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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.

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Topics in this field

molecular optimization · molecular design · molecular generation100 papers21 this week
protein language models · protein language · protein structure107 papers16 this week
machine learned interatomic · crystal structure prediction · learned interatomic potentials101 papers11 this week

Topics in this field

Active contributors · 90 days

Active contributors

Activity · 12 weeks

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arXiv cond-mat.str-elOct 12
Honeycomb Crystal in a Mass-Asymmetric Electron-Hole Bilayer
Shengdu Chai, Wangqian Miao, Yuqiang Li, Lei Wang, Xi Dai +1
A two-dimensional electron gas in a uniform neutralizing background forms a triangular Wigner crystal at low density. In a strongly mass-asymmetric electron-hole bilayer, localized heavy holes instead provide a nonuniform positive background that supports an electron crystal at densities two orders of magnitude higher than for a homogeneous electron gas in the same material. Here we show that correlated mobile electrons can overturn the preference for triangular order, stabilizing a honeycomb electron-hole crystal. Using the powerful real-space neural-network variational Monte Carlo in the Born-Oppenheimer limit with fixed holes, we find that increasing the density drives a transition from a triangular electron-hole crystal to a honeycomb crystal, which eventually melts into itinerant electrons coexisting with the honeycomb or the triangular hole lattice at fixed interlayer separation. Relative to triangular order, honeycomb order emerges when gains in electronic kinetic energy and electron-hole attraction outweigh its higher intralayer Coulomb repulsion, a threshold never reached in the rigid point-dipole model. Moreover, the honeycomb hole lattice supports paramagnetic,…
PDF arXiv
arXiv cs.LGOct 12
OctMole: Multiscale 3D Molecular Generation with Hierarchical Spatial Flows
Yu-Tong Jin, Yi-Yang Tian, Qiwei Ye, Peng-Shuai Wang
Generating accurate 3D molecules requires jointly determining a variable number of atoms, their identities, and geometry across spatial scales: global shape emerges coarsely, whereas chemical bonds demand fine local precision. Existing atom-based diffusion and flow models operate largely at a single scale, while dense spatial fields become costly at high resolution. We introduce OctMole, a multiscale octree flow framework for 3D molecular generation. A hierarchical occupancy flow progressively resolves sparse molecular support from coarse to fine, and a joint atom flow assigns atom types and continuous in-cell offsets to occupied leaves. This decomposition combines efficient global structure with subcell geometric precision, while cell corruption improves robustness to generated support. On QM9 and GEOM-DRUG, OctMole achieves strong chemical, distributional, and geometric quality, with particularly clear gains over Uni-3DAR on GEOM-DRUG and substantial efficiency gains over dense 3D generation. As an additional capability, intermediate occupancy states and selected regions provide spatial conditioning without task-specific retraining, supporting multiscale shape conditioning,…
PDF arXiv
arXiv cs.AIOct 12
PXRD-Bench: How Close Are We to Determining Crystal Structures from Powder Diffraction?
Dongyeop Woo, Nofit Segal, Nayoung Kim, Minkyu Kim, Rafael Gomez-Bombarelli +1
Determining crystal structures from powder X-ray diffraction (PXRD) would enable routine characterization of newly synthesized materials, including those absent from reference databases. Generative models offer a promising approach, but existing evaluations remain fragmented and largely assume single-phase samples with known composition. To fill this gap, we introduce PXRD-Bench, a unified benchmark that extends evaluation to unknown per-element atom counts and recovery of both structures in two-phase mixtures. It provides approximately 4.1 million training structures with simulated PXRD, tests generalization to unseen compositions and structural prototypes, and evaluates recovery from experimental PXRD after excluding structurally matching training entries. To provide a strong reference baseline, we also introduce Bragglite, a PXRD-to-structure model developed through a systematic study of PXRD modeling choices. It achieves a 44.2\% Top-1 match rate on experimental RRUFF patterns with known composition, 24.6\% above the strongest prior baseline. Further analysis yields several key findings: some models fail to benefit from experimental PXRD, while generalization to unseen…
PDF arXiv
arXiv cs.AIOct 12
RetroPlanner: Multi-Route Expansion and Multi-Objective Reasoning for LLM-Based Retrosynthesis Planning
Ye Rin Kim, Yongjun Jeong, Seongjun Yun, Hanbum Ko, Soohyun Oh +2
Multi-step retrosynthesis planning is often considered solved once a route to purchasable starting materials is found, but such a route should also be practical in real-world chemistry. Recent LLM-based planners formulate this process as sequential decision-making over an AND-OR graph, yet typically expand a single molecule per turn and are optimized for solvability alone, leaving alternative routes uncompared across the multiple objectives that determine practicality before the search budget is committed. We introduce RetroPlanner, an LLM-based planner that jointly compares multiple routes to steer the search toward higher synthesizability, as measured by reaction plausibility, round-trip consistency, and starting-material price. RetroPlanner is trained to reason over chemical evidence: structural progress from the target molecule, bond changes and reaction classes, where candidate routes diverge from one another, and how they rank across multiple objectives. Experiments on multi-step retrosynthesis benchmarks demonstrate that RetroPlanner recovers more alternative routes than prior LLM-based planners while improving synthetic route quality and maintaining a high success rate.
PDF arXiv
arXiv cs.LGOct 12
AutoNovo: Agentic Program Search Discovers Transferable Nucleic Acid Design Algorithms
Joel Shor, Subhashini Venugopalan
In-silico optimization of nucleic acids relies on predictive oracles that imperfectly capture biological function, so sequences optimized against one model may exploit model-specific artifacts and fail to generalize to independent models. Recent studies have shown that not all designers generalize equally well to independent models. In this work, we use agentic program search to iteratively propose, execute, evaluate, and revise code for nucleic-acid designers. We describe the successful strategies used to prompt the search. AutoNovo designers achieved the best observed mean among the evaluated methods on 3/3 DNA-design tasks in terms of in-silico performance, and 6/6 transfer tasks in terms of independent models. The designers come from a family of discovered nucleic acid designers rather than a single universal best designer. We plan to release the resulting designers. These results are the first steps in creating nucleic acid designers that maximize cross-model generalization, and thus improving the odds that in-silico designed sequences reflect real biology.
PDF arXiv
arXiv hep-exOct 11
RINO: Renormalization Group Distillation with No Labels
Zichun Hao, Raghav Kansal, Abhijith Gandrakota, Chang Sun, Haoyang Li +4
Supervised machine learning in high-energy physics (HEP) requires training on labeled simulations of particle collisions, which are known to be unfaithful to the underlying physics. This leads to significant inaccuracies and biases in the transfer of trained models to real data, limiting the power of deep learning methods. Self-supervised learning (SSL) is a promising alternative for pretraining directly on real, unlabeled data. However, existing techniques largely operate with inductive biases inspired by domains such as images and natural language. We propose RINO (Renormalization Group DIstillation with NO Labels), which, for the first time, exploits the fundamentally multi-scale renormalization group structure of high-energy jet formation as a physically grounded source of SSL views. We define teacher-student representations across energy scales using different levels of hierarchical clustering, aligned via DINO-style self-distillation. To mirror the background-dominated nature of real collider data, RINO pretrains exclusively on jets from quantum chromodynamics (QCD) processes and is evaluated on out-of-distribution (OOD) transfer to rare signal classes. In our controlled…
PDF arXiv

Papers

Topics in this field

molecular optimization · molecular design · molecular generation100 papers21 this week
protein language models · protein language · protein structure107 papers16 this week
machine learned interatomic · crystal structure prediction · learned interatomic potentials101 papers11 this week

Active contributors · 90 days

Recent papers

All in Research →

arXiv cond-mat.str-elOct 12
Honeycomb Crystal in a Mass-Asymmetric Electron-Hole Bilayer
Shengdu Chai, Wangqian Miao, Yuqiang Li, Lei Wang, Xi Dai +1
A two-dimensional electron gas in a uniform neutralizing background forms a triangular Wigner crystal at low density. In a strongly mass-asymmetric electron-hole bilayer, localized heavy holes instead provide a nonuniform positive background that supports an electron crystal at densities two orders of magnitude higher than for a homogeneous electron gas in the same material. Here we show that correlated mobile electrons can overturn the preference for triangular order, stabilizing a honeycomb electron-hole crystal. Using the powerful real-space neural-network variational Monte Carlo in the Born-Oppenheimer limit with fixed holes, we find that increasing the density drives a transition from a triangular electron-hole crystal to a honeycomb crystal, which eventually melts into itinerant electrons coexisting with the honeycomb or the triangular hole lattice at fixed interlayer separation. Relative to triangular order, honeycomb order emerges when gains in electronic kinetic energy and electron-hole attraction outweigh its higher intralayer Coulomb repulsion, a threshold never reached in the rigid point-dipole model. Moreover, the honeycomb hole lattice supports paramagnetic,…
PDF arXiv
arXiv cs.LGOct 12
OctMole: Multiscale 3D Molecular Generation with Hierarchical Spatial Flows
Yu-Tong Jin, Yi-Yang Tian, Qiwei Ye, Peng-Shuai Wang
Generating accurate 3D molecules requires jointly determining a variable number of atoms, their identities, and geometry across spatial scales: global shape emerges coarsely, whereas chemical bonds demand fine local precision. Existing atom-based diffusion and flow models operate largely at a single scale, while dense spatial fields become costly at high resolution. We introduce OctMole, a multiscale octree flow framework for 3D molecular generation. A hierarchical occupancy flow progressively resolves sparse molecular support from coarse to fine, and a joint atom flow assigns atom types and continuous in-cell offsets to occupied leaves. This decomposition combines efficient global structure with subcell geometric precision, while cell corruption improves robustness to generated support. On QM9 and GEOM-DRUG, OctMole achieves strong chemical, distributional, and geometric quality, with particularly clear gains over Uni-3DAR on GEOM-DRUG and substantial efficiency gains over dense 3D generation. As an additional capability, intermediate occupancy states and selected regions provide spatial conditioning without task-specific retraining, supporting multiscale shape conditioning,…
PDF arXiv
arXiv cs.AIOct 12
PXRD-Bench: How Close Are We to Determining Crystal Structures from Powder Diffraction?
Dongyeop Woo, Nofit Segal, Nayoung Kim, Minkyu Kim, Rafael Gomez-Bombarelli +1
Determining crystal structures from powder X-ray diffraction (PXRD) would enable routine characterization of newly synthesized materials, including those absent from reference databases. Generative models offer a promising approach, but existing evaluations remain fragmented and largely assume single-phase samples with known composition. To fill this gap, we introduce PXRD-Bench, a unified benchmark that extends evaluation to unknown per-element atom counts and recovery of both structures in two-phase mixtures. It provides approximately 4.1 million training structures with simulated PXRD, tests generalization to unseen compositions and structural prototypes, and evaluates recovery from experimental PXRD after excluding structurally matching training entries. To provide a strong reference baseline, we also introduce Bragglite, a PXRD-to-structure model developed through a systematic study of PXRD modeling choices. It achieves a 44.2\% Top-1 match rate on experimental RRUFF patterns with known composition, 24.6\% above the strongest prior baseline. Further analysis yields several key findings: some models fail to benefit from experimental PXRD, while generalization to unseen…
PDF arXiv
arXiv cs.AIOct 12
RetroPlanner: Multi-Route Expansion and Multi-Objective Reasoning for LLM-Based Retrosynthesis Planning
Ye Rin Kim, Yongjun Jeong, Seongjun Yun, Hanbum Ko, Soohyun Oh +2
Multi-step retrosynthesis planning is often considered solved once a route to purchasable starting materials is found, but such a route should also be practical in real-world chemistry. Recent LLM-based planners formulate this process as sequential decision-making over an AND-OR graph, yet typically expand a single molecule per turn and are optimized for solvability alone, leaving alternative routes uncompared across the multiple objectives that determine practicality before the search budget is committed. We introduce RetroPlanner, an LLM-based planner that jointly compares multiple routes to steer the search toward higher synthesizability, as measured by reaction plausibility, round-trip consistency, and starting-material price. RetroPlanner is trained to reason over chemical evidence: structural progress from the target molecule, bond changes and reaction classes, where candidate routes diverge from one another, and how they rank across multiple objectives. Experiments on multi-step retrosynthesis benchmarks demonstrate that RetroPlanner recovers more alternative routes than prior LLM-based planners while improving synthetic route quality and maintaining a high success rate.
PDF arXiv
arXiv cs.LGOct 12
AutoNovo: Agentic Program Search Discovers Transferable Nucleic Acid Design Algorithms
Joel Shor, Subhashini Venugopalan
In-silico optimization of nucleic acids relies on predictive oracles that imperfectly capture biological function, so sequences optimized against one model may exploit model-specific artifacts and fail to generalize to independent models. Recent studies have shown that not all designers generalize equally well to independent models. In this work, we use agentic program search to iteratively propose, execute, evaluate, and revise code for nucleic-acid designers. We describe the successful strategies used to prompt the search. AutoNovo designers achieved the best observed mean among the evaluated methods on 3/3 DNA-design tasks in terms of in-silico performance, and 6/6 transfer tasks in terms of independent models. The designers come from a family of discovered nucleic acid designers rather than a single universal best designer. We plan to release the resulting designers. These results are the first steps in creating nucleic acid designers that maximize cross-model generalization, and thus improving the odds that in-silico designed sequences reflect real biology.
PDF arXiv
arXiv hep-exOct 11
RINO: Renormalization Group Distillation with No Labels
Zichun Hao, Raghav Kansal, Abhijith Gandrakota, Chang Sun, Haoyang Li +4
Supervised machine learning in high-energy physics (HEP) requires training on labeled simulations of particle collisions, which are known to be unfaithful to the underlying physics. This leads to significant inaccuracies and biases in the transfer of trained models to real data, limiting the power of deep learning methods. Self-supervised learning (SSL) is a promising alternative for pretraining directly on real, unlabeled data. However, existing techniques largely operate with inductive biases inspired by domains such as images and natural language. We propose RINO (Renormalization Group DIstillation with NO Labels), which, for the first time, exploits the fundamentally multi-scale renormalization group structure of high-energy jet formation as a physically grounded source of SSL views. We define teacher-student representations across energy scales using different levels of hierarchical clustering, aligned via DINO-style self-distillation. To mirror the background-dominated nature of real collider data, RINO pretrains exclusively on jets from quantum chromodynamics (QCD) processes and is evaluated on out-of-distribution (OOD) transfer to rare signal classes. In our controlled…
PDF arXiv

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Fields · AI · updated 3m ago

Machine learned interatomic

Found by the topic model: machine learned interatomic, protein language models, molecular optimization.

48papers this week−39.2% vs last week

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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.