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.
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.
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…
We seek to automate the design of molecules based on specific chemical properties. In computational terms, this task involves continuous embedding and generation of molecular graphs. Our primary contribution is the direct realization of molecular graphs, a task previously approached by generating linear SMILES strings …
CORE optimizes molecules by copying or generating substructures, improving accuracy.
problem Inaccurate substructure prediction in molecule optimization.
method Copy & Refine (CORE) strategy combining scaffolding tree generation and adversarial training.
result Significant improvement in various molecule optimization metrics.
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.
SCAFFOLD improves Federated Learning by reducing client-drift and speeding up convergence.
problem Federated Learning's performance is limited by client-drift in heterogeneous data.
method SCAFFOLD uses control variates to correct client-drift and improve convergence.
result SCAFFOLD requires fewer communication rounds and is not affected by data heterogeneity.
Smooth fractal trees via analytic generators, preserving combinatorial and geometric properties.
problem Constructing smooth fractal trees from discrete models.
method Using analytic generator fields to integrate smooth vector fields in an internal state space, generating geometric curves as projections of generator trajectories.
result Analytic generators can represent any discrete tree specification and preserve the asymptotic limit geometry.
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.
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.
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.
In applications of machine learning to particle physics, a persistent challenge is how to go beyond discrimination to learn about the underlying physics. To this end, a powerful tool would be a framework for unsupervised learning, where the machine learns the intricate high-dimensional contours of the data upon which i…
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.
XIMP improves molecular property prediction by integrating multiple graph representations.
problem Graph neural networks struggle in data-scarce regimes and fail to surpass traditional methods.
method Cross-graph inter-message passing with multiple graph abstractions.
result XIMP outperforms state-of-the-art baselines across diverse molecular property tasks.
New algorithms improve distributed optimization under mild variance conditions.
problem Improving distributed optimization for large-scale machine learning problems.
method Revisited Federated Averaging and SCAFFOLD algorithms under a general variance condition.
result Established convergence results for smooth nonconvex objective functions under mild variance conditions.
The International Classification of Functioning, Disability, and Health for Children and Youth (ICF-CY) is a scaffold for designating and systematizing data on functioning and disability. It offers a standard semantic and a theoretical foundation for the demarcation and extent of wellbeing and infirmity. The multidimen…
We describe Venture, an interactive virtual machine for probabilistic programming that aims to be sufficiently expressive, extensible, and efficient for general-purpose use. Like Church, probabilistic models and inference problems in Venture are specified via a Turing-complete, higher-order probabilistic language desce…
Symbolic regression finds two projective invariants capturing most of the Ricci-flat metric variation.
problem Capturing the Ricci-flat metric variation on the Dwork quintic using a small number of projective invariants.
method Using symbolic regression on sampled points, the authors find two low-order symmetric features that capture most of the variation.
result A degree-3 polynomial in (p2,σ3) achieves held-out test R2=0.946. Scaff-PD improves fairness and robustness in federated learning with reduced communication.
problem Improving fairness and robustness in federated learning with limited communication.
method Scaff-PD uses a family of distributionally robust objectives and an accelerated primal dual algorithm with bias-corrected steps.
result Scaff-PD achieves significant gains in communication efficiency and convergence speed while maintaining fairness and robustness.
Conformal prediction fails to cover minority classes in imbalanced datasets, but a class-conditional fix improves coverage.
problem Conformal prediction fails to cover minority classes in imbalanced datasets, leading to poor performance on rare labels.
method Class-conditional conformal prediction to improve coverage of minority classes.
result Class-conditional conformal prediction restores minority coverage to target with a modest increase in prediction-set size.
OmniFold uses deep learning to deconvolve high-dimensional simulations.
problem Removing detector distortions and accounting for noise processes in high-dimensional simulations.
method OmniFold is a deep learning-based approach for maximum likelihood deconvolution.
result OmniFold can remove detector distortions and account for noise processes and acceptance effects.
Explainable machine learning (ML) enables human learning from ML, human appeal of automated model decisions, regulatory compliance, and security audits of ML models. Explainable ML (i.e. explainable artificial intelligence or XAI) has been implemented in numerous open source and commercial packages and explainable ML i…
Machine learning methods may have the potential to significantly accelerate drug discovery. However, the increasing rate of new methodological approaches being published in the literature raises the fundamental question of how models should be benchmarked and validated. We reanalyze the data generated by a recently pub…
Boosting meta-trees improve decision tree performance.
problem Overfitting in decision trees.
method Boosting approach to construct multiple meta-trees.
result Ensembles of meta-trees prevent overfitting.
Generates tubular and membranous shapes using curvature functionals.
problem Difficult analysis of tubular and membranous shapes.
method Modeling as curvature optimization problem, phase-field formulation, GPU algorithm.
result Wide continuum of shape textures discovered.
The paper studies geometric properties of quasi-trees and tree approximations.
problem Geometric properties and tree approximations of quasi-trees.
method Construction of a tree approximating quasi-trees, proving quasi-isometric properties.
result Every quasi-tree is (1,C)-quasi-isometric to a simplicial tree. Efficiently updates posterior tree distributions over meta-trees.
problem Updating posterior distributions over meta-trees efficiently.
method Batch updating method for posterior tree distributions.
result More efficient batch updating method.
We describe a method to infer dense depth from camera motion and sparse depth as estimated using a visual-inertial odometry system. Unlike other scenarios using point clouds from lidar or structured light sensors, we have few hundreds to few thousand points, insufficient to inform the topology of the scene. Our method …
New algorithm improves model generalization in structured biomedical domains.
problem Improving model generalization in structured biomedical domains.
method Proposes a new regret minimization (RGM) algorithm and its structured extension for better performance in diverse environments.
result Significantly outperforms previous state-of-the-art baselines on molecular property prediction, protein homology, and stability prediction.
This paper describes experiments, on two domains, to investigate the effect of averaging over predictions of multiple decision trees, instead of using a single tree. Other authors have pointed out theoretical and commonsense reasons for preferring the multiple tree approach. Ideally, we would like to consider predictio…
We introduce a novel incremental decision tree learning algorithm, Hoeffding Anytime Tree, that is statistically more efficient than the current state-of-the-art, Hoeffding Tree. We demonstrate that an implementation of Hoeffding Anytime Tree---"Extremely Fast Decision Tree", a minor modification to the MOA implementat…
We introduce block-tree graphs as a framework for deriving efficient algorithms on graphical models. We define block-tree graphs as a tree-structured graph where each node is a cluster of nodes such that the clusters in the graph are disjoint. This differs from junction-trees, where two clusters connected by an edge al…
This paper introduces TNTK to study infinite soft tree ensembles.
problem Understanding the behavior of infinite soft tree ensembles.
method Introduced Tree Neural Tangent Kernel (TNTK) to analyze infinite soft tree ensembles.
result Identified several non-trivial properties of infinite soft tree ensembles.
Paper analyzes soft tree ensembles using NTK, finding only leaf count matters.
problem Understanding impact of various tree architectures in ensemble learning.
method Formulated and analyzed Neural Tangent Kernel (NTK) for soft tree ensembles.
result Only the number of leaves at each depth is relevant for tree architecture in ensemble learning.
New molecular design model outperforms existing methods.
problem Designing valid, unique, and novel molecules.
method Adversarially Regularized Autoencoder (ARAE) combining latent variables from VAE and adversarial training from GAN.
result ARAE outperforms conventional models in validity, uniqueness, and novelty.
Researchers improve tree model recovery from noisy data.
problem Learning tree structured models from corrupted data.
method Linear latent tree models and continuous corruption model.
result Chow-Liu algorithm consistently learns tree from noisy data.
RAMBO optimizes multi-regime problems by discovering and modeling distinct energy basins.
problem Multi-regime problems in molecular conformation and drug discovery.
method Dirichlet Process Mixture of Gaussian Processes with adaptive hyperparameters and concentration parameters.
result Consistent improvements over state-of-the-art on multi-regime objectives.
Optimal survival trees ensemble reduces tree count and improves predictive performance.
problem Improving predictive performance in survival analysis.
method Grows a forest of optimal survival trees by ranking and selecting the best trees based on out-of-bag error.
result Reduces the number of trees in the ensemble while improving predictive performance.
Width trees link link invariants and bridge number.
problem Understanding link invariants through geometric structures.
method Associate width trees to links and use their geometric properties to bound link invariants.
result Width trees uniquely realize certain link invariants under specific conditions.
Paper studies ensemble probabilistic regression trees for smooth approximations.
problem Smooth approximations of regression functions.
method Ensemble versions of probabilistic regression trees.
result Ensemble probabilistic regression trees are consistent and perform well.
The task of translating between programming languages differs from the challenge of translating natural languages in that programming languages are designed with a far more rigid set of structural and grammatical rules. Previous work has used a tree-to-tree encoder/decoder model to take advantage of the inherent tree s…
Recently proposed budding tree is a decision tree algorithm in which every node is part internal node and part leaf. This allows representing every decision tree in a continuous parameter space, and therefore a budding tree can be jointly trained with backpropagation, like a neural network. Even though this continuity …
Event-based learning reduces communication in distributed networks.
problem Distributed learning with diverse data distributions and communication inefficiencies.
method A distributed learning algorithm using ADMM with event-triggered communication.
result The algorithm converges even with distinct local data distributions and achieves accelerated convergence in convex settings.
Characterizes fundamental groups of disjointly tree-graded spaces.
problem Understanding fundamental groups of complex geometric structures.
method Defines and analyzes disjointly tree-graded spaces, characterizing their fundamental groups.
result Fundamental groups of disjointly tree-graded spaces embed into inverse limits of free products of fundamental groups of pieces.
SBT model uses randomized sharding and sub-models to improve Bayesian Additive Regression Trees.
problem Improving efficiency and accuracy of Bayesian Additive Regression Trees.
method Randomized sharding, sub-models, intersection tree structure, optimal design.
result Theoretical optimal weights and worst-case complexity of SBT model.