相关论文: Presence-absence reasoning for evolutionary phenot…

Observability is a modelling property that describes the possibility of inferring the internal state of a system from observations of its output. A related property, structural identifiability, refers to the theoretical possibility of…

We propose a novel shape representation useful for analyzing and processing shape collections, as well for a variety of learning and inference tasks. Unlike most approaches that capture variability in a collection by using a template model…

Connecting the dynamics of biomolecular networks to experimentally measurable cell phenotypes remains a central challenge in systems biology. Here we introduce a model-based definition of phenotype as a partial steady state that is…

Type inference refers to the task of inferring the data type of a given column of data. Current approaches often fail when data contains missing data and anomalies, which are found commonly in real-world data sets. In this paper, we propose…

A natural phenomenon occurring in a living system is an outcome of the dynamics of the specific biological network underlying the phenomenon. The collective dynamics have both deterministic and stochastic components. The stochastic nature…

Understanding freely moving animal behavior is central to neuroscience, where pose estimation and behavioral understanding form the foundation for linking neural activity to natural actions. Yet both tasks still depend heavily on human…

Chronic viral infections can persist in an infected person for decades. From the perspective of the virus, a single infection can span thousands of generations, leading to a highly diverse population of viruses with its own complex…

As the public seeks greater accountability and transparency from machine learning algorithms, the research literature on methods to explain algorithms and their outputs has rapidly expanded. Feature importance methods form a popular class…

Humans and animals are constantly exposed to a continuous stream of sensory information from different modalities. At the same time, they form more compressed representations like concepts or symbols. In species that use language, this…

In mission-critical domains such as law enforcement and medical diagnosis, the ability to explain and interpret the outputs of deep learning models is crucial for ensuring user trust and supporting informed decision-making. Despite…

High-throughput data analyses are becoming common in biology, communications, economics and sociology. The vast amounts of data are usually represented in the form of matrices and can be considered as knowledge networks. Spectra-based…

Mutualistic interactions, where species interact to obtain mutual benefits, constitute an essential component of natural ecosystems. The use of ecological networks to represent the species and their ecological interactions allows the study…

An increasing number of dissident voices claim that the standard neo-Darwinian view of genes as 'leaders' and phenotypes as 'followers' during the process of adaptive evolution should be turned on its head. This idea is older than the…

In empirical studies, the data usually don't include all the variables of interest in an economic model. This paper shows the identification of unobserved variables in observations at the population level. When the observables are distinct…

Site occupancy models are routinely used to estimate the probability of species presence from either abundance or presence-absence data collected across sites with repeated sampling occasions. In the last two decades, a broad class of…

Automatic phenotyping is a task of identifying cohorts of patients that match a predefined set of criteria. Phenotyping typically involves classifying long clinical documents that contain thousands of tokens. At the same time, recent…

With the wide adoption of black-box models, instance-based \emph{post hoc} explanation tools, such as LIME and SHAP became increasingly popular. These tools produce explanations, pinpointing contributions of key features associated with a…

A finite set is "hidden" if its elements are not directly enumerable or if its size cannot be ascertained via a deterministic query. In public health, epidemiology, demography, ecology and intelligence analysis, researchers have developed a…

The goal of Science is to understand phenomena and systems in order to predict their development and gain control over them. In the scientific process of knowledge elaboration, a crucial role is played by models which, in the language of…

We consider cross-sectional genetic association studies (common and rare variants) where non-genetic information is available, or feasible to obtain for $N$ individuals, but where it is infeasible to genotype all $N$ individuals. We…