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.
Paper uses machine learning to identify key pathways for c-di-GMP in bacterial genomes.
Identifying altered pathways that are associated with specific cancer types can potentially bring a significant impact on cancer patient treatment. Accurate identification of such key altered pathways information can be used to develop novel therapeutic agents as well as to understand the molecular mechanisms of variou…
PKB framework boosts genomic data analysis by integrating pathway knowledge.
In this work, a machine learning approach for identifying the multi-omics metabolic regulatory control circuits inside the pathways is described. Therefore, the identification of bacterial metabolic pathways that are more regulated than others in term of their multi-omics follows from the analysis of these circuits . T…
The paper proposes a method to predict the performance of data-driven algorithms using surrogate models.
We present the Network-based Biased Tree Ensembles (NetBiTE) method for drug sensitivity prediction and drug sensitivity biomarker identification in cancer using a combination of prior knowledge and gene expression data. Our devised method consists of a biased tree ensemble that is built according to a probabilistic bi…
ISOKANN learns collective variables and effective dynamics for metastable transitions.
The paper identifies the best treatment to maximize NDPO, a key outcome in causal mediation analysis.
Paper relaxes faithfulness assumption for causal discovery using interventions.
Reliable identification of molecular biomarkers is essential for accurate patient stratification. While state-of-the-art machine learning approaches for sample classification continue to push boundaries in terms of performance, most of these methods are not able to integrate different data types and lack generalization…
The analysis of cancer genomic data has long suffered "the curse of dimensionality". Sample sizes for most cancer genomic studies are a few hundreds at most while there are tens of thousands of genomic features studied. Various methods have been proposed to leverage prior biological knowledge, such as pathways, to more…
Motivation: Identifying interaction clusters of large gene regulatory networks (GRNs) is critical for its further investigation, while this task is very challenging, attributed to data noise in experiment data, large scale of GRNs, and inconsistency between gene expression profiles and function modules, etc. It is prom…
Bayesian approach infers signaling pathways from data.
We categorise coherent band (aka nullification) pathways between knots and 2-component links. Additionally, we characterise the minimal coherent band pathways (with intermediates) between any two knots or 2-component links with small crossing number. We demonstrate these band surgeries for knots and links with small cr…
BioBO optimizes gene perturbation design using Bayesian optimization with biological priors.
Bayesian hypergraph inference models disease pathways from EHR data.
In many scientific studies, it becomes increasingly important to delineate the causal pathways through a large number of mediators, such as genetic and brain mediators. Structural equation modeling (SEM) is a popular technique to estimate the pathway effects, commonly expressed as products of coefficients. However, it …
Chemical reactions occur in energy, environmental, biological, and many other natural systems, and the inference of the reaction networks is essential to understand and design the chemical processes in engineering and life sciences. Yet, revealing the reaction pathways for complex systems and processes is still challen…
Motivation: Untargeted metabolomics comprehensively characterizes small molecules and elucidates activities of biochemical pathways within a biological sample. Despite computational advances, interpreting collected measurements and determining their biological role remains a challenge. Results: To interpret measurement…
Study relaxes identification assumptions for natural direct effects in non-randomized settings.
Motivated by an important insight from neural science, we propose a new framework for understanding the success of the recently proposed "maxout" networks. The framework is based on encoding information on sparse pathways and recognizing the correct pathway at inference time. Elaborating further on this insight, we pro…
Joint replacement is the most common inpatient surgical treatment in the US. We investigate the clinical pathway optimization for knee replacement, which is a sequential decision process from onset to recovery. Based on episodic claims from previous cases, we view the pathway optimization as an intelligence crowdsourci…
Complex systems may contain heterogeneous types of variables that interact in a multi-level and multi-scale manner. In this context, high-level layers may considered as groups of variables interacting in lower-level layers. This is particularly true in biology, where, for example, genes are grouped in pathways and two …
This research improves multitask learning by creating task-specific pathways.
New methods estimate causal effects through mediators, handling confounding without strict assumptions.
New method detects and compares folding pathways of knotted proteins.
We introduce tools to capture the dynamics of three different pathways, in which the synchronization of human decision-making could lead to turbulent periods and contagion phenomena in financial markets. The first pathway is caused when stock market indices, seen as a set of coupled integrate-and-fire oscillators, sync…
Deep reinforcement learning method finds rare events in complex systems.
New method makes neural networks transparent, revealing learning modes.
Simulates patient pathways to detect delayed rare disease diagnoses.
In this work, we developed a network inference method from incomplete data ("PathInf") , as massive and non-uniformly distributed missing values is a common challenge in practical problems. PathInf is a two-stages inference model. In the first stage, it applies a data summarization model based on maximum likelihood to …
New method analyzes complex multivariate pathways in high-dimensional data.
Bayesian method detects mesoscale structures in pathway data networks.
ESN model helps understand climate event impacts.
Paper proposes methods to handle missing data in online RL, improving efficiency and uncertainty capture.
RPPs improve deep learning models with soft equivariance constraints.
Computer-assisted synthesis planning aims to help chemists find better reaction pathways faster. Finding viable and short pathways from sugar molecules to value-added chemicals can be modeled as a retrosynthesis planning problem with a catalyst allowed. This is a crucial step in efficient biomass conversion. The tradit…
A key goal of computational personalized medicine is to systematically utilize genomic and other molecular features of samples to predict drug responses for a previously unseen sample. Such predictions are valuable for developing hypotheses for selecting therapies tailored for individual patients. This is especially va…
We consider the problem of learning fair decision systems in complex scenarios in which a sensitive attribute might affect the decision along both fair and unfair pathways. We introduce a causal approach to disregard effects along unfair pathways that simplifies and generalizes previous literature. Our method corrects …
Study optimizes climate adaptation strategies for NYC.
Exclusive Group Lasso improves feature selection in correlated biological data.
The goal of personalized decision making is to map a unit's characteristics to an action tailored to maximize the expected outcome for that unit. Obtaining high-quality mappings of this type is the goal of the dynamic regime literature. In healthcare settings, optimizing policies with respect to a particular causal pat…
Develops methods for GWAS of high dimensional phenotypes using summary statistics.
spex-LVM infers interpretable latent factors from biomedical data.
SENA-discrepancy-VAE interprets latent causal factors in biological pathways.
Proximal Mediation Analysis with Hidden Recanting Witnesses
A new method uses LLMs to discover causal pathways that affect fairness in machine learning.
Complex architectures of biological neural circuits, such as parallel processing pathways, has been behaviorally implicated in many cognitive studies. However, the theoretical consequences of circuit complexity on neural computation have only been explored in limited cases. Here, we introduce a mechanism by which direc…