New PEMs improve network inference from time-series data.
problem Causal inference from time-series data with trade-off between accuracy and feasibility.
method Infer networks via process motifs for lagged correlation in linear stochastic processes.
result Proposed PEMs achieve high accuracy and efficiency in network inference.
CAWs learn temporal network dynamics without node identities or edge attributes.
problem Learning temporal network dynamics without node identities or edge attributes.
method Causal Anonymous Walks (CAWs) using temporal random walks and hitting counts.
result CAW-N outperforms previous methods in predicting links over 6 real temporal networks.
Machine learning method characterizes network interference in A/B tests.
problem Compromised A/B test reliability due to network interference.
method Causal network motifs and machine learning models.
result Outperforms conventional methods in characterizing network interference.
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…
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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…
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…
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…
Networks are a fundamental model of complex systems throughout the sciences, and network datasets are typically analyzed through lower-order connectivity patterns described at the level of individual nodes and edges. However, higher-order connectivity patterns captured by small subgraphs, also called network motifs, de…
New framework for unbiased sampling of temporal networks.
problem Challenges in analyzing and modeling large, continuous temporal networks.
method General framework for unbiased temporal network sampling with online, single-pass algorithms and unbiased estimators.
result Effective algorithms for fast, accurate, and memory-efficient statistical estimation of temporal network patterns and properties.
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 …
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.
SEISM tests neural network features for regulatory genomics.
problem Testing neural network features for regulatory genomics.
method Selective inference procedure for sequence motifs.
result Sampling under specific parameters characterizes composite null hypothesis.
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…
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.
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…
A new GCN model detects cryptocurrency fraud by considering network evolution and balance theory.
problem Detecting fraud in evolving signed cryptocurrency trust networks.
method Motif-aware temporal GCN using balance theory and learnable weights.
result The model outperforms existing methods on bitcoin datasets.
In self-organizing networks, topology and dynamics coevolve in a continuous feedback, without exogenous driving. The World Trade Network (WTN) is one of the few empirically well documented examples of self-organizing networks: its topology strongly depends on the GDP of world countries, which in turn depends on the str…
RNA-binding proteins (RBPs) play crucial roles in many biological processes, e.g. gene regulation. Computational identification of RBP binding sites on RNAs are urgently needed. In particular, RBPs bind to RNAs by recognizing sequence motifs. Thus, fast locating those motifs on RNA sequences is crucial and time-efficie…
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 …
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.
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.
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.
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.
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.
Time Series Motif Discovery (TSMD) is defined as searching for patterns that are previously unknown and appear with a given frequency in time series. Another problem strongly related with TSMD is Word Segmentation. This problem has received much attention from the community that studies early language acquisition in ba…
A framework infers causal direction from symbolic sequences using compression measures.
problem Inferring causal direction from two observed discrete symbolic sequences.
method Lossless compressors for inferring context-free grammars (CFGs) and quantifying compression extent.
result Grammar inferred from one sequence better compresses the other sequence, indicating causal direction.
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.
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
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.
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…
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.
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…