相关论文: Evolution of Hierarchical Structure & Reuse in iGE…
Tree ensembles such as XGBoost are often preferred for discriminative tasks in mixed-type tabular data, due to their inductive biases, minimal hyperparameter tuning, and training efficiency. We argue that these qualities, when leveraged…
Molecular phylogenetic and phylogeographic reconstructions generally assume time-homogeneous substitution processes. Motivated by computational convenience, this assumption sacrifices biological realism and offers little opportunity to…
Deep generative models often perform poorly in real-world applications due to the heterogeneity of natural data sets. Heterogeneity arises from data containing different types of features (categorical, ordinal, continuous, etc.) and…
The hierarchical organisation of cell identity is a fundamental feature of animal development with rich and well-characterized experimental phenomenology, yet the mechanisms driving its emergence remain unknown. The regulation of cell…
When a biological system robustly corrects component-level errors, the direct pressure on component performance declines. Components may become less reliable, maintain more genetic variability, or drift neutrally in design, creating the…
The "developmental hourglass" describes a pattern of increasing morphological divergence towards earlier and later embryonic development, separated by a period of significant conservation across distant species (the "phylotypic stage").…
Time-series forecasting is one of the most active research topics in artificial intelligence. Applications in real-world time series should consider two factors for achieving reliable predictions: modeling dynamic dependencies among…
The control of nonlinear dynamical systems remains a major challenge for autonomous agents. Current trends in reinforcement learning (RL) focus on complex representations of dynamics and policies, which have yielded impressive results in…
The functionality of catalysts, enzymes, and supramolecular assemblies emerges not from individual molecules alone, but from the subtle interplay between multiple components arranged in complex systems. Designing such systems is a grand…
Large scale databases are available that contain homologous gene families constructed from hundreds of complete genome sequences from across the three domains of Life. Here we discuss approches of increasing complexity aimed at extracting…
Cognitive Diagnosis Models (CDMs) are a special family of discrete latent variable models that are widely used in modern educational, psychological, social and biological sciences. A key component of CDMs is a binary $Q$-matrix…
Bulk tissue RNA sequencing of heterogeneous samples provides averaged gene expression profiles, obscuring cell type-specific dynamics. To address this, we present a probabilistic hierarchical Bayesian model that deconvolves bulk RNA-seq…
Scientific discovery in biology is difficult due to the complexity of the systems involved and the expense of obtaining high quality experimental data. Automated techniques are a promising way to make scientific discoveries at the scale and…
Retrieval-augmented generation (RAG) methods can enhance the performance of LLMs by incorporating retrieved knowledge chunks into the generation process. In general, the retrieval and generation steps usually have different requirements for…
Many social and biological systems are characterized by enduring hierarchies, including those organized around prestige in academia, dominance in animal groups, and desirability in online dating. Despite their ubiquity, the general…
The largest source of systematic errors in the time-delay cosmography method likely arises from the lens model mass distribution, where an inaccurate choice of model could in principle bias the value of $H_0$. A Bayesian hierarchical…
The mutual influence of dynamics and structure is a central issue in complex systems. In this paper we study by simulation slow evolution of network under the feedback of a local-majority-rule opinion process. If performance-enhancing local…
As the amount and complexity of genetic information increases it is necessary that we explore some efficient ways of handling these data. This study takes the "divide and conquer" approach for analyzing high dimensional genomic data. Our…
The cell cycle is a tightly controlled process, yet its underlying genetic network shows marked differences across species. Which of the associated structural features follow solely from the ability to impose the appropriate gene expression…
Most complex systems are intrinsically dynamic in nature. The evolution of a dynamic complex system is typically represented as a sequence of snapshots, where each snapshot describes the configuration of the system at a particular instant…