Computational chemistry

Benchmarks archive 2025-07-28

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Most implemented papers archive 2025-07-28

30 shown of 48 papers with code (122 tagged with this task in all), ordered by repositories listed in the archive, not by stars (the archive holds no stars, so PwC's “Social” and “Latest” sorts cannot be reproduced). Papers without a page here are shown as plain text.

• Learning Gradient Fields for Molecular Conformation Generation
  9 May 2021 6 repositories listed Syntology ran 0 of 3 samples · 3 unverified · 3 pointer-only (licence)
  We study a fundamental problem in computational chemistry known as molecular conformation generation, trying to predict stable 3D structures from 2D molecular graphs.
• MACE: Higher Order Equivariant Message Passing Neural Networks for Fast and Accurate Force Fields
  15 Jun 2022 4 repositories listed Syntology ran 0 of 5 samples · 5 unverified
  In particular, we show that using four-body messages reduces the required number of message passing iterations to just two, resulting in a fast and highly parallelizable model, reaching or exceeding state-of-the-art…
• An Exploration of Conditioning Methods in Graph Neural Networks
  3 May 2023 3 repositories listed
  The flexibility and effectiveness of message passing based graph neural networks (GNNs) induced considerable advances in deep learning on graph-structured data.
• ChemCrow: Augmenting large-language models with chemistry tools
  11 Apr 2023 3 repositories listed Syntology ran 1 of 3 samples · 2 unverified
  Our agent autonomously planned and executed the syntheses of an insect repellent, three organocatalysts, and guided the discovery of a novel chromophore.
• End-to-End Differentiable Molecular Mechanics Force Field Construction
  2 Oct 2020 3 repositories listed
  Trained with arbitrary loss functions, it can construct entirely new force fields self-consistently applicable to both biopolymers and small molecules directly from quantum chemical calculations, with superior fidelity…
• Mitigating Exposure Bias in Score-Based Generation of Molecular Conformations
  21 Sep 2024 2 repositories listed Syntology ran 0 of 1 samples · 1 unverified
  In this work, we first propose a method for measuring exposure bias in SGMs used for molecular conformation generation, which confirms the significant existence of exposure bias in these models and measures its value.
• Spherical Channels for Modeling Atomic Interactions
  29 Jun 2022 2 repositories listed
  We propose the Spherical Channel Network (SCN) to model atomic energies and forces.
• Gold-standard solutions to the Schrödinger equation using deep learning: How much physics do we need?
  19 May 2022 2 repositories listed Syntology ran 2 of 2 samples · 0 unverified · 2 pointer-only (licence)
  Finding accurate solutions to the Schr\"odinger equation is the key unsolved challenge of computational chemistry.
• TorsionNet: A Reinforcement Learning Approach to Sequential Conformer Search
  12 Jun 2020 2 repositories listed Syntology ran 2 of 2 samples · 0 unverified
  Molecular geometry prediction of flexible molecules, or conformer search, is a long-standing challenge in computational chemistry.
• Chemception: A Deep Neural Network with Minimal Chemistry Knowledge Matches the Performance of Expert-developed QSAR/QSPR Models
  20 Jun 2017 2 repositories listed
  We then show how Chemception can serve as a general-purpose neural network architecture for predicting toxicity, activity, and solvation properties when trained on a modest database of 600 to 40, 000 compounds.
• Unlocking Chemical Insights: Superior Molecular Representations from Intermediate Encoder Layers
  6 Jun 2025 1 repository listed
  Specifically, using fixed embeddings from the optimal intermediate layers improved downstream performance by an average of 5.
• Integrating convolutional layers and biformer network with forward-forward and backpropagation training
  28 Feb 2025 1 repository listed
  Accurate molecular property prediction is crucial for drug discovery and computational chemistry, facilitating the identification of promising compounds and accelerating therapeutic development.
• Efficient and Scalable Density Functional Theory Hamiltonian Prediction through Adaptive Sparsity
  3 Feb 2025 1 repository listed Syntology ran 3 of 20 samples · 17 unverified
  Beyond Hamiltonian prediction, the proposed sparsification techniques also hold significant potential for improving the efficiency and scalability of other SE(3) equivariant networks, further broadening their…
• Towards Fast, Specialized Machine Learning Force Fields: Distilling Foundation Models via Energy Hessians
  15 Jan 2025 1 repository listed
  In this work, we introduce a method for transferring general-purpose representations from MLFF foundation models to smaller, faster MLFFs specialized to specific regions of chemical space.
• The dark side of the forces: assessing non-conservative force models for atomistic machine learning
  16 Dec 2024 1 repository listed Syntology ran 2 of 16 samples · 14 unverified · 12 pointer-only (licence)
  The use of machine learning to estimate the energy of a group of atoms, and the forces that drive them to more stable configurations, has revolutionized the fields of computational chemistry and materials discovery.
• Embrace rejection: Kernel matrix approximation by accelerated randomly pivoted Cholesky
  4 Oct 2024 1 repository listed Syntology ran 6 of 7 samples · 1 unverified
  Randomly pivoted Cholesky (RPCholesky) is an algorithm for constructing a low-rank approximation of a positive-semidefinite matrix using a small number of columns.
• Instruction-Based Molecular Graph Generation with Unified Text-Graph Diffusion Model
  19 Aug 2024 1 repository listed
  Recent advancements in computational chemistry have increasingly focused on synthesizing molecules based on textual instructions.
• Physics-Informed Weakly Supervised Learning for Interatomic Potentials
  23 Jul 2024 1 repository listed
  Our approach improves the accuracy of MLIPs applied to training tasks with sparse training data sets and reduces the need for pre-training computationally demanding models with large data sets.
• DeepMol: An Automated Machine and Deep Learning Framework for Computational Chemistr
  1 Jun 2024 1 repository listed
  The domain of computational chemistry has experienced a significant evolution due to the introduction of Machine Learning (ML) technologies.
• SE3Set: Harnessing equivariant hypergraph neural networks for molecular representation learning
  26 May 2024 1 repository listed Syntology ran 1 of 2 samples · 1 unverified · 2 pointer-only (licence)
  In this paper, we develop SE3Set, an SE(3) equivariant hypergraph neural network architecture tailored for advanced molecular representation learning.
• Molecular relaxation by reverse diffusion with time step prediction
  16 Apr 2024 1 repository listed Syntology ran 8 of 8 samples · 0 unverified
  As a remedy, we propose MoreRed, molecular relaxation by reverse diffusion, a conceptually novel and purely statistical approach where non-equilibrium structures are treated as noisy instances of their corresponding…
• ChemReasoner: Heuristic Search over a Large Language Model's Knowledge Space using Quantum-Chemical Feedback
  15 Feb 2024 1 repository listed Syntology ran 5 of 7 samples · 2 unverified · 7 pointer-only (licence)
  The discovery of new catalysts is essential for the design of new and more efficient chemical processes in order to transition to a sustainable future.
• T-Rex: Text-assisted Retrosynthesis Prediction
  26 Jan 2024 1 repository listed Syntology ran 1 of 2 samples · 1 unverified · 2 pointer-only (licence)
  As a fundamental task in computational chemistry, retrosynthesis prediction aims to identify a set of reactants to synthesize a target molecule.
• MLatom 3: Platform for machine learning-enhanced computational chemistry simulations and workflows
  31 Oct 2023 1 repository listed
  MLatom 3 is a program package designed to leverage the power of ML to enhance typical computational chemistry simulations and to create complex workflows.
• Monte Carlo Thought Search: Large Language Model Querying for Complex Scientific Reasoning in Catalyst Design
  22 Oct 2023 1 repository listed
  Discovering novel catalysts requires complex reasoning involving multiple chemical properties and resultant trade-offs, leading to a combinatorial growth in the search space.
• MolOpt: Autonomous Molecular Geometry Optimization using Multi-Agent Reinforcement Learning
  24 Aug 2023 1 repository listed
  We cast MGO as a MARL problem, where each agent corresponds to a single atom in the molecule.
• Beyond MD17: the reactive xxMD dataset
  22 Aug 2023 1 repository listed
  We show that the xxMD dataset involves diverse geometries which represent chemical reactions.
• Uncertainty Estimation for Molecules: Desiderata and Methods
  20 Jun 2023 1 repository listed
  Graph Neural Networks (GNNs) are promising surrogates for quantum mechanical calculations as they establish unprecedented low errors on collections of molecular dynamics (MD) trajectories.
• Symmetry-Informed Geometric Representation for Molecules, Proteins, and Crystalline Materials
  15 Jun 2023 1 repository listed Syntology ran 2 of 7 samples · 5 unverified
  Artificial intelligence for scientific discovery has recently generated significant interest within the machine learning and scientific communities, particularly in the domains of chemistry, biology, and material…
• Modeling Molecular Structures with Intrinsic Diffusion Models
  23 Feb 2023 1 repository listed
  Since its foundations, more than one hundred years ago, the field of structural biology has strived to understand and analyze the properties of molecules and their interactions by studying the structure that they take…

Syntology lines on 14 of the papers shown; no Syntology record for the others (a paper without an arXiv id cannot be joined to the graph, and absence from the graph layer is not a recorded non-run). “Ran” means the sample executed on a synthesized fixture, not that the paper's result was reproduced. Read from the graph 2026-09-24.