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To tackle the challenge of producing tractable phylogenetic trees in contexts where complete information is available, we introduce APOGeT: an online, pluggable, clustering algorithm for a stream of genomes. It is designed to run alongside…
Thrombus microstructure plays a critical role in determining the treatment success for thrombus-related diseases such as stroke and deep vein thrombosis. However, no in vivo diagnostic method can fully capture thrombus microstructure yet.…
Biological signals, such as electroencephalograms (EEG), play a crucial role in numerous clinical applications, exhibiting diverse data formats and quality profiles. Current deep learning models for biosignals are typically specialized for…
One popular assumption regarding biological systems is that traits have evolved to be optimized with respect to function. This is a standard goal in evolutionary computation, and while not always embraced in the biological sciences, is an…
This review focuses on microbiomes associated with residues within the context of other microbial habitats in cereal-producing agroecosystems such as phyllosphere or rhizosphere. We connect residue microbiome with the survival of…
Music stem generation, the task of producing musically-synchronized and isolated instrument audio clips, offers the potential of greater user control and better alignment with musician workflows compared to conventional text-to-music…
In complex ecosystems such as microbial communities, there is constant ecological and evolutionary feedback between the residing species and the environment occurring on concurrent timescales. Species respond and adapt to their surroundings…
This study introduces a framework for constructing enviromics matrices in mixed models to integrate genetic and environmental data to enhance phenotypic predictions in plant breeding. Enviromics utilizes diverse data sources, such as…
Recent advances in video generation have opened new avenues for macroscopic simulation of complex dynamic systems, but their application to microscopic phenomena remains largely unexplored. Microscale simulation holds great promise for…
Machine learning techniques play an important role in analyzing spectral data. The spectral data of fish biomass is useful in fish production, as it carries many important chemistry properties of fish meat. However, it is challenging for…
Providing a comprehensive view of the city operation and offering useful metrics for decision making is a well known challenge for urban risk analysis systems. Existing systems are, in many cases, generalizations of previous domain specific…
Multimodal Foundation Models (FMs) offer a path to learn general-purpose representations from heterogeneous ecological data, easily transferable to downstream tasks. However, practical biodiversity modelling remains fragmented; separate…
Stem cell regeneration is a vital biological process in self-renewing tissues, governing development and tissue homeostasis. Gene regulatory network dynamics are pivotal in controlling stem cell regeneration and cell type transitions.…
One trend in the recent healthcare transformations is people are encouraged to monitor and manage their health based on their daily diets and physical activity habits. However, much attention of the use of operational research and…
Recent technological advances and long-term data studies provide interaction data that can be modelled through dynamic networks, i.e a sequence of different snapshots of an evolving ecological network. Most often time is the parameter along…
We introduce the Robustness of Hierarchically Organized Time Series (RHiOTS) framework, designed to assess the robustness of hierarchical time series forecasting models and algorithms on real-world datasets. Hierarchical time series, where…
Human associated microbial communities exert tremendous influence over human health and disease. With modern metagenomic sequencing methods it is possible to follow the relative abundance of microbes in a community over time. These…
Rapid environmental change and advances in data-driven analysis highlight the need not only to use computational tools, but also to foster understanding of the natural world and inspire creativity. Photosynthesis, the process that fuels…
Drawing inspiration from honeybee swarms' nest-site selection process, we assess the ability of a kilobot robot swarm to replicate this captivating example of collective decision-making. Honeybees locate the optimal site for their new nest…
In a wide variety of natural systems, closely-related microbial strains coexist stably, resulting in high levels of fine-scale biodiversity. However, the mechanisms that stabilize this coexistence are not fully understood. Spatial…