model interpretability research, \textbf{circuit tracing} aims to identify which internal features causally contributed to a particular output and how they affected each other, with the goal of explaining the computations…
The displayed tree phylogenetic network model is shown to sit as a natural submodel of the graphical model associated to a directed acyclic graph (DAG). This representation allows to derive a number of results about the displayed tree…
Directed acyclic graph (DAG) has been widely employed to represent directional relationships among a set of collected nodes. Yet, the available data in one single study is often limited for accurate DAG reconstruction, whereas heterogeneous…
A new method to sort gene expression patterns into functional groups is presented. The method is based on a sorting algorithm using a non-local similarity score, which takes all other patterns in the dataset into account. The method is…
Learning a faithful directed acyclic graph (DAG) from samples of a joint distribution is a challenging combinatorial problem, owing to the intractable search space superexponential in the number of graph nodes. A recent breakthrough…
Several real problems ranging from text classification to computational biology are characterized by hierarchical multi-label classification tasks. Most of the methods presented in literature focused on tree-structured taxonomies, but only…
Interaction networks are of central importance in post-genomic molecular biology, with increasing amounts of data becoming available by high-throughput methods. Examples are gene regulatory networks or protein interaction maps. The main…
The promise of discovering a functional blueprint of a cellular system from large-scale and high-throughput sequence and experimental data is predicated on the belief that the same top-down investigative approach that proved successful in…
Community annotation of biological entities with concepts from multiple bio-ontologies has created large and growing repositories of ontology-based annotation data with embedded implicit relationships among orthogonal ontologies.…
Stratifying cancer patients based on their gene expression levels allows improving diagnosis, survival analysis and treatment planning. However, such data is extremely highly dimensional as it contains expression values for over 20000 genes…
Numerous social, medical, engineering and biological challenges can be framed as graph-based learning tasks. Here, we propose a new feature based approach to network classification. We show how dynamics on a network can be useful to reveal…
High-throughput experiments are shedding light on the topology of large regulatory networks and at the same time their functional states, namely the states of activation of the nodes (for example transcript or protein levels) in different…
Your computer is continuously executing programs, but does it really understand them? Not in any meaningful sense. That burden falls upon human knowledge workers, who are increasingly asked to write and understand code. They deserve to have…
Multiprocessor scheduling of hard real-time tasks modeled by directed acyclic graphs (DAGs) exploits the inherent parallelism presented by the model. For DAG tasks, a node represents a request to execute an object on one of the available…
The ability to reroute and control flow is vital to the function of venation networks across a wide range of organisms. By modifying individual edges in these networks, either by adjusting edge conductances or creating and destroying edges,…
Big Data architectures allow to flexibly store and process heterogeneous data, from multiple sources, in their original format. The structure of those data, commonly supplied by means of REST APIs, is continuously evolving. Thus data…