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.
Model accurately gates ocean microbes from high-frequency flow cytometry data.
Data obtained from Flow Cytometry present pronounced variability due to biological and technical reasons. Biological variability is a well-known phenomenon produced by measurements on different individuals, with different characteristics such as illness, age, sex, etc. The use of different settings for measurement, the…
Analysis of flow cytometry data is an essential tool for clinical diagnosis of hematological and immunological conditions. Current clinical workflows rely on a manual process called gating to classify cells into their canonical types. This dependence on human annotation limits the rate, reproducibility, and complexity …
Computational ghost imaging is an imaging technique in which an object is imaged from light collected using a single-pixel detector with no spatial resolution. Recently, ghost cytometry has been proposed for a high-speed cell-classification method that involves ghost imaging and machine learning in flow cytometry. Ghos…
Model predicts phytoplankton subpopulations based on environmental factors.
Paper uses optimal transport for low-dimensional representation of leukemia flow cytometry data.
A new clustering method estimates non-linear boundaries and automatically selects the number of clusters.
Researchers infer gene activity in dividing cells, accounting for protein inheritance and division history.
ROBOT framework solves regression without correspondence for large data and complex models.
Flow cytometry is often used to characterize the malignant cells in leukemia and lymphoma patients, traced to the level of the individual cell. Typically, flow cytometric data analysis is performed through a series of 2-dimensional projections onto the axes of the data set. Through the years, clinicians have determined…
Flow cytometry is a high-throughput technology used to quantify multiple surface and intracellular markers at the level of a single cell. This enables to identify cell sub-types, and to determine their relative proportions. Improvements of this technology allow to describe millions of individual cells from a blood samp…
Paper shows how to quantify uncertainty in medical ML models.
A new diffusion model encodes causal structures for better interventional sampling and edge inference.
This paper addresses challenges in flexibly modeling multimodal data that lie on constrained spaces. Such data are commonly found in spatial applications, such as climatology and criminology, where measurements are restricted to a geographical area. Other settings include domains where unsuitable recordings are discard…
We outline a representation for discrete multivariate distributions in terms of interventional potential functions that are globally normalized. This representation can be used to model the effects of interventions, and the independence properties encoded in this model can be represented as a directed graph that allows…
We conduct an axiomatic study of the problem of estimating the strength of a known causal relationship between a pair of variables. We propose that an estimate of causal strength should be based on the conditional distribution of the effect given the cause (and not on the driving distribution of the cause), and study d…
Sources of variability in experimentally derived data include measurement error in addition to the physical phenomena of interest. This measurement error is a combination of systematic components, originating from the measuring instrument, and random measurement errors. Several novel biological technologies, such as ma…
We propose a method for learning cyclic causal models from a combination of observational and interventional equilibrium data. Novel aspects of the proposed method are its ability to work with continuous data (without assuming linearity) and to deal with feedback loops. Within the context of biochemical reactions, we a…
We propose a simple method to learn linear causal cyclic models in the presence of latent variables. The method relies on equilibrium data of the model recorded under a specific kind of interventions ("shift interventions"). The location and strength of these interventions do not have to be known and can be estimated f…
The paper introduces a new kernel-based Maximum Mean Discrepancy (MMD) statistic for measuring the distance between two distributions given finitely-many multivariate samples. When the distributions are locally low-dimensional, the proposed test can be made more powerful to distinguish certain alternatives by incorpora…
Many biological data analysis processes like Cytometry or Next Generation Sequencing (NGS) produce massive amounts of data which needs to be processed in batches for down-stream analysis. Such datasets are prone to technical variations due to difference in handling the batches possibly at different times, by different …
Motivated by applications in computational advertising and systems biology, we consider the problem of identifying the best out of several possible soft interventions at a source node in an acyclic causal directed graph, to maximize the expected value of a target node (located downstream of ). Our setting im…
In systems biomedicine, an experimenter encounters different potential sources of variation in data such as individual samples, multiple experimental conditions, and multi-variable network-level responses. In multiparametric cytometry, which is often used for analyzing patient samples, such issues are critical. While c…
Is it possible to perform linear regression on datasets whose labels are shuffled with respect to the inputs? We explore this question by proposing several estimators that recover the weights of a noisy linear model from labels that are shuffled by an unknown permutation. We show that the analog of the classical least-…
The paper tackles high-dimensional mixed linear regression with unknown parameters and proposes methods for estimation, confidence intervals, and hypothesis testing.
The gold standard for discovering causal relations is by means of experimentation. Over the last decades, alternative methods have been proposed that can infer causal relations between variables from certain statistical patterns in purely observational data. We introduce Joint Causal Inference (JCI), a novel approach t…
Algorithm classifies point clouds using deep set linearized optimal transport.
We consider the inference of the structure of an undirected graphical model in an exact Bayesian framework. More specifically we aim at achieving the inference with close-form posteriors, avoiding any sampling step. This task would be intractable without any restriction on the considered graphs, so we limit our explora…
ALPODS AI diagnoses high-dimensional biomedical data with human-understandable explanations.
Fast nonparametric conditional independence testing via two-stage regression
Identifying components and estimating mixing weights in unlabeled finite mixtures under marginal independence.
We propose a new deep learning approach for medical imaging that copes with the problem of a small training set, the main bottleneck of deep learning, and apply it for classification of healthy and cancer cells acquired by quantitative phase imaging. The proposed method, called transferring of pre-trained generative ad…
Identifying dependency in multivariate data is a common inference task that arises in numerous applications. However, existing nonparametric independence tests typically require computation that scales at least quadratically with the sample size, making it difficult to apply them to massive data. Moreover, resampling i…
t-SNE and hierarchical clustering are popular methods of exploratory data analysis, particularly in biology. Building on recent advances in speeding up t-SNE and obtaining finer-grained structure, we combine the two to create tree-SNE, a hierarchical clustering and visualization algorithm based on stacked one-dimension…
There has been great interest recently in applying nonparametric kernel mixtures in a hierarchical manner to model multiple related data samples jointly. In such settings several data features are commonly present: (i) the related samples often share some, if not all, of the mixture components but with differing weight…
New method infers dynamical systems from population data.
New method recovers relative rates in spatial compositional data from IMS.
BlosSOM improves data visualization for large datasets.
Clustering high-dimensional data, such as images or biological measurements, is a long-standingproblem and has been studied extensively. Recently, Deep Clustering has gained popularity due toits flexibility in fitting the specific peculiarities of complex data. Here we introduce the Mixture-of-Experts Similarity Variat…
Despite fluorescent cell-labelling being widely employed in biomedical studies, some of its drawbacks are inevitable, with unsuitable fluorescent probes or probes inducing a functional change being the main limitations. Consequently, the demand for and development of label-free methodologies to classify cells is strong…
Scientific practice typically involves repeatedly studying a system, each time trying to unravel a different perspective. In each study, the scientist may take measurements under different experimental conditions (interventions, manipulations, perturbations) and measure different sets of quantities (variables). The res…
A new FFT-based method for fast rigid alignment of 2D closed curves.
New flows introduced for symplectic geometry.
The paper examines Ricci flows with closed and smooth tangent flows, proving uniqueness and characterizing ancient flows.
Proves uniqueness of geometric flow in various Riemannian manifolds.
Study of twisted Calabi flow connecting J-flow and Calabi flow on Kähler manifolds.
Investigate scalar curvature under geometric flows
Streets and Tian introduced pluriclosed flow and symplectic curvature flow in recent years. Here we construct a curvature flow to unify these two flows. We show the short time existence of our flow and exhibit an obstruction to long time existence.