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.
Bayesian approach infers signaling pathways from data.
Paper uses machine learning to identify key pathways for c-di-GMP in bacterial genomes.
A method clusters genes in large gene regulatory networks using semi-supervised hierarchical clustering.
Perfect adaptation in systems is identified and tested using graphical tools.
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…
DeepSIBA predicts biological effects of chemical structures using graph neural networks.
Signaling proteins are an important topic in drug development due to the increased importance of finding fast, accurate and cheap methods to evaluate new molecular targets involved in specific diseases. The complexity of the protein structure hinders the direct association of the signaling activity with the molecular s…
PKB framework boosts genomic data analysis by integrating pathway knowledge.
A new method uses LLMs to discover causal pathways that affect fairness in machine learning.
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…
Multiplicative noise, including dropout, is widely used to regularize deep neural networks (DNNs), and is shown to be effective in a wide range of architectures and tasks. From an information perspective, we consider injecting multiplicative noise into a DNN as training the network to solve the task with noisy informat…
An axiomatic approach to signal reconstruction is formulated, involving a sample consistent set and a guiding set, describing desired reconstructions. New frame-less reconstruction methods are proposed, based on a novel concept of a reconstruction set, defined as a shortest pathway between the sample consistent set and…
Paper proposes verifier engineering for improving foundation models.
PUMA interprets metabolomics data to predict pathway activity and assign chemical identities.
Machine learning identifies key metabolic control circuits in bacterial pathways.
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…
CRNN discovers chemical reaction pathways from data.
This paper extends compositional data analysis using graph signal processing.
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 …
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…
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.
We study the challenges of applying deep learning to gene expression data. We find experimentally that there exists non-linear signal in the data, however is it not discovered automatically given the noise and low numbers of samples used in most research. We discuss how gene interaction graphs (same pathway, protein-pr…
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.
Deep RL finds efficient pathways for sugar to chemicals.
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.
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 …
The paper proposes a method to predict the performance of data-driven algorithms using surrogate models.
Paper proposes methods to handle missing data in online RL, improving efficiency and uncertainty capture.
RPPs improve deep learning models with soft equivariance constraints.
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…
The paper proposes a method to estimate heterogeneous treatment effects using pretraining strategies.
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.
ISOKANN learns collective variables and effective dynamics for metastable transitions.
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…
RE enhances DL by learning model behavior, enabling iterative self-improvement.
Develops methods for GWAS of high dimensional phenotypes using summary statistics.