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.
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.
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.
Searching new molecules in areas like drug discovery often starts from the core structures of candidate molecules to optimize the properties of interest. The way as such has called for a strategy of designing molecules retaining a particular scaffold as a substructure. On this account, our present work proposes a scaff…
We describe the concept of logical scaffolds, which can be used to improve the quality of software that relies on AI components. We explain how some of the existing ideas on runtime monitors for perception systems can be seen as a specific instance of logical scaffolds. Furthermore, we describe how logical scaffolds ma…
Paper analyzes Scaffold algorithm for federated learning, proving linear speed-up with stochastic gradients.
problem Understanding the impact of stochastic gradients on the Scaffold algorithm's performance.
method Proved linear speed-up in the number of clients using a Markov chain analysis of global parameters and control variates.
result Scaffold achieves linear speed-up in the number of clients up to higher-order terms in the step size, but retains a higher-order bias.
Scaffolding sets improve predictor correctness across subsets.
problem Ensuring predictor correctness across multiple subsets.
method Inspired by neural nets, constructing scaffolding sets to ensure correctness.
result Scaffolding sets ensure predictor correctness, not just calibration.
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.
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.
Federated Averaging (FedAvg) has emerged as the algorithm of choice for federated learning due to its simplicity and low communication cost. However, in spite of recent research efforts, its performance is not fully understood. We obtain tight convergence rates for FedAvg and prove that it suffers from `client-drift' w…
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…
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.
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…
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.
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.
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 …
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.
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.
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.
TDS provides exact samples for conditional distributions in diffusion models.
problem Lack of exact sampling methods for diffusion models.
method Sequential Monte Carlo (SMC) algorithm with twisting technique.
result TDS offers more accurate approximations with fewer particles compared to heuristics.
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 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.
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.
Self-taught optimizer improves code generation using language models.
problem Improving code generation using language models.
method Recursive self-improvement of a scaffolding program that generates code.
result Improved scaffolding program generates programs with significantly better performance.
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…
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.
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…
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…
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…
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.
Co-Diffusion predicts drug-target affinity by learning latent manifolds and diffusion, improving generalization.
problem Cold-start regimes in drug-target affinity prediction due to label scarcity and domain shifts.
method Two-stage framework: latent manifold alignment and latent diffusion regularization.
result Significantly outperforms state-of-the-art baselines, especially in zero-shot generalization.
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.
The n-skeleton of the canonical cubulation C of Rn+2 into unit cubes is called the {\it canonical scaffolding} S. In this paper, we prove that any smooth, compact, closed, n-dimensional submanifold of Rn+2 with trivial normal bundle can be continuously isotoped by an amb…
In this paper we study topological surfaces as gridded surfaces in the 2-dimensional scaffolding of cubic honeycombs in Euclidean and hyperbolic spaces.
We study soft persistence (existence in subsequent temporal layers of motifs from the initial layer) of motif structures in Triangulated Maximally Filtered Graphs (TMFG) generated from time-varying Kendall correlation matrices computed from stock prices log-returns over rolling windows with exponential smoothing. We ob…
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 shows LIME and SHAP explanations can be fooled by adversarial attacks.
problem Reliability of post hoc explanation methods like LIME and SHAP.
method Adversarial attack technique to hide classifier biases.
result Popular explanation techniques can be fooled into generating biased explanations.
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.