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Open problems in Machine learned interatomic

Reliable geometric reasoning from protein structures1 paper raises it · 2 address it
Frontier models excel at metadata lookup but struggle with numeric geometry tasks, which are critical for structural biology.
Effective integration of biological foundation model inputs1 paper raises it · 1 addresses it
Biological reasoning models often ignore foundation model inputs, relying instead on text, which limits their accuracy and interpretability.
- When Do Biological Reasoning Models Use Their Biological Inputs?raises
- Does Learning Protein Folding Generalize to Broader Reasoning?addresses
Scalable and robust protein sequence and structure generation1 paper raises it · 2 address it
Autoregressive models for protein generation are weak, and current representations lack contextual semantics or efficient discrete encodings.
- Learning Latent Protein Languages for Autoregressive Generationraises · addresses
- recAMPLIFY: Large-Scale Pretraining of Recursive Protein Language Modelsaddresses
Durable and selective pretraining data filtering1 paper raises it · 1 addresses it
Filtering pretraining data can degrade performance on specific domains, but fine-tuning can easily undo these effects, limiting its long-term utility.
- The Effectiveness and Durability of Pretraining Data Filtering in Protein Language Modelsraises · addresses
Stable evaluation metrics for gene perturbation models1 paper raises it · 0 address it
Heterogeneous metrics and DE gene subsets lead to unstable rankings, undermining fair comparisons across methods.
- A Pitfall in the Evaluation of Gene Perturbation Modelsraises

Named by an AI from these papers' abstracts.

Open problems

Recently funded

Topics in this field

molecular optimization · molecular design · molecular generation100 papers19 this week
protein language models · protein language · protein structure107 papers16 this week
machine learned interatomic · crystal structure prediction · learned interatomic potentials101 papers10 this week

Topics in this field

Active contributors · 90 days

Active contributors

Activity · 12 weeks

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arXiv physics.chem-phOct 8
MolP2SBench: Do LLMs Really Reason from Molecular Properties to Structure?
Yuhang Xie, Zhiyi Shi, Zeyi Zhang, Zhisheng Qi, Yushun Dong +2
Large language models (LLMs) are increasingly used in molecular discovery and structure elucidation, where decisions depend on physical observations. Existing evaluations primarily focus on end-to-end molecular reconstruction, where correct predictions do not necessarily indicate reliance on the supplied properties. We introduce MolP2SBench, a benchmark for molecular property-to-structure (P2S) reasoning in LLMs. Each task presents a masked molecular scaffold with given properties and asks the model to select the missing structure from plausible candidates. We shuffle or replace properties to test reliance on correct property-structure pairing and responsiveness to counterfactual property changes. A channel-wise leaderboard uses Property-Grounded Recovery (PGR), giving equal weight to source and counterfactual recovery. Evaluating seven models, we find that LLMs can use physical properties for structure prediction, but performance varies substantially across property types. Higher accuracy with a property does not necessarily imply greater responsiveness to it: a model may benefit more from $^1$H NMR than from $^{13}$C NMR, yet be less likely to change its prediction when the…
PDF arXiv
arXiv cs.LGOct 7
ASPIRE: Saddle-Point Discovery through Set Prediction and Physical Refinement
Yucheng Zhao, Quanyou Zhang, Shaoxiang Qin, Haixuan Xu, Xiongye Xiao
Predicting thermally activated diffusion and defect evolution with event-driven models requires identifying atomic rearrangement mechanisms and their activation barriers. Discovering the associated saddle points is a major computational bottleneck: multiple rearrangements may originate from one metastable state, while costly local searches can fail or repeatedly converge to the same saddle. To address this challenge, we introduce ASPIRE (Atomistic Saddle-Point Inference with Refinement for Events), a framework that predicts a set of saddle candidates from a single initial atomic environment and refines them through Dimer searches on the original interatomic potential. The framework's equivariant set predictor, Ev-Quiformer, integrates (i) geometry-conditioned scalar-vector event slots for generating multiple saddle-point proposals and (ii) a decoder that maps each slot to a full atomic displacement field by combining atom, slot, and anchor-relative vectors with invariant coefficients. We also contribute two datasets: (i) BCCFE4VACAV-4000, comprising 4,000 four-vacancy body-centered cubic iron configurations and 65,450 reference events grouped by initial state for set supervision…
PDF arXiv
arXiv physics.chem-phOct 7
Looking Under the Streetlight: Evaluation in Generative Molecular Dynamics
Simon Olsson, Frank Noé, Grant M. Rotskoff, Kresten Lindorff-Larsen
This position paper argues that the generative molecular dynamics (GenMD) community is not properly evaluating its progress: current evaluations let a model match what is reported while being arbitrarily wrong on what was claimed, which risks over-claiming advantage over classical baselines. This reflects a structural misalignment between common evaluation practices and the scientific tasks the field sets for itself. The reason is that the ground truth---exhaustive molecular dynamics on the systems of interest---is computationally costly, and this cost is what motivates the field. With ground truth inaccessible, evaluation drifts toward convenient proxies, and the resulting norms entrench easily. We identify misaligned evaluation patterns that persist as a community-level equilibrium, and propose concrete observables, reporting standards, and benchmark designs, both computational and experimental, that better reflect what GenMD aspires to deliver. Our aim is to give the field shared language and tools for evaluation that match its scientific ambitions before today's conventions calcify into norms.
PDF arXiv
arXiv cs.LGOct 7
NEMORA: Neural Equivariant Multipole Operators for Long-Range Atomistic Learning
Jay L. Kaplan, Samuel Varner, Rebecca Willett, Juan J. de Pablo
Equivariant graph neural networks have emerged as foundational architectures for machine-learned interatomic potentials, approaching quantum-chemical accuracy at a fraction of the computational cost. These models describe local atomic environments accurately, but finite spatial cutoffs truncate long-range information flow, and stacking message-passing layers can lead to over-smoothing and over-squashing. Existing long-range extensions either prescribe a fixed analytical propagation kernel, restrict long-range communication to scalars or degree-preserving channels, are only approximately equivariant, or incur super-linear computational cost. Combining learnable long-range equivariant transport with multiscale many-body expressivity and efficient scaling for larger systems remains a central challenge. We introduce Neural Equivariant Multipole Operators (NEMORA), a neural equivariant extension of the Fast Multipole Method (FMM) for learning long-range tensorial representations. NEMORA generalizes the FMM's analytical multipole expansion and translation operators to learned equivariant counterparts on an adaptive spatial hierarchy. Its operators couple angular degrees and form…
PDF arXiv
arXiv physics.chem-phOct 7
LLM-Assisted Generation of Transparent, Open-Source Multiphysics Models of Electrochemical Devices
Sebastian Castro, Maya F. Schuchert, Spencer A. McCluskey, Eric W. Lees, Justin C. Bui
Multiphysics continuum models are powerful tools for studying electrochemical devices, enabling in silico reactor design and resolution of local pH, potential, and concentration fields that govern device performance but are difficult to measure experimentally. However, constructing such models requires substantial numerical expertise or reliance on proprietary software. Here, we show that frontier large language model agents can remove this implementation burden while keeping the underlying physics under researcher control. Using one-dimensional electrochemical CO2 reduction to CO in a porous gas diffusion electrode as a test case, we develop a machine-readable, human-specified modeling harness containing governing equations, parameters, numerical methods, logical build stages, and human-verifiable checkpoints. From this specification, the agent reproducibly constructs complete multiphysics models in open-source Julia. Independently built models, including fully autonomous agent-built models, agree with an equivalent COMSOL implementation to within 0.7% of the peak CO partial current density, and with one another to within 0.04%. Systematically planted errors demonstrate the…
PDF arXiv
arXiv cs.LGOct 7
PoreML: A Data-Driven Framework for Learning Multiphase Flow in Porous Media
Chunyang Wang, Mingrui Zhang, Yuyan Zhang, Linqi Zhu, Xin Ju +3
Multiphase flow in porous microstructures is central to CO$_2$ storage, fuel-cell operation, and flip-chip packaging. Predicting these flows remains challenging because wettability and complex pore geometry govern the nonlinear evolution of fluid interfaces. Machine learning holds substantial promise for advancing the field, but progress is constrained by scarce time-resolved 3D datasets and a lack of a unified workflow for training and evaluating models. To fill this critical gap, we introduce PoreML, an open-source framework unifying data generation, model training, and evaluation grounded in pore-scale physics. The framework comprises three core components. (a) A modern GPU-native lattice Boltzmann solver, validated against analytical solutions and published experiments, enables reproducible data generation. (b) A 3.3 TB dataset contains 560 simulation runs and 158,546 stored time steps across four application-driven scenarios. These trajectories span synthetic structures and geometries derived from micro-CT scans of real materials, covering diverse wetting conditions and viscosity ratios. (c) A unified learning framework evaluates one-step prediction and autoregressive…
PDF arXiv

Papers

Topics in this field

molecular optimization · molecular design · molecular generation100 papers19 this week
protein language models · protein language · protein structure107 papers16 this week
machine learned interatomic · crystal structure prediction · learned interatomic potentials101 papers10 this week

Active contributors · 90 days

Activity · 12 weeks

Coming with more sources: repos

Open problems in Machine learned interatomic

Reliable geometric reasoning from protein structures1 paper raises it · 2 address it
Frontier models excel at metadata lookup but struggle with numeric geometry tasks, which are critical for structural biology.
Effective integration of biological foundation model inputs1 paper raises it · 1 addresses it
Biological reasoning models often ignore foundation model inputs, relying instead on text, which limits their accuracy and interpretability.
- When Do Biological Reasoning Models Use Their Biological Inputs?raises
- Does Learning Protein Folding Generalize to Broader Reasoning?addresses
Scalable and robust protein sequence and structure generation1 paper raises it · 2 address it
Autoregressive models for protein generation are weak, and current representations lack contextual semantics or efficient discrete encodings.
- Learning Latent Protein Languages for Autoregressive Generationraises · addresses
- recAMPLIFY: Large-Scale Pretraining of Recursive Protein Language Modelsaddresses
Durable and selective pretraining data filtering1 paper raises it · 1 addresses it
Filtering pretraining data can degrade performance on specific domains, but fine-tuning can easily undo these effects, limiting its long-term utility.
- The Effectiveness and Durability of Pretraining Data Filtering in Protein Language Modelsraises · addresses
Stable evaluation metrics for gene perturbation models1 paper raises it · 0 address it
Heterogeneous metrics and DE gene subsets lead to unstable rankings, undermining fair comparisons across methods.
- A Pitfall in the Evaluation of Gene Perturbation Modelsraises

Named by an AI from these papers' abstracts.

Recent papers

All in Research →

arXiv physics.chem-phOct 8
MolP2SBench: Do LLMs Really Reason from Molecular Properties to Structure?
Yuhang Xie, Zhiyi Shi, Zeyi Zhang, Zhisheng Qi, Yushun Dong +2
Large language models (LLMs) are increasingly used in molecular discovery and structure elucidation, where decisions depend on physical observations. Existing evaluations primarily focus on end-to-end molecular reconstruction, where correct predictions do not necessarily indicate reliance on the supplied properties. We introduce MolP2SBench, a benchmark for molecular property-to-structure (P2S) reasoning in LLMs. Each task presents a masked molecular scaffold with given properties and asks the model to select the missing structure from plausible candidates. We shuffle or replace properties to test reliance on correct property-structure pairing and responsiveness to counterfactual property changes. A channel-wise leaderboard uses Property-Grounded Recovery (PGR), giving equal weight to source and counterfactual recovery. Evaluating seven models, we find that LLMs can use physical properties for structure prediction, but performance varies substantially across property types. Higher accuracy with a property does not necessarily imply greater responsiveness to it: a model may benefit more from $^1$H NMR than from $^{13}$C NMR, yet be less likely to change its prediction when the…
PDF arXiv
arXiv cs.LGOct 7
ASPIRE: Saddle-Point Discovery through Set Prediction and Physical Refinement
Yucheng Zhao, Quanyou Zhang, Shaoxiang Qin, Haixuan Xu, Xiongye Xiao
Predicting thermally activated diffusion and defect evolution with event-driven models requires identifying atomic rearrangement mechanisms and their activation barriers. Discovering the associated saddle points is a major computational bottleneck: multiple rearrangements may originate from one metastable state, while costly local searches can fail or repeatedly converge to the same saddle. To address this challenge, we introduce ASPIRE (Atomistic Saddle-Point Inference with Refinement for Events), a framework that predicts a set of saddle candidates from a single initial atomic environment and refines them through Dimer searches on the original interatomic potential. The framework's equivariant set predictor, Ev-Quiformer, integrates (i) geometry-conditioned scalar-vector event slots for generating multiple saddle-point proposals and (ii) a decoder that maps each slot to a full atomic displacement field by combining atom, slot, and anchor-relative vectors with invariant coefficients. We also contribute two datasets: (i) BCCFE4VACAV-4000, comprising 4,000 four-vacancy body-centered cubic iron configurations and 65,450 reference events grouped by initial state for set supervision…
PDF arXiv
arXiv physics.chem-phOct 7
Looking Under the Streetlight: Evaluation in Generative Molecular Dynamics
Simon Olsson, Frank Noé, Grant M. Rotskoff, Kresten Lindorff-Larsen
This position paper argues that the generative molecular dynamics (GenMD) community is not properly evaluating its progress: current evaluations let a model match what is reported while being arbitrarily wrong on what was claimed, which risks over-claiming advantage over classical baselines. This reflects a structural misalignment between common evaluation practices and the scientific tasks the field sets for itself. The reason is that the ground truth---exhaustive molecular dynamics on the systems of interest---is computationally costly, and this cost is what motivates the field. With ground truth inaccessible, evaluation drifts toward convenient proxies, and the resulting norms entrench easily. We identify misaligned evaluation patterns that persist as a community-level equilibrium, and propose concrete observables, reporting standards, and benchmark designs, both computational and experimental, that better reflect what GenMD aspires to deliver. Our aim is to give the field shared language and tools for evaluation that match its scientific ambitions before today's conventions calcify into norms.
PDF arXiv
arXiv cs.LGOct 7
NEMORA: Neural Equivariant Multipole Operators for Long-Range Atomistic Learning
Jay L. Kaplan, Samuel Varner, Rebecca Willett, Juan J. de Pablo
Equivariant graph neural networks have emerged as foundational architectures for machine-learned interatomic potentials, approaching quantum-chemical accuracy at a fraction of the computational cost. These models describe local atomic environments accurately, but finite spatial cutoffs truncate long-range information flow, and stacking message-passing layers can lead to over-smoothing and over-squashing. Existing long-range extensions either prescribe a fixed analytical propagation kernel, restrict long-range communication to scalars or degree-preserving channels, are only approximately equivariant, or incur super-linear computational cost. Combining learnable long-range equivariant transport with multiscale many-body expressivity and efficient scaling for larger systems remains a central challenge. We introduce Neural Equivariant Multipole Operators (NEMORA), a neural equivariant extension of the Fast Multipole Method (FMM) for learning long-range tensorial representations. NEMORA generalizes the FMM's analytical multipole expansion and translation operators to learned equivariant counterparts on an adaptive spatial hierarchy. Its operators couple angular degrees and form…
PDF arXiv
arXiv physics.chem-phOct 7
LLM-Assisted Generation of Transparent, Open-Source Multiphysics Models of Electrochemical Devices
Sebastian Castro, Maya F. Schuchert, Spencer A. McCluskey, Eric W. Lees, Justin C. Bui
Multiphysics continuum models are powerful tools for studying electrochemical devices, enabling in silico reactor design and resolution of local pH, potential, and concentration fields that govern device performance but are difficult to measure experimentally. However, constructing such models requires substantial numerical expertise or reliance on proprietary software. Here, we show that frontier large language model agents can remove this implementation burden while keeping the underlying physics under researcher control. Using one-dimensional electrochemical CO2 reduction to CO in a porous gas diffusion electrode as a test case, we develop a machine-readable, human-specified modeling harness containing governing equations, parameters, numerical methods, logical build stages, and human-verifiable checkpoints. From this specification, the agent reproducibly constructs complete multiphysics models in open-source Julia. Independently built models, including fully autonomous agent-built models, agree with an equivalent COMSOL implementation to within 0.7% of the peak CO partial current density, and with one another to within 0.04%. Systematically planted errors demonstrate the…
PDF arXiv
arXiv cs.LGOct 7
PoreML: A Data-Driven Framework for Learning Multiphase Flow in Porous Media
Chunyang Wang, Mingrui Zhang, Yuyan Zhang, Linqi Zhu, Xin Ju +3
Multiphase flow in porous microstructures is central to CO$_2$ storage, fuel-cell operation, and flip-chip packaging. Predicting these flows remains challenging because wettability and complex pore geometry govern the nonlinear evolution of fluid interfaces. Machine learning holds substantial promise for advancing the field, but progress is constrained by scarce time-resolved 3D datasets and a lack of a unified workflow for training and evaluating models. To fill this critical gap, we introduce PoreML, an open-source framework unifying data generation, model training, and evaluation grounded in pore-scale physics. The framework comprises three core components. (a) A modern GPU-native lattice Boltzmann solver, validated against analytical solutions and published experiments, enables reproducible data generation. (b) A 3.3 TB dataset contains 560 simulation runs and 158,546 stored time steps across four application-driven scenarios. These trajectories span synthetic structures and geometries derived from micro-CT scans of real materials, covering diverse wetting conditions and viscosity ratios. (c) A unified learning framework evaluates one-step prediction and autoregressive…
PDF arXiv

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Machine learned interatomic

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