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…
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.
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…
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.
As machine learning black boxes are increasingly being deployed in domains such as healthcare and criminal justice, there is growing emphasis on building tools and techniques for explaining these black boxes in an interpretable manner. Such explanations are being leveraged by domain experts to diagnose systematic error…
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.
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.
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. 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 …
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…
Deep generative models are attracting great attention as a new promising approach for molecular design. All models reported so far are based on either variational autoencoder (VAE) or generative adversarial network (GAN). Here we propose a new type model based on an adversarially regularized autoencoder (ARAE). It basi…
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.
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.
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.
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.
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.
FedElasticNet reduces communication costs and handles client drift in FL.
problem Expensive communication costs and client drift issues in federated learning.
method Leverages elastic net regularizers to sparsify local updates and limit client drift.
result FedElasticNet effectively resolves communication cost and client drift problems.
LLM-based trading systems vary in execution realism and reproducibility.
problem LLM-based trading systems vary in execution realism and reproducibility.
method Reproducibility audit of 30 trade-relevant primary studies.
result LLM-based trading systems vary in execution realism and reproducibility.
Molecule optimization is about generating molecule Y with more desirable properties based on an input molecule X. The state-of-the-art approaches partition the molecules into a large set of substructures S and grow the new molecule structure by iteratively predicting which substructure from S to add. However, s…
SLEDGE algorithm reduces gradient computation errors in optimization.
problem Accumulated errors in gradient estimation methods for large-scale optimization.
method Single-loop method for finite-sum nonconvex optimization without periodic gradient refresh.
result Achieves nearly optimal gradient complexity and second-order optimality.
New federated learning methods improve model performance on non-IID data.
problem Improving model performance on non-IID decentralized data.
method Proposed Federated AGMs using adaptive gradient methods with first-order and second-order momenta.
result The proposed Federated AGMs converge to a first-order stationary point under non-IID and unbalanced data settings for nonconvex optimization.
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…
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.
Bayesian nonparametric models for data with heterogeneous particles.
problem Deconvolving data with heterogeneous particles, like voter tallies in elections.
method Nonparametric deconvolution models (NDMs) using two tiers of Dirichlet processes.
result NDMs can recover how factor distributions vary locally for each observation.
ASCEND discovers causal relationships in multi-omics data by leveraging known hierarchical structure.
problem Causal inference in high-dimensional multi-omics data, especially when ignoring the hierarchical structure.
method Two-tiered divide-and-conquer strategy with ancestral conditioning sets.
result Achieves polynomial-time complexity and accurately recovers ancestral relationships.
Develops probabilistic models for gene regulatory network inference.
problem Challenges in reconstructing gene regulatory networks from genome-wide data.
method Two complementary frameworks: PMF-GRN and GLM-Prior.
result Probabilistic inference refines regulatory estimates with quantified uncertainty.
Deep learning predicts tissue properties from cell-laden hydrogels.
problem Predicting tissue properties from cell-laden hydrogels.
method Developed a process for generating mould designs, created a training set of 6500 cases, trained a deep learning model (pix2pix).
result Deep learning makes excellent predictions and is significantly faster than biophysical methods.
Modof-pipe optimizes molecules by modifying a single site, outperforming state-of-the-art methods.
problem Improving drug candidates' properties through chemical modification.
method Deep generative model Modof over molecular graphs for molecule optimization.
result Modof-pipe achieves significant improvements in octanol-water partition coefficient and molecule similarity constraints.
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.
PTOPOFL uses topological descriptors to protect privacy in federated learning.
problem Privacy and data reconstruction attacks in federated learning.
method PTOPOFL replaces gradient communication with persistent homology feature vectors for privacy and topology-guided aggregation.
result PTOPOFL achieves higher AUC and reduces reconstruction risk compared to gradient sharing.
AI agents on social networks rarely engage in extended conversations.
problem Understanding the persistence of interactions in AI-agent social networks.
method Analysis of Moltbook, a social network of AI agents, using interaction half-life and spectral tests.
result Most comments on Moltbook receive a direct reply within seconds, indicating a ``fast response or silence'' regime.
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.
Framework improves clinical timeline reconstruction from text and tables.
problem Temporal precision and event timing in clinical narratives and EHRs.
method Retrieval-augmented multimodal alignment framework.
result Consistently improves absolute timestamp accuracy and temporal concordance.
EDINET-Bench evaluates LLMs on complex financial tasks using Japanese financial statements.
problem Challenges in evaluating LLMs on financial tasks due to specialized expertise and scarce benchmarks.
method Developed EDINET-Bench, an open-source Japanese financial benchmark for LLMs on tasks like fraud detection and earnings forecasting.
result State-of-the-art LLMs perform only marginally better than logistic regression in financial tasks, highlighting the need for more realistic benchmarks.
Polynomial chaos surrogates quantify epistemic uncertainty in AI-driven scientific models.
problem Uncertainty in reward estimates hinders interpretability in sequential generative models.
method Fit polynomial chaos expansions to trained models to propagate epistemic uncertainty and quantify sensitivity.
result Interpretable decomposition of reward components driving generative decisions.
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…