arXiv subjects

Nataliya Sokolovska

Publications and source records attributed to Nataliya Sokolovska.

11 recordsLinked to original sources

arXiv2026

Finetuning-Free Diffusion Model with Adaptive Constraint Guidance for Inorganic Crystal Structure Generation

Generative diffusion models have emerged as powerful tools for the discovery of inorganic crystal structures, yet steering their sampling process toward user-defined physical and chemical objectives remains challenging. We present a computational framework that integrates adaptive constraint guidance into a pre-trained crystal diffusion model, enabling the generation of candidate structures that satisfy targeted structural and chemical requirements without model retraining. The approach incorporates differentiable constraint functions directly during sampling, providing an interpretable mechanism for expert-driven exploration of the crystal structure space. To assess the reliability of generated candidates, we introduce a multi-stage validation workflow combining descriptor-based analysis, duplicate removal, comparison with reference crystal databases, graph neural network energy prediction, and thermodynamic stability evaluation through convex-hull analysis. The framework is applied to several classes of inorganic compounds and to constraints involving atomic volume, local coordination environments, and near-neighbor structural motifs. Results demonstrate that adaptive guidance effectively redirects the sampling distribution toward structures exhibiting the desired characteristics while preserving chemical plausibility. Subsequent validation reveals which generated candidates remain viable after energetic and thermodynamic screening. The proposed methodology provides a practical and transparent strategy for incorporating expert knowledge into crystal generative models and establishes a general computational framework for constrained materials discovery.

cond-mat.mtrl-sci↗

arXiv2025

Quantitative evaluation of methods to analyze motion changes in single-particle experiments

The analysis of live-cell single-molecule imaging experiments can reveal valuable information about the heterogeneity of transport processes and interactions between cell components. These characteristics are seen as motion changes in the particle trajectories. Despite the existence of multiple approaches to carry out this type of analysis, no objective assessment of these methods has been performed so far. Here, we report the results of a competition to characterize and rank the performance of these methods when analyzing the dynamic behavior of single molecules. To run this competition, we implemented a software library that simulates realistic data corresponding to widespread diffusion and interaction models, both in the form of trajectories and videos obtained in typical experimental conditions. The competition constitutes the first assessment of these methods, providing insights into the current limitations of the field, fostering the development of new approaches, and guiding researchers to identify optimal tools for analyzing their experiments.

cond-mat.soft↗

arXiv2025

Bottom-up Iterative Anomalous Diffusion Detector (BI-ADD)

In recent years, the segmentation of short molecular trajectories with varying diffusive properties has drawn particular attention of researchers, since it allows studying the dynamics of a particle. In the past decade, machine learning methods have shown highly promising results, also in changepoint detection and segmentation tasks. Here, we introduce a novel iterative method to identify the changepoints in a molecular trajectory, i.e., frames, where the diffusive behavior of a particle changes. A trajectory in our case follows a fractional Brownian motion and we estimate the diffusive properties of the trajectories. The proposed BI-ADD combines unsupervised and supervised learning methods to detect the changepoints. Our approach can be used for the analysis of molecular trajectories at the individual level and also be extended to multiple particle tracking, which is an important challenge in fundamental biology. We validated BI-ADD in various scenarios within the framework of the AnDi2 Challenge 2024 dedicated to single particle tracking. Our method is implemented in Python and is publicly available for research purposes.

cs.LG↗

arXiv2023

False membership rate control in mixture models

The clustering task consists in partitioning elements of a sample into homogeneous groups. Most datasets contain individuals that are ambiguous and intrinsically difficult to attribute to one or another cluster. However, in practical applications, misclassifying individuals is potentially disastrous and should be avoided. To keep the misclassification rate small, one can decide to classify only a part of the sample. In the supervised setting, this approach is well known and referred to as classification with an abstention option. In this paper the approach is revisited in an unsupervised mixture model framework and the purpose is to develop a method that comes with the guarantee that the false membership rate (FMR) does not exceed a pre-defined nominal level $α$. A plug-in procedure is proposed, for which a theoretical analysis is provided, by quantifying the FMR deviation with respect to the target level $α$ with explicit remainder terms. Bootstrap versions of the procedure are shown to improve the performance in numerical experiments.

math.ST↗

arXiv2023

Data-Driven Score-Based Models for Generating Stable Structures with Adaptive Crystal Cells

The discovery of new functional and stable materials is a big challenge due to its complexity. This work aims at the generation of new crystal structures with desired properties, such as chemical stability and specified chemical composition, by using machine learning generative models. Compared to the generation of molecules, crystal structures pose new difficulties arising from the periodic nature of the crystal and from the specific symmetry constraints related to the space group. In this work, score-based probabilistic models based on annealed Langevin dynamics, which have shown excellent performance in various applications, are adapted to the task of crystal generation. The novelty of the presented approach resides in the fact that the lattice of the crystal cell is not fixed. During the training of the model, the lattice is learned from the available data, whereas during the sampling of a new chemical structure, two denoising processes are used in parallel to generate the lattice along the generation of the atomic positions. A multigraph crystal representation is introduced that respects symmetry constraints, yielding computational advantages and a better quality of the sampled structures. We show that our model is capable of generating new candidate structures in any chosen chemical system and crystal group without any additional training. To illustrate the functionality of the proposed method, a comparison of our model to other recent generative models, based on descriptor-based metrics, is provided.

physics.comp-ph↗

arXiv2020

Supervised deep learning prediction of the formation enthalpy of the full set of configurations in complex phases: the $σ-$phase as an example

Machine learning (ML) methods are becoming integral to scientific inquiry in numerous disciplines, such as material sciences. In this manuscript, we demonstrate how ML can be used to predict several properties in solid-state chemistry, in particular the heat of formation of a given complex crystallographic phase (here the $σ-$phase, $tP30$, $D8_{b}$). Based on an independent and unprecedented large first principles dataset containing about 10,000 $σ-$compounds with $n=14$ different elements, we used a supervised learning approach, to predict all the $\sim$500,000 possible configurations within a mean absolute error of 23 meV/at ($\sim$2 kJ.mol$^{-1}$) on the heat of formation and $\sim$0.06 Ang. on the tetragonal cell parameters. We showed that neural network regression algorithms provide a significant improvement in accuracy of the predicted output compared to traditional regression techniques. Adding descriptors having physical nature (atomic radius, number of valence electrons) improves the learning precision. Based on our analysis, the training database composed of the only binary-compositions plays a major role in predicting the higher degree system configurations. Our result opens a broad avenue to efficient high-throughput investigations of the combinatorial binary calculation for multicomponent prediction of a complex phase.

cond-mat.mtrl-sci↗

arXiv2020

Latent Instrumental Variables as Priors in Causal Inference based on Independence of Cause and Mechanism

Causal inference methods based on conditional independence construct Markov equivalent graphs, and cannot be applied to bivariate cases. The approaches based on independence of cause and mechanism state, on the contrary, that causal discovery can be inferred for two observations. In our contribution, we challenge to reconcile these two research directions. We study the role of latent variables such as latent instrumental variables and hidden common causes in the causal graphical structures. We show that the methods based on the independence of cause and mechanism, indirectly contain traces of the existence of the hidden instrumental variables. We derive a novel algorithm to infer causal relationships between two variables, and we validate the proposed method on simulated data and on a benchmark of cause-effect pairs. We illustrate by our experiments that the proposed approach is simple and extremely competitive in terms of empirical accuracy compared to the state-of-the-art methods.

cs.LG↗

arXiv2019

CrystalGAN: Learning to Discover Crystallographic Structures with Generative Adversarial Networks

Our main motivation is to propose an efficient approach to generate novel multi-element stable chemical compounds that can be used in real world applications. This task can be formulated as a combinatorial problem, and it takes many hours of human experts to construct, and to evaluate new data. Unsupervised learning methods such as Generative Adversarial Networks (GANs) can be efficiently used to produce new data. Cross-domain Generative Adversarial Networks were reported to achieve exciting results in image processing applications. However, in the domain of materials science, there is a need to synthesize data with higher order complexity compared to observed samples, and the state-of-the-art cross-domain GANs can not be adapted directly. In this contribution, we propose a novel GAN called CrystalGAN which generates new chemically stable crystallographic structures with increased domain complexity. We introduce an original architecture, we provide the corresponding loss functions, and we show that the CrystalGAN generates very reasonable data. We illustrate the efficiency of the proposed method on a real original problem of novel hydrides discovery that can be further used in development of hydrogen storage materials.

cs.LG↗

arXiv2018

Disease Classification in Metagenomics with 2D Embeddings and Deep Learning

Deep learning (DL) techniques have shown unprecedented success when applied to images, waveforms, and text. Generally, when the sample size ($N$) is much bigger than the number of features ($d$), DL often outperforms other machine learning (ML) techniques, often through the use of Convolutional Neural Networks (CNNs). However, in many bioinformatics fields (including metagenomics), we encounter the opposite situation where $d$ is significantly greater than $N$. In these situations, applying DL techniques would lead to severe overfitting. Here we aim to improve classification of various diseases with metagenomic data through the use of CNNs. For this we proposed to represent metagenomic data as images. The proposed Met2Img approach relies on taxonomic and t-SNE embeddings to transform abundance data into "synthetic images". We applied our approach to twelve benchmark data sets including more than 1400 metagenomic samples. Our results show significant improvements over the state-of-the-art algorithms (Random Forest (RF), Support Vector Machine (SVM)). We observe that the integration of phylogenetic information alongside abundance data improves classification. The proposed approach is not only important in classification setting but also allows to visualize complex metagenomic data. The Met2Img is implemented in Python.

cs.CV↗

arXiv2017

Deep Learning for Metagenomic Data: using 2D Embeddings and Convolutional Neural Networks

Deep learning (DL) techniques have had unprecedented success when applied to images, waveforms, and texts to cite a few. In general, when the sample size (N) is much greater than the number of features (d), DL outperforms previous machine learning (ML) techniques, often through the use of convolution neural networks (CNNs). However, in many bioinformatics ML tasks, we encounter the opposite situation where d is greater than N. In these situations, applying DL techniques (such as feed-forward networks) would lead to severe overfitting. Thus, sparse ML techniques (such as LASSO e.g.) usually yield the best results on these tasks. In this paper, we show how to apply CNNs on data which do not have originally an image structure (in particular on metagenomic data). Our first contribution is to show how to map metagenomic data in a meaningful way to 1D or 2D images. Based on this representation, we then apply a CNN, with the aim of predicting various diseases. The proposed approach is applied on six different datasets including in total over 1000 samples from various diseases. This approach could be a promising one for prediction tasks in the bioinformatics field.

cs.CV↗

arXiv2010

Efficient Learning of Sparse Conditional Random Fields for Supervised Sequence Labelling

Conditional Random Fields (CRFs) constitute a popular and efficient approach for supervised sequence labelling. CRFs can cope with large description spaces and can integrate some form of structural dependency between labels. In this contribution, we address the issue of efficient feature selection for CRFs based on imposing sparsity through an L1 penalty. We first show how sparsity of the parameter set can be exploited to significantly speed up training and labelling. We then introduce coordinate descent parameter update schemes for CRFs with L1 regularization. We finally provide some empirical comparisons of the proposed approach with state-of-the-art CRF training strategies. In particular, it is shown that the proposed approach is able to take profit of the sparsity to speed up processing and hence potentially handle larger dimensional models.

cs.LG↗