定量方法
Depth of anesthesia is a complex but important vital state to analyze during a surgery or other procedure. One parameter to estimate this state is the bispectral index (BIS), a value ranging from 0 to 100 with a target of 40 to 60 for a…
Energy landscapes provide a common framework for describing learning, embryonic development, and collective dynamics. Although such landscapes may evolve over time, their dynamics are typically prescribed externally rather than generated by…
Background: Dynamic programming in biological sequence analysis computes probabilities or partition functions by summing over exponentially many latent paths, alignments, derivation trees, or RNA secondary structures. Their backward and…
Genetic testing reports coding variants far faster than they can be interpreted, and placing a variant in its biophysical context, the domain it perturbs, whether its residue is buried or exposed, whether it lies near a disulfide bond or a…
A model predictive controller (MPC) is used to construct a virtual assistant to aid a physician in prescribing cortisol replacement therapy for patients with adrenal insufficiency (AI). AI, also known as hypocortisolism, is a condition that…
The push toward large language models for biology (BioLM) has created a need for training corpora that can endow models with a genuine understanding of biology. However, existing biological resources, such as molecular databases, protein…
Current computational approaches for drug design typically focus on generating molecules conditioned on specific targets or general molecular properties, often neglecting the influence of disease context on target behavior and therapeutic…
Perfusion imaging guides clinical evaluation of stroke and brain tumors by characterizing tissue-level hemodynamics. Routine quantification relies on manual arterial input function (AIF) selection followed by deconvolution, producing…
Ramkrishna, Kompala, and Tsao proposed the cybernetic model of microbial growth, in which cells allocate enzyme synthesis resources according to a matching rule that mimics rational decision-making. The matching rule was later shown to be…
Large language models (LLMs) demonstrate remarkable reasoning capabilities, yet their stateless architecture fundamentally limits deployment in long-horizon research workflows requiring multi-session continuity and quantitative rigor. Here…
Many biological processes are governed by complex dynamical mechanisms that remain incompletely understood despite increasing volumes of experimental data. Biologically-informed neural networks (BINNs) seek to address this challenge by…
Diffuse large B-cell lymphoma (DLBCL) is an aggressive form of non-Hodgkin lymphoma with a high recurrence rate. The molecular profiling of DLBCL tumors culminated in several immunohistochemistry algorithms for prognostic stratification.…
ssys is a Python package for exact algebraic recasting of supported ODE models into S-system or Generalized Mass Action form. It reads Antimony and SBML models, introduces auxiliary variables through symbolic lifting, and validates…
Understanding the differences between individual instances of the same complex system remains a central challenge, particularly in biological contexts. Parenclitic networks constitute a suitable means to detect deviations in correlations…
DNA methylation (DNAm) serves as one of the most robust molecular biomarkers of biological aging. While conventional epigenetic clocks accurately predict chronological age from high-dimensional CpG profiles, they treat aging as a static…
Codon harmonization aims to adapt the coding sequences for heterologous expression while preserving the native-like patterns of frequent and rare codons that may influence local translation dynamics and co-translational protein folding.…
Microbial keratitis requires rapid pathogen identification to guide treatment, but culture- and PCR-based diagnostics are slow and resource-intensive. We developed a triple-phase multimodal framework for bacterial-versus-fungal keratitis…
Models of complex systems often have many parameters, yet are constrained by far fewer experimentally accessible observables: similar activity can emerge from coordinated parameter changes. We formalize these compatible parameter sets as…
The baboon (Papio) is an invaluable resource within nonhuman primate research, having the advantage of being a cercopithecoid (Old World monkey) with one of the largest brains among non-hominid primates. In order to facilitate comparative…
We study how to recover candidate circadian-clock regulators of pituitary hormone genes that are important for women's health but do not show a clear 24-hour rhythm in bulk tissue, aiming to nominate clock-linked regulatory targets that…