Mathematical pipeline identifies structural homology of knotted proteins.
problem Quantification and classification of protein structures, especially knotted proteins, require noise-free and complete data.
method Developed a geometric framework using persistent homology to analyze protein structures.
result Persistent homology accurately represents structural homology of knotted proteins and identifies geometric features of protein entanglement.
Topological data analysis classifies encrypted bits with success.
problem Classifying encrypted data with traditional machine learning methods.
method Persistent homology for generating topological features, machine learning pipeline.
result Successfully classifies encrypted data, outperforming classical models.
Unreduced PDs can perform similarly to reduced PDs in machine learning tasks.
problem Ignoring much of the information in persistence diagrams in machine learning pipelines.
method Developed methods to generate topological feature vectors from unreduced boundary matrices.
result Unreduced PDs can perform on par with, and sometimes outperform, fully-reduced PDs in machine learning tasks.
Pipeline learns topological features for protein stability prediction.
problem Predicting protein stability using topological features.
method Data-driven method to learn topological features, comparing with expert features.
result Topological features achieve 92%-99% of SME-based models' performance.
PipeDream-2BW accelerates large model training by 20x with minimal memory usage.
problem Training large models requires memory beyond single accelerator capacity.
method Pipeline parallelism, weight gradient coalescing, double buffering.
result Accelerates large model training by up to 20x.
TopoFisher learns topological summaries by maximizing Fisher information, improving parameter efficiency and inference quality.
problem Simulation-based inference misses key information in low-order statistics, especially for non-Gaussian fields.
method TopoFisher uses a differentiable persistent-homology pipeline that learns topological summaries by maximizing local Gaussian Fisher information.
result TopoFisher recovers much of the available information and outperforms fixed topological vectorizations in weak gravitational lensing.
New method enhances graph neural networks using contractions and hourglass persistence.
problem Limitations of traditional persistent homology in graph neural networks.
method Hourglass Persistence, Contraction Homology, contractions as a topological operation.
result Hourglass Persistence boosts expressivity, learnability, and stability in graph representation learning.
AgensFlow learns multi-agent coordination policies from experience.
problem Difficult coordination choices in multi-agent systems built on LLMs.
method Online policy learning from repeated trajectories, treating decisions as learnable.
result Learned routing improves coordination-heavy workflows over static wiring.
This work classifies monodromy in vineyards using singularity theory.
problem Understanding and predicting monodromy in vineyards for topological data analysis.
method Using a connection with singularity theory, the study classifies monodromy in vineyards of 1-manifolds in R^2.
result Monodromy in vineyards occurs only if they contain a specific singularity of the distance function.
We present a way to use Topological Data Analysis (TDA) for machine learning tasks on grayscale images. We apply persistent homology to generate a wide range of topological features using a point cloud obtained from an image, its natural grayscale filtration, and different filtrations defined on the binarized image. We…
AVATAR uses a surrogate model to quickly evaluate ML pipelines, saving time and resources.
problem Time-consuming evaluation of ML pipelines limits exploration of complex models.
method AVATAR employs a surrogate model to assess pipeline validity without execution.
result AVATAR accelerates ML pipeline evaluation, improving efficiency in complex scenarios.
New method detects and compares folding pathways of knotted proteins.
problem Understanding the function of knots in protein folding.
method Topological analysis of protein knotoid distributions and entanglement.
result Reveals unique folding pathway for shallow knotted Carbonic Anhydrases.
This paper introduces TDA and TSI for better business analytics.
problem Nonlinear, multi-scale business datasets under-represented by traditional tools.
method Topological Data Analysis (TDA) and Topological Stability Index (TSI).
result TSI reveals structural variability in business data.
A new penalty-free method optimizes portfolios without quantum annealing penalties.
problem Optimizing portfolios with quantum annealing penalties.
method Removing the penalty term and using a classical feasibility projector.
result Significant reduction in chain-break fractions and post-processed regret.
Hyperparameter tuning of multi-stage pipelines introduces a significant computational burden. Motivated by the observation that work can be reused across pipelines if the intermediate computations are the same, we propose a pipeline-aware approach to hyperparameter tuning. Our approach optimizes both the design and exe…
Stable density-based clustering via multiparameter persistence.
problem Density-based clustering stability to data perturbations.
method Degree-Rips construction, correspondence-interleaving distance, multiparameter stability analysis.
result Persistable pipeline yields stable, consistent density-based clustering.
Classical Machine Learning (ML) pipelines often comprise of multiple ML models where models, within a pipeline, are trained in isolation. Conversely, when training neural network models, layers composing the neural models are simultaneously trained using backpropagation. We argue that the isolated training scheme of ML…
Study proposes a statistical testing framework for evaluating clustering pipelines.
problem Quantifying the statistical reliability of clustering results from data analysis pipelines.
method Selective inference-based statistical testing framework for clustering pipelines.
result The proposed test controls the type I error rate and is effective in validating clustering results.
New method robustifies topological data analysis against outliers.
problem Outliers make topological data analysis unstable.
method Proposed a robust distance function (MoM Dist) for persistent homology.
result MoM Dist sublevel filtrations and weighted filtrations are consistent estimators in adversarial settings.
New method detects dynamical system changes in time series data.
problem Detecting changes in time series data structures.
method Weighted Ordinal Partition Network (OPN) with topological data analysis (TDA).
result Improved accuracy and resilience to noise in dynamic state detection.
Investigates fairness in pipeline models where individuals may drop out.
problem Fairness in pipeline models where individuals may drop out and subsequent stages depend on remaining individuals.
method Rigorous framework for evaluating fairness guarantees, showing that naïve auditing is insufficient and dependence must exist between stages.
result Fairness in pipelines can be arbitrary, even with just two stages, and requires dependence between stages.
Persistent homology analysis provides means to capture the connectivity structure of data sets in various dimensions. On the mathematical level, by defining a metric between the objects that persistence attaches to data sets, we can stabilize invariants characterizing these objects. We outline how so called contour fun…
Data science relies on pipelines that are organized in the form of interdependent computational steps. Each step consists of various candidate algorithms that maybe used for performing a particular function. Each algorithm consists of several hyperparameters. Algorithms and hyperparameters must be optimized as a whole …
A method for vectorizing persistence diagrams simplifies topological data analysis.
problem Challenges in integrating persistence diagrams into machine learning pipelines.
method Quantized Persistence and Integral transforms of Diagrams (Qupid) using binning and discrete transforms.
result Qupid preserves highly competitive performances compared to state-of-the-art methods across various classification tasks.
Automates supervised learning pipeline design with matrix and tensor factorization.
problem Designing effective supervised learning pipelines with many choices.
method Uses matrix and tensor factorization to model pipeline search space and develops greedy experiment design protocols.
result Demonstrates the effectiveness of the approach on real-world classification problems.
Data science relies on pipelines that are organized in the form of interdependent computational steps. Each step consists of various candidate algorithms that maybe used for performing a particular function. Each algorithm consists of several hyperparameters. Algorithms and hyperparameters must be optimized as a whole …
New model optimizes oil product distribution via pipelines.
problem Optimizing oil product distribution via pipelines.
method Discrete-time mixed integer linear programming model.
result Significant reductions in pipeline operational cost.
Pipeline decomposes portfolio optimization problems into smaller, solvable subproblems.
problem Large-scale portfolio optimization with constraints.
method Decomposition pipeline with preprocessing, clustering, and risk rebalancing.
result Pipeline reduces problem size by 80% and computation time.
Paper proposes a statistical test for feature selection pipelines using selective inference.
problem Assessing the significance of feature selection pipelines in data analysis.
method Selective inference technique applied to feature selection pipelines composed of various algorithms.
result The proposed statistical test controls false positive feature selection probabilities.
New approach identifies and explains errors in machine learning pipelines.
problem Challenges in identifying and explaining errors in complex machine learning pipelines.
method Uses iteration and provenance to automatically infer root causes of failures.
result Significantly improves precision and recall compared to state-of-the-art methods.
Pipelined Backpropagation trains large models without batches efficiently.
problem Training large models efficiently on hardware with limited batch sizes.
method Fine-grained Pipelined Backpropagation with Spike Compensation and Linear Weight Prediction.
result Fine-grained Pipelined Backpropagation with a batch size of one matches the accuracy of SGD for multiple networks.
In this paper we study the real time deployment of deep learning algorithms in low resource computational environments. As the use case, we compare the accuracy and speed of neural networks for smile detection using different neural network architectures and their system level implementation on NVidia Jetson embedded p…
Unified pipeline classifies time series using complex networks and persistent homology.
problem Classifying univariate time series using various graph constructions and metrics.
method Time series to graph, graph to dissimilarity matrix, filtration to persistence diagrams, vectorization to features.
result Persistence-based features are robust to noise and optimal graph type depends on signal structure.
Study reveals similarities in knowledge flows between pharmaceutical and AI industries.
problem Understanding the dynamics of drug pipelines in global pharmaceutical industry.
method Multilayer network analysis of drug pipeline, global supply chain, and ownership data.
result Proven similarities in knowledge flows between pharmaceutical and AI industries.
Modyn automates continuous ML model training on growing datasets.
problem Continuous model retraining is costly and impractical.
method Data-centric ML platform with policies for continuous training.
result Modyn enables high throughput training with sample-level data selection.
TODS automates time series outlier detection with customizable pipelines.
problem Automated detection of outliers in time series data.
method Modular system with 70 primitives for data processing, time series analysis, and detection algorithms. GUI and data-driven searcher for pipeline design.
result Automated discovery and construction of effective outlier detection pipelines.
Hungarian text processing improved with efficient, accurate NLP pipelines.
problem Improving text processing for Hungarian language.
method Implemented in spaCy framework, focusing on efficiency and accuracy.
result Near state-of-the-art performance in all text preprocessing steps.
With the rapid adoption of machine learning techniques for large-scale applications in science and engineering comes the convergence of two grand challenges in visualization. First, the utilization of black box models (e.g., deep neural networks) calls for advanced techniques in exploring and interpreting model behavio…
A rigorous ML pipeline for binary classification in biomedical studies, focusing on pancreatic cancer.
problem Handling bias in ML models for complex biomedical data.
method Customizable ML analysis pipeline with 9 algorithms, hyperparameter optimization, and thorough evaluation.
result Comparison of ML algorithms to ExSTraCS, highlighting interpretability and bias handling.
Pipeline parallelism (PP) when training neural networks enables larger models to be partitioned spatially, leading to both lower network communication and overall higher hardware utilization. Unfortunately, to preserve the statistical efficiency of sequential training, existing PP techniques sacrifice hardware efficien…
Pipeline for comparing trading algorithms in finance and crypto.
problem Disconnected research and applications in algorithmic trading.
method General pipeline for designing, programming, and evaluating trading strategies.
result Systematic comparison of trading algorithms in finance and crypto.
This paper explores how different audio signal representations affect topological signatures and their predictive power.
problem The impact of different signal representations on topological signatures and their predictive power.
method The study compares three different signal representations (embedding, spectrogram, and spectrogram zeroes) and evaluates their topological signatures for speaker gender, vowel type, and individual prediction.
result Topological signatures from spectrogram zeroes offer the best improvement for gender prediction, and different representations are complementary.
RL pipeline simplifies knot diagrams, including very hard unknots.
problem Simplifying complex knot diagrams, especially very hard unknots.
method Reinforcement learning for move proposals and heuristic navigation of Reidemeister moves.
result Trained agent simplifies diagrams, including a 41#910 link to a three-step unknotting process. This paper explores how LLMs can improve pipeline-based conversational agents.
problem Limitations of pipeline-based conversational agents in human-like conversations.
method Investigated LLMs' capabilities in two phases: design and development, and operations.
result LLMs can enhance pipeline-based agents in various tasks like data generation, intent classification, and auto-correction.
Much of the work in metalearning has focused on classifier selection, combined more recently with hyperparameter optimization, with little concern for data preprocessing. Yet, it is generally well accepted that machine learning applications require not only model building, but also data preprocessing. In other words, p…
Pipeline selects best RL policy from limited data.
problem Selecting best RL policy from small datasets.
method Task- and method-agnostic pipeline using multiple data splits.
result Pipeline produces higher-performing policies.
Machine learning pipeline potentially consists of several stages of operations like data preprocessing, feature engineering and machine learning model training. Each operation has a set of hyper-parameters, which can become irrelevant for the pipeline when the operation is not selected. This gives rise to a hierarchica…
The paper presents a method for analyzing shape graphs using specific features.
problem Analyzing geometric and topological variations in shape graphs.
method Curated set of topological, geometric, and directional features for shape graph analysis.
result The feature representation is effective for tasks like group comparison and classification.