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.
Quantum computing promises faster bioinformatics, but challenges remain.
Method uses network biology to construct gene expression models for cancer.
We compute Khovanov homology for tangles using TQFT.
We address the problem of parameter estimation in models of systems biology from noisy observations. The models we consider are characterized by simultaneous deterministic nonlinear differential equations whose parameters are either taken from in vitro experiments, or are hand-tuned during the model development process…
DAG-FOCI learns causal relationships without parametric assumptions.
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…
hyperSBINN improves drug cardiosafety assessment by efficiently modeling cardiac action potentials.
Polynomial-time algorithm finds short non-orientable loops intersecting graph edges up to 30 times.
Complex behaviour in many systems arises from the stochastic interactions of spatially distributed particles or agents. Stochastic reaction-diffusion processes are widely used to model such behaviour in disciplines ranging from biology to the social sciences, yet they are notoriously difficult to simulate and calibrate…
DECAT framework evaluates multimodal models for shared biology, detecting confounders and false positives.
COMRECGC finds common recourse for global counterfactual explanations in GNNs.
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.
Two simulation-based methods improve optimal sampling design in systems biology.
New algorithm optimizes matrix reordering for noisy disordered matrices.
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…
A scalable Bayesian inference method for mixed-effects models in systems biology.
In an effort to overcome the data deluge in computational biology and bioinformatics and to facilitate bioinformatics research in the era of big data, we identify some of the most influential algorithms that have been widely used in the bioinformatics community. These top data mining and machine learning algorithms cov…
ProGen models protein sequences for synthetic biology.
Several real problems ranging from text classification to computational biology are characterized by hierarchical multi-label classification tasks. Most of the methods presented in literature focused on tree-structured taxonomies, but only few on taxonomies structured according to a Directed Acyclic Graph (DAG). In thi…
MSBM extends SB for multi-marginal trajectory inference.
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…
Extracts factors from Treasury yields using ML techniques.
In Classical Knot Theory and in the new Theory of Quantum Invariants substantial effort was directed toward the search for unknotting moves on links. We solve, in this note, several classical problems concerning unknotting moves. Our approach uses a new concept, Burnside groups of links, which establishes unexpected re…
nUDEs use neural networks to model biology without negative values.
Estimates support in distributions with sampling artifacts and errors.
Genomics has revolutionized biology, enabling the interrogation of whole transcriptomes, genome-wide binding sites for proteins, and many other molecular processes. However, individual genomic assays measure elements that interact in vivo as components of larger molecular machines. Understanding how these high-order in…
The objectives of this "perspective" paper are to review some recent advances in sparse feature selection for regression and classification, as well as compressed sensing, and to discuss how these might be used to develop tools to advance personalized cancer therapy. As an illustration of the possibilities, a new algor…
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…
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. …
We introduce a new discriminant analysis method (Empirical Discriminant Analysis or EDA) for binary classification in machine learning. Given a dataset of feature vectors, this method defines an empirical feature map transforming the training and test data into new data with components having Gaussian empirical distrib…
X-SHAP assesses multiplicative variable contributions in machine learning models.
BioBO optimizes gene perturbation design using Bayesian optimization with biological priors.
Graph kernels assess graph similarity for various applications.
We study the sample complexity of learning a high-dimensional simplex from a set of points uniformly sampled from its interior. Learning of simplices is a long studied problem in computer science and has applications in computational biology and remote sensing, mostly under the name of `spectral unmixing'. We theoretic…
High dimensional time series are endemic in applications of machine learning such as robotics (sensor data), computational biology (gene expression data), vision (video sequences) and graphics (motion capture data). Practical nonlinear probabilistic approaches to this data are required. In this paper we introduce the v…
Kernel-based support vector machines (SVMs) are supervised machine learning algorithms for classification and regression problems. We introduce a method to train SVMs on a D-Wave 2000Q quantum annealer and study its performance in comparison to SVMs trained on conventional computers. The method is applied to both synth…
Detection of dense cycles in graphs reveals a gap between easy detection and hard recovery.
In a range of fields including the geosciences, molecular biology, robotics and computer vision, one encounters problems that involve random variables on manifolds. Currently, there is a lack of flexible probabilistic models on manifolds that are fast and easy to train. We define an extremely flexible class of exponent…
Graphs arise naturally in many real-world applications including social networks, recommender systems, ontologies, biology, and computational finance. Traditionally, machine learning models for graphs have been mostly designed for static graphs. However, many applications involve evolving graphs. This introduces import…
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…
Geometric modeling for human food and chemical sensitivities.
An important task for many if not all the scientific domains is efficient knowledge integration, testing and codification. It is often solved with model construction in a controllable computational environment. In spite of that, the throughput of in-silico simulation-based observations become similarly intractable for …
Parallel algorithm speeds up Jones polynomial computation.
Large-scale computational experiments, often running over weeks and over large datasets, are used extensively in fields such as epidemiology, meteorology, computational biology, and healthcare to understand phenomena, and design high-stakes policies affecting everyday health and economy. For instance, the OpenMalaria f…
BaMANI uses ensemble learning to improve Bayesian network inference.
PolytopeWalk library efficiently samples high-dimensional polytopes.