Paper proposes DTW-SOM for visual exploration of time-series motifs.
problem Exploring motifs extracted by time-series motif discovery algorithms.
method Adapted Self-Organizing Map (DTW-SOM) using Dynamic Time Warping distance.
result DTW-SOM effectively visualizes motifs from time-series data.
Proposes VILMAP for finding motifs and segmenting words in time series.
problem Finding motifs and segmenting words in time series data.
method Self-Organizing Maps with variable input length.
result VILMAP identifies motifs of varying lengths and avoids catastrophic forgetting.
The discovery of time series motifs has emerged as one of the most useful primitives in time series data mining. Researchers have shown its utility for exploratory data mining, summarization, visualization, segmentation, classification, clustering, and rule discovery. Although there has been more than a decade of exten…
New method discovers time series motifs under DTW, significantly reducing computations.
problem Discovering time series motifs under DTW is computationally challenging.
method Exact scalable method using novel lower bounds hierarchy.
result Prunes up to 99.99% of DTW computations under realistic settings.
TF-MoDISco (Transcription Factor Motif Discovery from Importance Scores) is an algorithm for identifying motifs from basepair-level importance scores computed on genomic sequence data. This technical note focuses on version v0.5.6.5. The implementation is available at https://github.com/kundajelab/tfmodisco/tree/v0.5.6…
Paper discovers manoeuvres from vehicle telematics data.
problem Analyzing driving behaviour from vehicle data.
method Used motif detection in time-series with a modified EMD algorithm.
result Validated motif discovery for complex manoeuvres.
MotiFiesta learns network motifs efficiently.
problem Efficiently identifying network motifs in real-world datasets.
method Formulated as a node labelling task, using machine learning.
result Demonstrated efficient motif discovery on challenging datasets.
MDF represents time series motifs as images for improved classification.
problem Classifying time series data with high-order patterns.
method Motif Difference Field (MDF) using Fully Convolutional Networks (FCN).
result MDF outperforms other methods on UCR time series datasets.
Complex systems, such as airplanes, cars, or financial markets, produce multivariate time series data consisting of a large number of system measurements over a period of time. Such data can be interpreted as a sequence of states, where each state represents a prototype of system behavior. An important problem in this …
New model generates larger molecules more effectively.
problem Previous graph generation techniques struggle with larger molecules.
method Hierarchical graph encoder-decoder using structural motifs.
result Model significantly outperforms previous baselines on molecule generation tasks.
HiGraphDTI learns drug and target representations from molecular graphs to predict DTIs.
problem Inaccurate drug-target interaction prediction due to insufficient chemical information extraction.
method Hierarchical graph representation learning to extract chemical information from atoms, motifs, and molecules.
result HiGraphDTI outperforms state-of-the-art methods in DTI prediction and interaction interpretation.
The last decade has seen a flurry of research on all-pairs-similarity-search (or, self-join) for text, DNA, and a handful of other datatypes, and these systems have been applied to many diverse data mining problems. Surprisingly, however, little progress has been made on addressing this problem for time series subseque…
Motivation: Prediction of the interaction affinity between proteins and compounds is a major challenge in the drug discovery process. WideDTA is a deep-learning based prediction model that employs chemical and biological textual sequence information to predict binding affinity. Results: WideDTA uses four text-based inf…
Method finds motifs in knowledge graphs, revealing their structure.
problem Identifying meaningful subunits in knowledge graphs.
method Inspired by simple graphs, the approach uses compression techniques to find motifs.
result Motifs found reflect the basic structure of the graph.
Improved scaffold generation for protein motifs using SE(3) flow matching.
problem Lack of structural diversity in generated scaffolds for protein motifs.
method Extended FrameFlow for motif-scaffolding with motif amortization and motif guidance.
result 2.5 times more designable and unique motif-scaffolds compared to state-of-the-art.
Networks are a fundamental tool for modeling complex systems in a variety of domains including social and communication networks as well as biology and neuroscience. Small subgraph patterns in networks, called network motifs, are crucial to understanding the structure and function of these systems. However, the role of…
Researchers create exact minimal surfaces with helical motifs in biological structures.
problem Analyzing helical motifs in minimal surfaces of biological structures.
method Developed a method to construct exact minimal surfaces with arbitrary helical motifs.
result Exact minimal surfaces with helical motifs can be created and analyzed.
New clustering methods use motifs to organize networks.
problem Organizing directed graphs efficiently.
method Construct clustering methods parametrized by motifs.
result New clustering methods can organize networks.
MMGAN creates graphs with higher-order motifs for better network simulation.
problem Generative models fail to capture higher-order connectivity patterns in real-world networks.
method Combines multiple biased random walks to capture different motif structures.
result Outperforms NetGAN at creating graphs with accurate network motif statistics.
Behaviors of several laboratory animals can be modeled as sequences of stereotyped behaviors, or behavioral motifs. However, identifying such motifs is a challenging problem. Behaviors have a multi-scale structure: the animal can be simultaneously performing a small-scale motif and a large-scale one (e.g. \textit{chewi…
odeN efficiently approximates multiple temporal motifs in large networks.
problem Efficiently counting multiple temporal motifs in large temporal networks.
method odeN is a sampling-based algorithm that provides accurate probabilistic approximations of motif counts.
result odeN provides accurate approximations of motif counts in a fraction of the time needed by state-of-the-art methods.
Computational approaches to transcription factor binding site identification have been actively researched for the past decade. Negative examples have long been utilized in de novo motif discovery and have been shown useful in transcription factor binding site search as well. However, understanding of the roles of nega…
Synthetic Petri Dish predicts neural architecture performance faster.
problem Expensive NAS evaluation process with ground-truth data.
method Instantiates motifs in small networks, evaluates with few synthetic samples.
result Significantly higher accuracy in predicting motif performance.
FoundCause: Causal Discovery with Latent Confounders from Observational Data
problem Causal discovery from observational data
method FoundCause, an amortized causal discovery model trained on synthetic data
result FoundCause outperforms classical and amortized methods on real-world datasets
A motif-based framework identifies local spillover structures in financial markets.
problem Aggregate risk spillovers obscure local interaction patterns in systemic risk.
method Develops a motif-based framework using multiscale backbones and colored motifs.
result Motif-based portfolios outperform traditional benchmarks on risk-adjusted returns.
New method learns diverse protein scaffolds for motif design.
problem Designing long, diverse protein scaffolds for specific motifs.
method E(3)-equivariant graph neural network for diffusion modeling.
result First to guarantee conditional sampling from diffusion models.
PGEL learns embeddings to diversify protein motifs while maintaining biological function.
problem Generating diverse protein structures while preserving biological function.
method Embedding learning framework that enhances motif diversity in a diffusion model's frozen denoiser.
result PGEL achieves greater structural diversity, better designability, and improved self-consistency compared to partial diffusion.
Model improves robustness of neural network sequences without transition failures.
problem Learning and generating complex sequences of motor primitives without interference.
method Inspired by thalamocortical circuit, uses specific module for motif transitions.
result Improved robustness of sequence generation with no transition failures.
New method clusters weighted directed networks using motifs.
problem Clustering directed networks fails to consider higher-order structure and edge weights.
method Motif-based weighted spectral clustering with new matrix formulae.
result Scalable and effective clustering on large graphs and real-world data.
New method uses diffusion models to generate proteins with specific motifs.
problem Generating proteins with specific functional substructures (motifs) using diffusion models.
method Adapting SMC-aided diffusion posterior samplers to zero-shot scaffolding tasks.
result Proposed potentials and samplers improve performance in generating proteins with desired motifs.
Proposes a motif-preserving Graph Neural Network for financial default prediction.
problem Weak connectivity and imbalance in motif patterns in graph-based models.
method MotifGNN with curriculum learning to capture higher-order topology structures.
result Significantly improved financial default prediction accuracy on public and industrial datasets.
In this paper, we introduce the notion of motif closure and describe higher-order ranking and link prediction methods based on the notion of closing higher-order network motifs. The methods are fast and efficient for real-time ranking and link prediction-based applications such as web search, online advertising, and re…
Generalized belief propagation converges to optimal solutions on graphs with motifs.
problem Understanding belief propagation on loopy graphs.
method Study of generalized belief propagation on graphs with motifs.
result Generalized belief propagation converges to the global optimum of the Bethe free energy.
BaGGLS models biological interactions using Bayesian shrinkage for interpretability.
problem Interpreting complex interactions in high-dimensional biological data.
method Bayesian group global-local shrinkage prior with variational approximation.
result BaGGLS outperforms other methods in interaction detection and scalability.
Paper constructs motifs from planar tilings for DP weaves and polycatenanes.
problem Creating complex entangled structures from periodic tilings.
method Combinatorial methodology using polygonal link transformations.
result Predicting the type of motif from a given tiling and polygonal link method.
The paper models musical motif transformations in Beethoven's works.
problem Understanding how motifs transform in symbolic music.
method Developed a probabilistic framework using Conditional Random Fields.
result Identified patterns of motif transformations and their co-occurrences.
UrbanRhythm reveals urban dynamics from mobility data.
problem Understanding changing urban activities over time.
method Extracting staying, leaving, arriving attributes; using Saak transform; clustering for city states; motif analysis for short-term regularity.
result Characterized urban dynamics as city state transformations over time.
The study identifies persistent motifs in stock correlations for sector-neutral portfolio diversification.
problem Forecasting and diversification of sector-neutral portfolios using long-term correlations.
method Analysis of Triangulated Maximally Filtered Graphs (TMFG) generated from rolling windows of stock price log-returns, identifying persistent motifs.
result Persistent motifs in stock correlations can be used to forecast and diversify sector-neutral portfolios, reducing volatility.
When analyzing the genome, researchers have discovered that proteins bind to DNA based on certain patterns of the DNA sequence known as "motifs". However, it is difficult to manually construct motifs due to their complexity. Recently, externally learned memory models have proven to be effective methods for reasoning ov…
When each data point is a large graph, graph statistics such as densities of certain subgraphs (motifs) can be used as feature vectors for machine learning. While intuitive, motif counts are expensive to compute and difficult to work with theoretically. Via graphon theory, we give an explicit quantitative bound for the…
New approach learns latent motifs in networks for mesoscale structure analysis.
problem Understanding large-scale behavior in complex systems through mesoscale structures.
method Network dictionary learning (NDL) combining network sampling and nonnegative matrix factorization.
result Networks can be approximated using a small set of latent motifs.
When learning a hidden Markov model (HMM), sequen- tial observations can often be complemented by real-valued summary response variables generated from the path of hid- den states. Such settings arise in numerous domains, includ- ing many applications in biology, like motif discovery and genome annotation. In this pape…
KCoreMotif clusters large networks efficiently by exploiting k-core decomposition and motifs.
problem Efficiently clustering large networks for trust evaluation.
method Exploits k-core decomposition and motifs to perform motif-based spectral clustering on k-core subgraphs.
result The proposed algorithm is accurate and efficient for large networks.
This paper classifies periodic weaves and their universal cover, extending Tait's conjectures.
problem Classifying periodic weaves and their universal cover in thickened surfaces.
method Introducing hyperbolic periodic weaves, extending Tait's conjectures, and using a generalized Kauffman bracket polynomial.
result Tait's conjectures are extended to minimal reduced alternating weaving motifs.
Paper defines and analyzes mathematical equivalence of periodic tangles.
problem Understanding the equivalence of periodic tangles.
method Established mathematical framework, characterized isotopies, generalized results.
result Characterization of DP tangle equivalence based on motifs.
Bayesian network models are finding success in characterizing enzyme-catalyzed reactions, slow conformational changes, predicting enzyme inhibition, and genomics. In this work, we apply them to statistical modeling of peptides by simultaneously identifying amino acid sequence motifs and using a motif-based model to cla…
In this paper, we consider the problem of fast and efficient indexing techniques for sequences evolving in non-Euclidean spaces. This problem has several applications in the areas of human activity analysis, where there is a need to perform fast search, and recognition in very high dimensional spaces. The problem is ma…
We study trade-based manipulation of stock prices from the perspective of complex trading networks constructed by using detailed information of trades. A stock trading network consists of nodes and directed links, where every trader is a node and a link is formed from one trader to the other if the former sells shares …