Search

Translational research requires data at multiple scales of biological organization. Advancements in sequencing and multi-omics technologies have increased the availability of these data, but researchers face significant integration challenges. Knowledge graphs (KGs) are used to model complex phenomena, and methods exist to construct them automatically. However, tackling complex biomedical integration problems requires flexibility in the way knowledge is modeled. Moreover, existing KG construction methods provide robust tooling at the cost of fixed or limited choices among knowledge representation models. PheKnowLator (Phenotype Knowledge Translator) is a semantic ecosystem for automating the FAIR (Findable, Accessible, Interoperable, and Reusable) construction of ontologically grounded KGs with fully customizable knowledge representation. The ecosystem includes KG construction resources (e.g., data preparation APIs), analysis tools (e.g., SPARQL endpoints and abstraction algorithms), and benchmarks (e.g., prebuilt KGs and embeddings). We evaluated the ecosystem by systematically comparing it to existing open-source KG construction methods and by analyzing its computational performance when used to construct 12 large-scale KGs. With flexible knowledge representation, PheKnowLator enables fully customizable KGs without compromising performance or usability.

Generative artificial intelligence models can be a valuable aid to music composition and live performance, both to aid the professional musician and to help democratize the music creation process for hobbyists. Here we present a novel method that, given an English word or phrase, generates 2 compasses of a 4-piece drum pattern that embodies the "mood" of the given language cue, or that could be used for an audiovisual scene described by the language cue. We envision this tool as composition aid for electronic music and audiovisual soundtrack production, or an improvisation tool for live performance. In order to produce the training samples for this model, besides manual annotation of the "scene" or "mood" terms, we have designed a novel method to extract the consensus drum track of any song. This consists of a 2-bar, 4-piece drum pattern that represents the main percussive motif of a song, which could be imported into any music loop device or live looping software. These two key components (drum pattern generation from a generalizable input, and consensus percussion extraction) present a novel approach to computer-aided composition and provide a stepping stone for more comprehensive rhythm generation.

As data structures and mathematical objects used for complex systems modeling, hypergraphs sit nicely poised between on the one hand the world of network models, and on the other that of higher-order mathematical abstractions from algebra, lattice theory, and topology. They are able to represent complex systems interactions more faithfully than graphs and networks, while also being some of the simplest classes of systems representing topological structures as collections of multidimensional objects connected in a particular pattern. In this paper we discuss the role of (undirected) hypergraphs in the science of complex networks, and provide a mathematical overview of the core concepts needed for hypernetwork modeling, including duality and the relationship to bicolored graphs, quantitative adjacency and incidence, the nature of walks in hypergraphs, and available topological relationships and properties. We close with a brief discussion of two example applications: biomedical databases for disease analysis, and domain-name system (DNS) analysis of cyber data.

Knowledge-based biomedical data science (KBDS) involves the design and implementation of computer systems that act as if they knew about biomedicine. Such systems depend on formally represented knowledge in computer systems, often in the form of knowledge graphs. Here we survey the progress in the last year in systems that use formally represented knowledge to address data science problems in both clinical and biological domains, as well as on approaches for creating knowledge graphs. Major themes include the relationships between knowledge graphs and machine learning, the use of natural language processing, and the expansion of knowledge-based approaches to novel domains, such as Chinese Traditional Medicine and biodiversity., Comment: Manuscript 43 pages with 3 tables; Supplemental material 43 pages with 3 tables