A locally-built, LLM-digested index of recent arXiv papers in quant finance, geometry/topology, and statistical ML — keyword search served straight from SQLite on this machine.
Method uses network biology to construct gene expression models for cancer.
nUDEs use neural networks to model biology without negative values.
Two simulation-based methods improve optimal sampling design in systems biology.
hyperSBINN improves drug cardiosafety assessment by efficiently modeling cardiac action potentials.
Quantum computing promises faster bioinformatics, but challenges remain.
A scalable Bayesian inference method for mixed-effects models in systems biology.
New method learns cell trajectories and network interactions from single-cell data.
CHANI learns classification tasks with local transformations inspired by biology.
COMRECGC finds common recourse for global counterfactual explanations in GNNs.
Physics analogies explain machine learning overfitting control.
DECAT framework evaluates multimodal models for shared biology, detecting confounders and false positives.
ABI adapts to graph data for fast, scalable inference.
New bound for neural nets on non-iid data.
DHRL learns interpretable features from visual data.
Biology has changed radically in the last two decades, transitioning from a descriptive science into a design science. Synthetic biology allows us to bioengineer cells to synthesize novel valuable molecules such as renewable biofuels or anticancer drugs. However, traditional synthetic biology approaches involve ad-hoc …
Optimal algorithm selects biological models without prior info.
A new method for inferring latent states in Markov jump processes.
Popular online enrichment analysis tools from the field of molecular systems biology provide users with the ability to submit their experimental results as gene sets for individual analysis. Such queries are kept private, and have never before been considered as a resource for integrative analysis. By harnessing gene s…
The aim of this chapter is twofold. In the first part we will provide a brief overview of the mathematical and statistical foundations of graphical models, along with their fundamental properties, estimation and basic inference procedures. In particular we will develop Markov networks (also known as Markov random field…
Critical learning periods found in deep linear networks too.
Capsule Networks have great potential to tackle problems in structural biology because of their attention to hierarchical relationships. This paper describes the implementation and application of a Capsule Network architecture to the classification of RAS protein family structures on GPU-based computational resources. …
ProGen models protein sequences for synthetic biology.
DAMNETS generates complex network dynamics models.
Graphical modelling has a long history in statistics as a tool for the analysis of multivariate data, starting from Wright's path analysis and Gibbs' applications to statistical physics at the beginning of the last century. In its modern form, it was pioneered by Lauritzen and Wermuth and Pearl in the 1980s, and has si…
In this paper, we provide conditions which ensure that stochastic Lipschitz BSDEs admit Malliavin differentiable solutions. We investigate the problem of existence of densities for the first components of solutions to general path-dependent stochastic Lipschitz BSDEs and obtain results for the second components in part…
Networks are a fundamental model of complex systems throughout the sciences, and network datasets are typically analyzed through lower-order connectivity patterns described at the level of individual nodes and edges. However, higher-order connectivity patterns captured by small subgraphs, also called network motifs, de…
Automated method simplifies stochastic chemical reaction network analysis.
New technologies have enabled the investigation of biology and human health at an unprecedented scale and in multiple dimensions. These dimensions include a myriad of properties describing genome, epigenome, transcriptome, microbiome, phenotype, and lifestyle. No single data type, however, can capture the complexity of…
BaMANI uses ensemble learning to improve Bayesian network inference.
FEPS models agents to learn and act in complex environments without deep neural networks.
In many applications, multivariate samples may harbor previously unrecognized heterogeneity at the level of conditional independence or network structure. For example, in cancer biology, disease subtypes may differ with respect to subtype-specific interplay between molecular components. Then, both subtype discovery and…
The methods of statistical physics are widely used for modelling complex networks. Building on the recently proposed Equilibrium Expectation approach, we derive a simple and efficient algorithm for maximum likelihood estimation (MLE) of parameters of exponential family distributions - a family of statistical models, th…
Structure learning in random fields has attracted considerable attention due to its difficulty and importance in areas such as remote sensing, computational biology, natural language processing, protein networks, and social network analysis. We consider the problem of estimating the probabilistic graph structure associ…
Design of experiments improves validation of biomolecular networks.
Despite an explosion in the number of experimentally determined, atomically detailed structures of biomolecules, many critical tasks in structural biology remain data-limited. Whether performance in such tasks can be improved by using large repositories of tangentially related structural data remains an open question. …
We consider the problem of joint modelling of metabolic signals and gene expression in systems biology applications. We propose an approach based on input-output factorial hidden Markov models and propose a structured variational inference approach to infer the structure and states of the model. We start from the class…
Paper proves multiplicative weight updates can train neural networks without learning rate tuning.
As proteins with similar structures often have similar functions, analysis of protein structures can help predict protein functions and is thus important. We consider the problem of protein structure classification, which computationally classifies the structures of proteins into pre-defined groups. We develop a weight…
New model for detecting communities in weighted bipartite networks.
X-SHAP assesses multiplicative variable contributions in machine learning models.
Reconstructing network connectivity from the collective dynamics of a system typically requires access to its complete continuous-time evolution although these are often experimentally inaccessible. Here we propose a theory for revealing physical connectivity of networked systems only from the event time series their i…
Recently, there has been a growing interest in network research, especially in these fields of biology, computer science, and sociology. It is natural to address complex financial issues such as the European sovereign debt crisis from the perspective of network. In this article, we construct a network model according t…
BioBO optimizes gene perturbation design using Bayesian optimization with biological priors.
Networks are a fundamental tool for modeling complex systems in a variety of domains including social and communication networks as well as biology and neuroscience. Small subgraph patterns in networks, called network motifs, are crucial to understanding the structure and function of these systems. However, the role of…
Using back-propagation and its variants to train deep networks is often problematic for new users. Issues such as exploding gradients, vanishing gradients, and high sensitivity to weight initialization strategies often make networks difficult to train, especially when users are experimenting with new architectures. Her…
Bayesian method predicts future network configurations from past snapshots.
GNNS uses graph neural networks to efficiently estimate subgraph frequency distributions.
Protein function prediction is the important problem in modern biology. In this paper, the un-normalized, symmetric normalized, and random walk graph Laplacian based semi-supervised learning methods will be applied to the integrated network combined from multiple networks to predict the functions of all yeast proteins …