GCDM generates valid large 3D molecules and optimizes existing molecules.
problem Lack of geometric properties in 3D molecule generation models.
method Introduces Geometry-Complete Diffusion Model (GCDM) using equivariant GNNs.
result Significantly outperforms existing models in 3D molecule generation and optimization.
Rotationally equivariant convolutions improve molecular property prediction.
problem Predicting molecular properties using graph neural networks.
method Ablation study with rotationally equivariant and invariant convolutions on QM9 data set.
result Rotationally equivariant layers decrease test error by an average of 23%.
Graph Neural Networks (GNNs) achieve an impressive performance on structured graphs by recursively updating the representation vector of each node based on its neighbors, during which parameterized transformation matrices should be learned for the node feature updating. However, existing propagation schemes are far fro…
In this work, we extend the SchNet architecture by using weighted skip connections to assemble the final representation. This enables us to study the relative importance of each interaction block for property prediction. We demonstrate on both the QM9 and MD17 dataset that their relative weighting depends strongly on t…
Equivariant graph neural networks predict electron density for molecules, liquids, and solids.
problem Predicting electron density for molecules, liquids, and solids using machine learning.
method Equivariant graph neural networks for predicting electron density at query points.
result The model predicts electron density with accuracy beyond state of the art and significantly faster than traditional DFT methods.
A new graph model HMG and neural network HMGNN improve molecule property predictions.
problem Predicting quantum mechanical properties of molecules with limited consideration of many-body interactions.
method Introducing heterogeneous molecular graphs (HMG) and building HMGNN on neural message passing scheme.
result HMGNN achieves state-of-the-art performance in 9 out of 12 tasks on the QM9 dataset.
Much of the recent work on learning molecular representations has been based on Graph Convolution Networks (GCN). These models rely on local aggregation operations and can therefore miss higher-order graph properties. To remedy this, we propose Path-Augmented Graph Transformer Networks (PAGTN) that are explicitly built…
Transformer adapts to graphs with adaptive attention and auto-regressive decoding.
problem Transformers struggle with graph data due to non-sequential nature.
method Proposes GRAT, a Transformer variant with adaptive attention and auto-regressive decoding.
result GRAT achieves state-of-the-art performance on molecule property predictions and generation tasks.
Neural message passing on molecular graphs is one of the most promising methods for predicting formation energy and other properties of molecules and materials. In this work we extend the neural message passing model with an edge update network which allows the information exchanged between atoms to depend on the hidde…
Paper improves molecular property prediction using denoising autoencoders.
problem Limited data for molecular property prediction from 3D structures.
method Pre-training via denoising for learning molecular force fields.
result Achieves new state-of-the-art performance on QM9 dataset.
Study evaluates uncertainty quantification for atomistic neural networks, revealing complex relationships between error and uncertainty.
problem Uncertainty quantification for predictions of atomistic neural networks.
method Modified PhysNet NN architecture, evaluated with various metrics, analyzed QM9 and tautomerization reaction databases.
result Error and uncertainty are not linearly related; redundancy and noise complicate predictions, especially for small changes.
SE(3)-Transformers maintain equivariance for 3D data under rotations and translations.
problem Ensuring stable and predictable performance in 3D data under transformations.
method Introducing a self-attention module that is equivariant under continuous 3D roto-translations.
result The SE(3)-Transformer outperforms non-equivariant and non-attention models on real-world datasets.
Discrete structure rules for validating molecular structures are usually limited to fulfillment of the octet rule or similar simple deterministic heuristics. We propose a model, inspired by language modeling from natural language processing, with the ability to learn from a collection of undirected molecular graphs, en…
A new unpooling layer enhances graph generation in molecular models.
problem Efficient graph generation for complex models like molecules.
method Trainable unpooling layer that enlarges and restructures graphs.
result The unpooling layer improves graph generation in molecular models.
Constant-curvature Riemannian manifolds (CCMs) have been shown to be ideal embedding spaces in many application domains, as their non-Euclidean geometry can naturally account for some relevant properties of data, like hierarchy and circularity. In this work, we introduce the CCM adversarial autoencoder (CCM-AAE), a pro…
Sparse molecular representations improve interpretability in graph neural networks.
problem Difficulty in understanding which molecular graph aspects drive deep learning predictions.
method Constrain weights in a graph convolutional neural network using the Gini index to maximize representation inequality.
result The Gini-constrained approach does not degrade evaluation metrics and allows for interpretable representation combination.
E-NFs generate molecules and their positions while preserving Euclidean symmetries.
problem Generating molecules with their positions while preserving Euclidean symmetries.
method Integrating E(n) graph neural networks into a differential equation to create an invertible equivariant function.
result E-NFs significantly outperform baselines and existing methods in log-likelihood for particle systems and molecules.
A novel method computes Wigner kernels for atomic environments, achieving state-of-the-art accuracy.
problem Efficiently describing local atomic environments in materials science.
method Computes fully equivariant and body-ordered kernels iteratively, independent of basis.
result Achieves state-of-the-art accuracy on the QM9 benchmark dataset.
New method calibrates uncertainty in molecular property predictions.
problem Uncalibrated uncertainty estimates in molecular property predictions.
method Message Passing Neural Networks with calibrated probabilistic predictive distribution.
result Accurate molecular formation energy predictions with well-calibrated uncertainty.
A new method predicts electron density accurately from atom-centered models.
problem Predicting electron density accurately from atom-centered models.
method Gradient-based approach to minimize loss function in an optimized sparse feature space.
result Extremely accurate predictions of electron density and total energies.
A new method for generating sets and graphs without requiring exchangeability.
problem Generating exchangeable distributions for sets and graphs is challenging.
method Top-n creation, a differentiable generation mechanism that selects relevant points from a latent vector.
result Top-n method outperforms i.i.d. generation in various tasks.
A Graph Neural Network model for generating molecular graphs.
problem Designing new drug molecules efficiently and cost-effectively.
method Sequential molecular graph generator based on Graph Neural Networks.
result The model can generate molecular graphs without overfitting and outperforms existing methods.
Advances in deep neural network (DNN) based molecular property prediction have recently led to the development of models of remarkable accuracy and generalization ability, with graph convolution neural networks (GCNNs) reporting state-of-the-art performance for this task. However, some challenges remain and one of the …
Novel flows generate molecules without post-processing.
problem Generating new molecules efficiently and without post-processing issues.
method Continuous normalizing E(3)-equivariant flows based on node ODEs coupled as a graph PDE.
result Generated samples achieve state-of-the-art performance on QM9 and ZINC250K benchmarks.
Introduces Spectral Graph Network combining spatial and spectral message passing.
problem Relational reasoning in graph structured data.
method Applies message passing to both spatial and spectral domains of a graph.
result Promotes efficient training with fewer iterations and robustness to edge dropout.
VecMol generates 3D molecules as continuous vector fields, overcoming modality and geometry constraints.
problem Challenges in generating 3D molecules, especially in drug discovery and materials science.
method VecMol reimagines molecular representation by modeling 3D molecules as continuous vector fields over Euclidean space, parameterized by a neural field and generated using a latent diffusion model.
result Vector-field-based representations show promise for 3D molecular generation, validated on benchmarks.
Deep generative models for graph-structured data offer a new angle on the problem of chemical synthesis: by optimizing differentiable models that directly generate molecular graphs, it is possible to side-step expensive search procedures in the discrete and vast space of chemical structures. We introduce MolGAN, an imp…
A new autoregressive model learns the order of graph generation tasks.
problem Generating graphs in a meaningful order when the canonical order is not obvious.
method Introduces a variant of autoregressive models that dynamically decides the autoregressive order based on data.
result Achieves state-of-the-art results on molecular graph generation benchmarks.
HLTF generates chemically valid 3D molecules with improved topology control.
problem Generating chemically valid 3D molecules is challenging due to bond topology errors.
method HLTF uses a latent multi-scale plan for global context and a constraint-aware sampler to suppress topology-driven failures.
result HLTF achieves high validity and uniqueness on QM9 and GEOM-DRUGS datasets.
Improves generative models by optimizing rewards and sample editing.
problem Efficiently generating high-reward samples with structural constraints.
method Introduces MDM-VGB, a discrete diffusion sampler that augments unmasking generation with reward-guided remasking.
result MDM-VGB achieves quadratic complexity and robustness to noise, outperforming heuristics like best-of-N. We introduce weighted atom-centered symmetry functions (wACSFs) as descriptors of a chemical system's geometry for use in the prediction of chemical properties such as enthalpies or potential energies via machine learning. The wACSFs are based on conventional atom-centered symmetry functions (ACSFs) but overcome the un…
DimeNet uses directional message passing to improve molecular predictions.
problem Lack of directional information in graph neural networks for molecules.
method Directional message passing, rotationally equivariant embeddings, spherical functions.
result DimeNet outperforms previous GNNs by 76% on MD17 and 31% on QM9.
Dependent MMD coresets help compare multiple related datasets.
problem Comparing multiple related datasets for insights into model generalization.
method Dependent MMD coresets for collections of datasets.
result Dependent MMD coresets facilitate comparison and understanding of multiple related datasets.
SCARY dataset generates complex causal scenarios for causality research.
problem Lack of complexity in existing causal datasets.
method Synthetic dataset with 40 scenarios, three seeds, and two data generation mechanisms.
result Provides a valuable resource for realistic causal discovery.
MusPy is a toolkit for symbolic music generation, providing tools for dataset management and analysis.
problem Facilitating the creation and analysis of symbolic music datasets.
method Development of an open-source Python library (MusPy) with features for dataset management, data I/O, preprocessing, and model evaluation. Demonstrated through statistical analysis and cross-dataset generalizability experiments.
result MusPy's dataset analysis reveals varying degrees of cross-genre representation across different music datasets.
In this paper, we propose a data collaboration analysis method for distributed datasets. The proposed method is a centralized machine learning while training datasets and models remain distributed over some institutions. Recently, data became large and distributed with decreasing costs of data collection. If we can cen…
StyleDiff compares unlabeled datasets using disentangled image spaces.
problem Mismatches between development and real-world datasets lead to inaccurate predictions.
method Uses disentangled image spaces and focuses on attributes to compare datasets.
result Accurately detects and presents differences between datasets.
In this paper, we propose a novel method for generating a synthetic dataset obeying Gaussian distribution. Compared to the commonly used benchmark datasets with unknown distribution, the synthetic dataset has an explicit distribution, i.e., Gaussian distribution. Meanwhile, it has the same characteristics as the benchm…
New framework assesses graph-learning datasets for better evaluation.
problem Insufficient evaluation of graph-learning datasets and methods.
method Introduces Rings framework for dataset ablations and proposes performance separability and mode complementarity measures.
result Demonstrates utility of Rings framework for graph-learning dataset evaluation.
This paper introduces a new dataset called "ToyADMOS" designed for anomaly detection in machine operating sounds (ADMOS). To the best our knowledge, no large-scale datasets are available for ADMOS, although large-scale datasets have contributed to recent advancements in acoustic signal processing. This is because anoma…
In this paper, we disseminate a new handwritten digits-dataset, termed Kannada-MNIST, for the Kannada script, that can potentially serve as a direct drop-in replacement for the original MNIST dataset. In addition to this dataset, we disseminate an additional real world handwritten dataset (with 10k images), which we …
In this paper, we introduce the Fairness GAN, an approach for generating a dataset that is plausibly similar to a given multimedia dataset, but is more fair with respect to protected attributes in allocative decision making. We propose a novel auxiliary classifier GAN that strives for demographic parity or equality of …
MTL method uses unlabeled data with pseudo labels to improve classification with disjoint datasets.
problem Improving classification performance with disjoint labeled datasets using unlabeled data.
method Proposes MTL-SA method to select and augment unlabeled data with confident pseudo labels and close distribution to labeled data.
result Extensive experiments show the effectiveness of MTL-SA method in improving classification performance.
The study examines dataset usage patterns in machine learning research.
problem Lack of attention to dataset dynamics in machine learning research.
method Analysis of dataset usage patterns across machine learning subcommunities and time periods (2015-2020).
result Increasing concentration on fewer and fewer datasets, significant adoption from other tasks, and concentration across the field on datasets introduced by elite institutions.
Method embeds numeric tabular datasets into a shared vector space for similarity and retrieval.
problem Lack of meaningful representation for numeric tabular datasets in large language models.
method Structured exploratory data analysis descriptors, sentence transformer embedding, CCA for cross-dataset alignment.
result Total P@1 score of 0.9 across 15 datasets, robust nearest-neighbor retrieval and cluster structure.
This paper presents the recently published Cerema AWP (Adverse Weather Pedestrian) dataset for various machine learning tasks and its exports in machine learning friendly format. We explain why this dataset can be interesting (mainly because it is a greatly controlled and fully annotated image dataset) and present base…
Two large medical dialogue datasets for improving healthcare.
problem Improving healthcare through better dialogue systems.
method Building two large-scale medical dialogue datasets: MedDialog-EN and MedDialog-CN.
result The datasets are the largest medical dialogue datasets to date.
Dataset distillation is a method for reducing dataset sizes by learning a small number of synthetic samples containing all the information of a large dataset. This has several benefits like speeding up model training, reducing energy consumption, and reducing required storage space. Currently, each synthetic sample is …