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.
DECAT framework evaluates multimodal models for shared biology, detecting confounders and false positives.
Federated learning improves bioinformatics by sharing data legally.
New model captures complex relationships from experimental data.
Paper presents a method to align unpaired samples across different modalities.
Multiplex networks, a special type of multilayer networks, are increasingly applied in many domains ranging from social media analytics to biology. A common task in these applications concerns the detection of community structures. Many existing algorithms for community detection in multiplexes attempt to detect commun…
Stable cooperation emerges in fluctuating environments.
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.
Motivated by an application in computational biology, we consider low-rank matrix factorization with -constraints on one of the factors and optionally convex constraints on the second one. In addition to the non-convexity shared with other matrix factorization schemes, our problem is further complicated by a c…
Two simulation-based methods improve optimal sampling design in systems biology.
Massively multi-label prediction/classification problems arise in environments like health-care or biology where very precise predictions are useful. One challenge with massively multi-label problems is that there is often a long-tailed frequency distribution for the labels, which results in few positive examples for t…
Quantum computing promises faster bioinformatics, but challenges remain.
A scalable Bayesian inference method for mixed-effects models in systems biology.
ProGen models protein sequences for synthetic biology.
Method uses network biology to construct gene expression models for cancer.
Probabilistic matrix factorization (PMF) is a powerful method for modeling data associated with pairwise relationships, finding use in collaborative filtering, computational biology, and document analysis, among other areas. In many domains, there is additional information that can assist in prediction. For example, wh…
Elucidating the genetic basis of human diseases is a central goal of genetics and molecular biology. While traditional linkage analysis and modern high-throughput techniques often provide long lists of tens or hundreds of disease gene candidates, the identification of disease genes among the candidates remains time-con…
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…
nUDEs use neural networks to model biology without negative values.
In the era of big data, analysts usually explore various statistical models or machine learning methods for observed data in order to facilitate scientific discoveries or gain predictive power. Whatever data and fitting procedures are employed, a crucial step is to select the most appropriate model or method from a set…
Research on probabilistic models of networks now spans a wide variety of fields, including physics, sociology, biology, statistics, and machine learning. These efforts have produced a diverse ecology of models and methods. Despite this diversity, many of these models share a common underlying structure: pairwise intera…
MNIST-Nd offers synthetic datasets to benchmark clustering across dimensions.
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.
Bayesian network structure learning algorithms with limited data are being used in domains such as systems biology and neuroscience to gain insight into the underlying processes that produce observed data. Learning reliable networks from limited data is difficult, therefore transfer learning can improve the robustness …
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…
Certain research strands can yield "forbidden knowledge". This term refers to knowledge that is considered too sensitive, dangerous or taboo to be produced or shared. Discourses about such publication restrictions are already entrenched in scientific fields like IT security, synthetic biology or nuclear physics researc…
New 3D protein analysis methods improve accuracy.
X-SHAP assesses multiplicative variable contributions in machine learning models.
BioBO optimizes gene perturbation design using Bayesian optimization with biological priors.
Geometric modeling for human food and chemical sensitivities.
The estimation of covariance matrices of gene expressions has many applications in cancer systems biology. Many gene expression studies, however, are hampered by low sample size and it has therefore become popular to increase sample size by collecting gene expression data across studies. Motivated by the traditional me…
Exploratory cancer drug studies test multiple tumor cell lines against multiple candidate drugs. The goal in each paired (cell line, drug) experiment is to map out the dose-response curve of the cell line as the dose level of the drug increases. We propose Bayesian Tensor Filtering (BTF), a hierarchical Bayesian model …
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…
New algorithm optimizes matrix reordering for noisy disordered matrices.
DAG-FOCI learns causal relationships without parametric assumptions.
COMRECGC finds common recourse for global counterfactual explanations in GNNs.
Physics analogies explain machine learning overfitting control.
We consider continuous time Markovian processes where populations of individual agents interact stochastically according to kinetic rules. Despite the increasing prominence of such models in fields ranging from biology to smart cities, Bayesian inference for such systems remains challenging, as these are continuous tim…
Understanding functional organization of genetic information is a major challenge in modern biology. Following the initial publication of the human genome sequence in 2001, advances in high-throughput measurement technologies and efficient sharing of research material through community databases have opened up new view…
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…
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…
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…
Quantitative modeling of post-transcriptional regulation process is a challenging problem in systems biology. A mechanical model of the regulatory process needs to be able to describe the available spatio-temporal protein concentration and mRNA expression data and recover the continuous spatio-temporal fields. Rigorous…
We compute Khovanov homology for tangles using TQFT.
New method learns cell trajectories and network interactions from single-cell data.
DHRL learns interpretable features from visual data.
In this paper, we show how simple logistic growth that was studied intensively during the last 200 years in many domains of science could be extended in a rather simple way and with these extensions is capable to produce a collection of behaviors widely observed in an enormous number of real-life systems in Economics, …