Vast Chemical Space

RNA design consists of discovering a nucleotide sequence that optimizes predefined criteria, such as secondary structure. It is useful for synthetic biology, medicine, and nanotechnology. We propose Montparnasse, a Monte Carlo search framework based on Generalized Nested Rollout Policy Adaptation, augmented with a problem-specific prior, slow and long adaptation at level 1, and a lexicographic multicriteria evaluation. Montparnasse solves all 100 puzzles of the Eterna100 V1 benchmark consistently faster than DesiRNA, the previous state of the art, across all time limits, reaching full coverage more than three times faster overall. On messenger RNA secondary structure optimization for hemoglobin alpha, it identifies sequences with more paired bases than the MFE-optimal solution of LinearDesign.

Protein structure generative models excel at predicting single protein static structures from sequence, but routinely fail to capture the correct conformational state of protein complexes, critical for protein design and induced proximity modalities such as antibodies and PROTACs. While structural proteomics techniques like Cross-Linking Mass Spectrometry (XL-MS) and Hydrogen-Deuterium Exchange (HDX-MS) offer valuable spatial and dynamic insights, integrating these sparse, heterogeneous measurements into these models remains an open challenge. Here, we bridge this gap by combining structural proteomics data with the rich biophysical priors learned by pretrained diffusion models. We introduce AIMS-Fold, an inference-time guided-diffusion framework that actively steers the generative sampling trajectory using differentiable physical potentials derived from XL-MS spatial restraints and HDX-MS solvent accessibility profiles. We demonstrate that these structural methods individually enhance predictive accuracy, and their integration yields synergistic improvement. Crucially, by leveraging these experimental restraints, AIMS-Fold achieves higher accuracy on challenging induced proximity targets than purely computational, unguided state-of-the-art models like Boltz-2. This establishes our framework as a powerful, integrative computational approach for the structure based drug design of induced proximity drugs. Evaluation code will be made publicly available upon publication.

Accurately predicting crystal properties is critical for accelerating materials discovery, but it is often limited by scarce labeled data and costly theoretical calculations. To alleviate this, we propose UNATE (Unsupervised Atomic Embedding), a framework that leverages structural information extracted from unlabeled crystal structures. UNATE integrates an unsupervised denoising autoencoder with self-supervised contrastive learning to learn robust atomic representations, which are then used as input features for downstream property prediction. Experimental results show that replacing raw atomic numbers with UNATE-pretrained node embeddings yields a 2.7% improvement over the full-data baseline. Notably, the benefits become more pronounced in scenarios with limited labeled data, reaching improvements of up to 10% when only 25% of the labeled data is used.

Designing a single molecule that modulates two targets is a promising strategy for polypharmacology, but it remains substantially harder than standard single-target generation because one candidate must satisfy two binding requirements while preserving drug-likeness and synthesizability. Existing dual-target generative methods typically introduce dual-target capability by either retraining the generator or intervening in the diffusion process during sampling. The former can be costly and difficult to stabilize when dual-target supervision is sparse, while the latter may be sensitive to denoising-time target balancing and competing update directions. These limitations motivate a generator-preserving alternative that keeps the pretrained prior intact: can dual-target candidates instead be recovered from the input space of a frozen single-target diffusion model, without modifying its parameters or denoising dynamics? We formulate this task as a constrained multi-objective optimization problem and propose REUSE, a hierarchical evolutionary input-space search framework that combines pair-conditioned exploration with structured multi-stage selection to enforce dual-target affinity, chemical quality, and diversity. Experiments show that, compared with methods that modify the diffusion process, REUSE consistently improves dual-target affinity and balance, achieving a 20.9-percentage-point gain in Dual High Affinity over the strongest prior baseline while maintaining competitive molecular quality.

The generation of accurate 3D molecular conformations is a pivotal challenge in computational chemistry and drug discovery. Recently, diffusion and flow matching models have achieved remarkable success. However, there is a critical misalignment between their mathematical formulation and the physical reality of molecules. Existing approaches predominantly treat molecules as unstructured point clouds in Cartesian space, overlooking the intrinsic hierarchical mechanics where bond lengths and bond angles are relatively stiff, whereas torsion angles constitute the dominant flexible degrees of freedom. This lack of manifold awareness forces models to relearn fundamental geometric constraints from scratch, often leading to physically implausible intermediate structures. To address this, we propose GO-Flow that aligns generative modeling with molecular geometry via manifold decomposition. Instead of forcing motion through Euclidean space, GO-Flow decomposes the generation process into three physically motivated subspaces: translation space with linear optimal transport, rotation space with geodesic flows on $SO(3)$, and conformation space with entropic optimal transport. This decomposition injects geometric inductive biases and makes the generative paths better aligned with molecular degrees of freedom. When combined with equivariant neural architectures, it encourages rotation-consistent generation and improves geometric validity. Extensive experiments on GEOM-Drugs and GEOM-QM9 demonstrate that GO-Flow achieves state-of-the-art generation quality. Notably, by learning straighter probability paths on the correct manifolds naturally, our method enables high-fidelity sampling with as few as 50 steps, effectively bridging the gap between structural precision and computational efficiency.

Not all clinically relevant adverse effects are structurally inferable from molecular graphs - regardless of model quality or architectural complexity. This study introduces an operational taxonomy of the structural information limits that prevent structure-based toxicity prediction, independent of the learning algorithm employed. Graph Neural Networks (GNNs) have emerged as a natural approach for molecular toxicity prediction, operating directly on atomic connectivity without the information loss inherent to fixed-length fingerprints. However, the fraction of a drug's known pharmacological profile that is actually inferable from molecular structure remains systematically underexplored. A systematic case study using acetylsalicylic acid (ASA, Aspirin) - one of the most comprehensively characterized drugs in pharmacology - serves as model compound. A Message Passing Neural Network (MPNN) is trained on the Tox21 benchmark and GNNExplainer is applied to characterize atom-level attribution. Results indicate that molecular structure explains approximately 45% (5/11) of known ASA adverse effects. A four-category Gap Taxonomy (GAP-1 through GAP-4) is introduced distinguishing between principally non-encodable effects, data gaps arising from Missing Not At Random (MNAR) mechanisms, assay panel mismatches, and representation errors. The MNAR gap is empirically quantified via a systematic ChEMBL query (42 documented assays, 0 retrievable bioactivity entries). An attention pooling experiment localizes the representation error to the MPNN message passing layers rather than the aggregation step. The Gap Taxonomy has direct implications for drug safety signal detection and regulatory frameworks including Good Pharmacovigilance Practice (GVP) guidelines and New Approach Methodologies (NAMs). Structural limits identified are confirmed in a companion DDI ablation study.

Property-conditional molecular generation should produce valid, diverse molecules while responding to continuous target values at low sampling cost. We introduce DriftingMol, a two-stage framework that adapts drifting models to a SELFIES latent molecular space. A frozen SELFIES beta-VAE provides the latent space, and the hidden representation of its decoder serves as the drift feature map. In decoder-coupled drift, decoder weights remain fixed, but drift gradients are backpropagated through the decoder feature map to a DiT generator, inducing a pullback metric aligned with molecular decoding. On ZINC250K, the default setting achieves QED Spearman correlation 0.493 with 94.7% uniqueness, while the strongest decoder-coupled condition reaches 0.510. Under protocol-matched four-property conditioning, decoder-coupled drift reaches mean Spearman correlation up to 0.598. Across 15 controlled variants, models that preserve the gradient path through decoder features achieve higher correlations than the tested latent-space, random-feature, and external-feature drift variants, while detached or stop-gradient decoder controls yield near-zero QED correlation and very low uniqueness. These results indicate that decoder-coupled drift is a useful low-cost mechanism for property-biased molecular generation, requiring one generator evaluation and one frozen decoder pass.

Obtaining consistent explanations for machine learning on molecular graphs requires predictions and attributions to be aligned with chemical identity. However, chemically equivalent drawings of the same molecule can induce different molecular representations, leading to inconsistent predictions and explanations. Here, we introduce InChIfied Invariants, a class of node, edge, and graph features based on the International Chemical Identifier (InChI) and designed to be invariant under transformations that preserve chemical identity. Using one million molecular graphs from PubChem Substances, we show that InChIfied Invariants produce identical representations for chemically equivalent graphs in 99.62% of cases, whereas standard Daylight invariants do so in only 0.35% of cases. Across MoleculeNet tasks, InChIfied Invariants preserve predictive performance while significantly improving prediction consistency across alternative graph depictions of the same molecules. We further perform a quantitative attribution analysis and show that explanations produced with standard molecular featurization methods vary substantially across chemically equivalent graphs, while InChIfied Invariants enforce consistent attributions by construction. We release open-source software implementing InChIfied Invariants, which can be used as a drop-in replacement for standard molecular graph features.

Stochastic process-based molecular graph generators have become the state of the art for template-free single-step retrosynthesis. However, these models are typically trained only on product-reactant pairs, thereby acquiring chemistry-relevant representations in an indirect and implicit manner. Meanwhile, recent advances in computer vision demonstrate that offering representation guidance to a generator can effectively distill semantics from pretrained encoders into DiTs, substantially improving both convergence and generation quality. Whether similar gains extend to the retrosynthesis task, and what graph-specific design choices can make them work, remains an open question. To address these questions, we conduct a systematic empirical study over a unified design space spanning teacher molecular representations, endpoint and granularity choices, injection depths in the denoiser, correspondence strategies and guidance scheme. Guided by these considerations, we develop Graph-oriented Representation Guidance (GRG), which achieves 58.6 / 77.2 / 83.4 / 87.1 top-1 / 3 / 5 / 10 accuracy on USPTO-50k, while increasing diversity to 15.5, both substantially outperforming the adopted base generator. Notably, GRG consistently improves all top-k metrics in out-of-distribution settings, suggesting that representation guidance facilitates the acquisition of intrinsic chemical semantics. Meanwhile, the introduced representation guidance reduces the number of epochs by 35% and the wall-clock time by 30% to reach comparable performance. In addition, we introduce a simple yet effective representation-similarity-based reranking mechanism, which further improves the top of the ranked list without training an additional verifier.

Ordinary differential equation models of biochemical reactions are often formulated as stoichiometric systems in which the dynamics arise from a collection of interacting processes. A central challenge is that the functional form of each process is rarely known a priori and may be difficult to infer from data. We propose biochemically informed neural ordinary differential equations (BINODEs), a neural-ODE framework that retains the stoichiometric structure of mechanistic models while representing individual processes by neural networks. In BINODEs, the outputs of neural network processes (NNPs) are mapped to state derivatives through a linear layer analogous to a stoichiometric matrix. This architecture allows biological side information, such as process-specific inputs, sign constraints, and monotonicity assumptions, to be built directly into the model. We characterize the approximation properties of NNPs for several standard biochemical rate laws and show that the proposed framework recovers both trajectories and process-level structure in Monod, Lotka--Volterra, pharmacokinetic, and ultradian endocrine models. These results suggest that BINODEs offer a useful compromise between mechanistic interpretability and data-driven flexibility for modeling partially known biochemical or biological dynamical systems.

Nucleic acids are increasingly recognized as therapeutic targets beyond conventional protein-centered drug discovery, yet accurate and efficient docking of small molecules to nucleic acid structures remains challenging. Physics-based docking methods often show limited accuracy and efficiency, whereas deep learning approaches are constrained by the scarcity of experimentally resolved nucleic acid-ligand complexes. Here, we present NucleoDock, a deep learning framework for nucleic acid-small molecule docking. To address data scarcity, NucleoDock combines physics-guided large-scale pretraining on millions of docking-generated synthetic complexes with fine-tuning on curated experimental co-crystal structures. It further integrates sequence- and structure-informed nucleotide representations with atomistic three-dimensional features to capture both biological context and binding-site geometry. A mixture density network-based geometric scoring head is used to model conditional interaction-distance distributions for pose ranking. On an external benchmark of 125 nucleic acid-ligand complexes, NucleoDock achieved a top-1 success rate of 56 percent at an RMSD cutoff of 2.0 Angstrom, outperforming rDock with 29 percent, while generating 100 poses in approximately 5 seconds per complex. Retrospective virtual screening on the ROBIN benchmark further showed improved early enrichment. NucleoDock represents a step toward bridging the methodological gap between protein- and nucleic acid-directed computational drug discovery.

Protein-ligand modeling underpins computational drug discovery and molecular design. Existing protein-ligand benchmarks typically evaluate whether a protein and ligand interact and how strongly they bind, through tasks such as binary binding prediction and affinity regression. However, these evaluations provide limited evidence of whether models can localize binding sites or identify the non-covalent interactions underlying molecular recognition. To address this gap, we introduce InteractBind, a large-scale protein-ligand dataset comprising approximately 100k protein-ligand pairs, together with a benchmark for fine-grained evaluation. The core fine-grained task is that of binding-site localization, which uses protein-residue and ligand-atom interaction maps spanning six major types of non-covalent interactions to assess whether model-derived interaction maps localize binding sites. InteractBind further includes binding affinity and protein similarity-controlled splits to support realistic generalization assessment. Using InteractBind, we evaluate eight existing sequence-based and interaction-aware models, assessing binary binding prediction and binding-site localization. Results reveal limited binding-site localization despite strong binary binding prediction, with marked variation across non-covalent interaction types. Overall, InteractBind establishes a benchmark paradigm that encourages the development of more interpretable and physically grounded protein-ligand models.

Scientific discovery is a closed-loop process in which hypotheses guide data acquisition and observations refine the hypothesis space. Yet most approaches reduce discovery to supervised learning over fixed datasets, where limited observations can support multiple plausible mechanisms that fit locally but fail to generalize. Thus, the key challenge is selecting informative observations to resolve uncertainty, shifting the focus from static inference to adaptive data acquisition. To address this, we propose LLM-AutoSciLab, a closed-loop framework that couples hypothesis generation with hypothesis-conditioned experiment selection and mechanism refinement. Rather than fitting models to passively collected data, LLM-AutoSciLab iteratively proposes plausible hypotheses, selects informative experiments to distinguish or refine them, and updates its state using the resulting evidence. To evaluate dynamic, closed-loop scientific discovery with active data acquisition, we introduce ActiveSciBench, comprising two datasets: ActiveSciBench-Chem with 57 enzyme-kinetics tasks and ActiveSciBench-GRN with 45 gene-regulatory-network tasks. These datasets model discovery as a budget-constrained process requiring adaptive experiment design, variable selection, and recovery of true mechanisms. Across NewtonBench, ActiveSciBench-Chem, and ActiveSciBench-GRN, LLM-AutoSciLab outperforms prior methods, achieving 67.6% and 35.1% symbolic accuracy on NewtonBench and ActiveSciBench-Chem, respectively, and 31.1% exact graph recovery on ActiveSciBench-GRN. Moreover, hypothesis-guided experimentation is 2-5x more sample-efficient than the strongest competing baselines. Code and data are available at: https://github.com/scientific-discovery/LLM-AutoSciLab

Drug discovery is a lengthy and resource-intensive process composed of multiple stages. Among these stages, lead optimization plays a critical role in transforming early hit compounds into viable drug candidates. This stage requires improving ADMET-related properties through subtle structural refinement while preserving key molecular substructures responsible for binding affinity to disease targets. Recent advances in artificial intelligence have shown promise in accelerating various aspects of drug discovery; however, most existing approaches to lead optimization rely on one-step molecular optimization, which fail to account for the long-term consequences of sequential design decisions. To address this limitation, we propose TRACE, a trajectory-aware, LLM-reasoning agent for molecular lead optimization that formulates tool selection as a sequential decision-making problem over action trajectories. Given a lead molecule and an optimization objective, TRACE makes trajectory-aware decisions over molecular optimization tools, enabling forward-looking refinement under structural constraints. Experiments on multiple ADMET optimization tasks show that our agent achieves higher optimization success, larger property improvements, and higher validity, while preserving molecular similarity compared to baseline models.

We present Epicure, a family of three sibling skip-gram ingredient embeddings retrained from scratch on a multilingual recipe corpus. We aggregate 4.14M recipes from 11 sources spanning seven languages, English, Chinese, Russian, Vietnamese, Spanish, Turkish, Indonesian, German, and Indian-English, and normalise the raw ingredient strings to 1,790 canonical entries via an LLM-augmented pipeline. A 203,508-edge ingredient-ingredient NPMI graph and an 80,019-edge typed FlavorDB ingredient-compound graph, 2,247 typed compound nodes across 15 categories, seed three Metapath2Vec variants that share architecture and hyperparameters and differ only in the random-walk schema: Cooc walks the co-occurrence graph only, Chem walks the typed compound metapaths only, and Core blends both via injected ingredient-ingredient walks at controlled mixing, placing each model at a distinct point on the chemistry-vs-recipe-context spectrum.

Large Language Models (LLMs) are central to the one-for-all intelligent paradigm, but they face a fundamental challenge when dealing with heterogeneous scientific data such as molecules: the inherent gap between discrete linguistic symbols and topological molecular or continuous reaction data leads to significant information loss and semantic noise in text-based reasoning. We propose SciCore-Mol, a modular framework that bridges this gap through three deeply integrated pluggable cognitive modules: a topology-aware perception module, a latent diffusion-based molecular generation module, and a reaction-aware reasoning module. Each module is coupled to the LLM backbone through learned representation interfaces, enabling richer information exchange than is possible with text-only tool feedback. Our experiments on diverse chemical tasks demonstrate that SciCore-Mol achieves strong comprehensive performance across molecular understanding, generation, reaction prediction, and general chemistry knowledge, with an 8B-parameter open-source system that is competitive with and in several dimensions surpasses proprietary large models. This work provides a systematic blueprint for equipping LLMs with scientific expertise through decoupled, pluggable, and flexibly orchestrated modules, with direct implications for drug design, chemical synthesis, and broader scientific discovery.

Stellar spectra encode key information on the physical properties and chemical compositions of stars. Accurate stellar parameter determination is essential for addressing major questions such as galaxy and stellar evolution. Large-scale spectroscopic surveys have accumulated unprecedented spectral data. Traditional feature extraction or model-fitting approaches struggle with high-dimensional, massive datasets, limited generalization, and computational inefficiency. Recent advances in large language models demonstrate strong generalization and feature-learning in tasks like natural language processing, DNA/RNA sequence analysis, and protein/chemical parsing. Stellar spectra are continuous sequential signals, enabling the transfer of language models to stellar spectroscopy. Here, we propose a two-stage large language model framework for stellar parameter inference, achieving accurate estimation of effective temperature, surface gravity, metallicity, and abundances of ~20 chemical elements. Scaling-law analyses show systematic performance improvements with increasing data, providing a scalable framework for forthcoming large-scale surveys.

Recent advances in generative modeling show that pretrained representations can improve generation as conditioning features or alignment targets. Motivated by this, we study protein representations for predicting structures beyond conventional function annotation. We propose TriProRep, a structure-aware pretraining method that jointly models three aligned residue-level views: amino-acid identity, backbone geometry, and local full-atom geometry, discretely encoded via VQ-VAE tokenizers. By pretraining to recover original tokens from generator-corrupted views, TriProRep learns to distinguish plausible but incorrect cross-view augmentations from the original protein. We further introduce RepSP, a benchmark for evaluating protein representations in structure-predictive settings. RepSP tests three uses of representations: homodimer co-folding from apo-chain representations, residue-level prediction of homodimer-derived interaction properties, and representation-aligned monomer structure prediction. Across these tasks, TriProRep improves over sequence-only and prior structure-aware representation models, while maintaining competitive performance on conventional benchmarks.

LLM agents have incredible potential for scientific discovery applications. However, the performance of LLM agents on real-world, small molecule drug design (SMDD) tasks across diverse chemistries and targets is unclear. Current evaluation methods are either ad hoc, too simple for real-world discovery, limited in scale, or restricted to single-turn question answering. In effort to standardize the evaluation of LLM agents on small molecule design, we introduce SMDD-Bench, a challenging, multi-turn, long-horizon agentic benchmark consisting of 502 guaranteed-solvable task instances spanning 5 task types: 2D Pharmacophore Identification, Interaction Point Discovery, Scaffold Hopping, Lead Optimization, and Fragment Assembly. SMDD-Bench tasks span a wide region of chemical space and involve 102 unique protein targets. Completely solving the benchmark would require having strong chemical and biological reasoning and 3D intuition, understanding specialized tool use, and displaying planning expertise over a limited number of oracle calls. We benchmark 7 frontier open and closed source LLMs and find even the most performant LLM, GPT5.4, solves only 40.2% of tasks. We hope SMDD-Bench provides a standardized testbed to invigorate the field towards training and evaluating LLM agents for fully autonomous computational drug design. We host a public leaderboard at smddbench.com .

Computational antibody CDR design methods condition on antigen structure to generate binding loops. Yet, the existing architectures conflate two fundamentally distinct sub-problems: identifying which CDR positions will contact the antigen, and selecting amino acids at those positions. This forces models to learn contact reasoning implicitly through uniform message passing, diluting antigen signal across all positions equally. We introduce ConTact, a contact-then-act architecture that explicitly decomposes CDR design into three cascaded stages: learning surface complementarity fingerprints, predicting CDR-antigen contacts, and injecting contact-gated antigen features into the prediction head. A distance-biased cross-attention module encodes geometric priors favoring spatial neighbors, while a contact-weighted cross-entropy loss concentrates gradient signal on binding-critical positions. On the CHIMERA-Bench dataset, ConTact achieves the lowest backbone RMSD on every split (a 5 to 6% improvement over the best baseline) and the best fraction of native contacts, interface RMSD, and epitope F1 on the antigen-fold and temporal splits, while remaining competitive on the harder epitope-group split. The source code is available at: https://github.com/mansoor181/ConTact.git

Accurate registration between a prior model and the real scene is essential for high-precision robotic manipulation, yet optical methods suffer from long calibration chains, line-of-sight constraints, and fabrication errors. We propose a calibration-free alternative that reformulates contact registration as complementary-shape docking between the object and the probe's swept volume, explicitly accounting for probe geometry and leveraging both contact and non-contact evidence. Our solver integrates a global-to-local search via 3D FFT correlation over low-discrepancy SO(3) samples, then followed by continuous SE(3) refinement using Lie-algebra updates and analytic contact sensitivities. This pipeline yields efficient exploration and metric-grade convergence without fragile point correspondences. Simulation across free-form meshes achieved sub-0.04 mm and sub-0.4° accuracy and robustness to pose noise and contact loss. On a tooth-preparation robot, our method attained 0.42 mm and 3.75°, outperforming an optical tracker registration while requiring no external sensors. These results demonstrate a practical and precise registration strategy for surgical and industrial robots.

Materials discovery and biomedical translation increasingly require models that can reason across composition, processing, structure, biological response, manufacturability, safety, and governance constraints. Existing materials and biomedical data ecosystems are powerful but remain poorly coupled for AI-guided discovery. Here we present AIMBio, a conceptual framework for an AI-native, FAIR, and governance-aware decision layer that links materials provenance, biomedical context, knowledge graphs, uncertainty-aware machine learning, and human-in-the-loop active learning. The framework formulates biomedical-materials discovery as constrained multi-objective optimization under uncertainty and introduces practical requirements for metadata, model documentation, risk-tiered governance, evaluation metrics, and phased implementation. To make the roadmap testable, we add a minimum viable prototype specification and a worked pilot for AI-guided nanomaterials for drug delivery. AIMBio is positioned as exploratory and preclinical discovery infrastructure, not as clinical decision-support software; any clinical or regulated-device use would require separate validation, change control, and regulatory review. The central contribution is a publishable platform blueprint for converting fragmented materials and biomedical records into auditable, experimentally actionable, and translationally responsible discovery workflows.

Precision oncology requires predicting which drugs will suppress a specific tumor from its molecular profile, but drug-blind sensitivity prediction has plateaued despite increasingly complex drug representations. Here we show that this stagnation reflects a metric artifact rather than a representational bottleneck. The standard benchmark, global Pearson r, is dominated by between-drug potency differences that a trivial drug-mean predictor captures without any cell-specific learning. Per-drug Pearson r, which isolates within-drug cell ranking, reveals that no drug encoding improves over cell-only features across four independent datasets. A controlled experiment channeling mechanism-of-action identity as either a drug feature or a training-distribution constraint identifies the cause. Supplying MoA as a feature yields negligible benefit, whereas using it to stratify training raises per-drug r substantially for targeted kinase inhibitors, because pan-cancer co-training suppresses pathway-specific sensitivity signals. Mechanism-stratified training and response matching from pilot observations provide two deployable strategies that together recover the principal sources of predictive gain in drug-blind sensitivity prediction.

Large language models can predict real-valued quantities from heterogeneous inputs such as text, code, and molecular strings, but most training objectives score each decoded floating-point number independently, improving point estimates without ensuring calibrated predictive distributions. This limits applications requiring candidate ranking or uncertainty estimation. We introduce Distribution-Aware Reward, an on-policy reinforcement learning objective whose main contribution is to train language models to produce better predictive distributions for regression tasks, rather than only optimizing individual decoded outputs against scalar targets. Our method treats multiple decoded samples as an empirical predictive distribution, evaluates it with the Continuous Ranked Probability Score, and assigns leave-one-out credit based on each rollout's marginal contribution to distribution quality, rewarding predictions that are both accurate and appropriately dispersed. We evaluate our method on a controlled Gaussian-mixture task, code performance prediction, and molecular property prediction from SMILES strings. Across tasks, our method improves over supervised fine-tuning and pointwise reinforcement learning baselines, with strong rank-correlation gains, including a 6-point Spearman improvement on KBSS. On MoleculeNet, it uses only SMILES strings yet remains competitive with strong graph-based and 3D molecular models. Further analyses show that our method mitigates rollout diversity collapse and improves uncertainty diagnostics, suggesting that directly optimizing predictive distributions makes language model regression more robust and better calibrated.

Automated extraction of materials composition-property data from scientific literature has advanced considerably with the development of large language model-based pipelines; however, existing frameworks remain limited to textual and tabular content, overlooking the substantial proportion of quantitative property data reported exclusively in scientific figures. Here, we extend ComProScanner, a fully end-to-end multi-agent framework for automated composition-property database construction, with a native vision-language model (VLM) based figure extraction capability. The extension introduces a FigureExtractor utility for caption-keyword-based figure filtering across all supported publishers, and a GraphExtractorTool agent that passes extracted figures to a configurable VLM to recover composition-property pairs from scientific charts and plots. Four VLMs are selected for evaluation on the basis of the LMArena Diagram leaderboard with an input cost criterion of less than $1.50 per million tokens. Benchmarking on 50 piezoelectric ceramic articles from the established $d_{33}$ test corpus demonstrates that Gemini-3-Flash-Preview achieves the highest performance with a composition accuracy of 0.97 and a normalised F1 score of 0.97, whilst remaining the most cost-effective model among the four evaluated. We additionally introduce a range-based value error threshold parameter into the evaluation framework, providing a more physically meaningful assessment of numeric property values extracted from figures than exact value matching. These contributions establish VLM-integrated ComProScanner as the first materials-specific, fully automated, multimodal literature mining platform capable of extracting structured composition-property data from text, tables, and figures within a single unified pipeline.

Predicting protein-ligand binding affinity remains intractable for multi-domain proteins, where inter-domain dynamics govern molecular recognition. Existing geometric deep learning methods typically treat proteins as monolithic static graphs, suffering from rigid-body assumptions and aleatoric noise in flexible regions. To address this, we introduced HCLBind, a self-supervised framework that decouples geometric representation learning from affinity regression. HCLBind leverages a general-to-specific pre-training paradigm on the Q-BioLiP database to learn a robust physical grammar of binding. We propose a novel hierarchical decoy strategy: the model learns local physicochemical constraints through protein coordinate perturbation in single-domain proteins and global conformational geometry through inter-domain rotation in multi-domain complexes. Our hybrid architecture integrates a domain-gated graph attention network and cross-modal attention to explicitly prioritize domain interfaces. Furthermore, we employ LoRA on protein and ligand foundation models, ensuring efficient optimization while preserving evolutionary knowledge. Experiments on PDBBind demonstrate that HCLBind effectively learns discriminative interface features and provides robust uncertainty estimation, overcoming the limitations of standard supervised learning. The code is available at https://github.com/jiankliu/HCLBind.

Accurately identifying metabolites i.e. small molecules from mass spectrometry data remains a core challenge in metabolomics, with broad applications in drug discovery, environmental analysis, and clinical research. We address the Molecule Retrieval task, which consists in recovering the chemical structure of a metabolite from its MS/MS spectrum given a set of candidate molecules. While the recent release of benchmark datasets such as MassSpecGym and Spectraverse has considerably accelerated the development of novel machine learning approaches, the complexity of data preprocessing pipelines and the lack of unified implementations make methods and results difficult to reproduce and compare. We make three contributions. First, we propose a unified framework encompassing recent approaches based on representation alignment and contrastive learning. Second, we introduce MSAlign, inspired by multimodal alignment in vision-language models, which learns a shared representation space by aligning two frozen foundation models (DreaMS for mass spectra and ChemBERTa for molecules) through lightweight MLP projections trained with a candidate-based contrastive objective. MSAlign is simple to implement, fast to train and consistently outperforms existing approaches across all benchmarks. Third, we investigate a long-standing evaluation problem: data splitting strategies in molecule retrieval implicitly trade off data leakage against domain shift. We formalize this tension by introducing a quantitative measure of distribution shift, and use it to evaluate splitting strategies in existing benchmarks. All datasets, splits, candidate sets, and a unified implementation of MSAlign and baselines are publicly released to support reproducible research.

Protein-protein interactions (PPIs) govern nearly all cellular processes, yet computational methods for identifying binding partners typically produce ranked predictions without mechanistic justification. This creates a fundamental barrier to adoption because biologists cannot assess whether predictions reflect genuine biochemical insight or spurious correlations. We present \textbf{Protein Thoughts}, a framework that reformulates PPI discovery as an interpretable search problem with explicit reasoning. The system decomposes binding evidence into four biologically meaningful signals: sequence similarity reflecting evolutionary relationships, structural complementarity capturing geometric fit, interface balance, and chemical compatibility encoding residue-level interactions. Rather than collapsing these signals into an opaque score, we preserve their individual contributions through a transparent value function that enables both ranking and auditing. To navigate large candidate spaces efficiently, we introduce hypothesis-guided entropy-regularized Tree-of-Thoughts search. A fine-tuned language model generates search directives from embedding-derived features, classifying candidates as high-priority, exploratory, or skippable. These directives condition a Boltzmann policy that balances exploitation with entropy-driven exploration, while hypothesis-aware pruning prevents premature abandonment of promising candidates. For candidates exhibiting score disagreement, hypothesis-conditioned embedding-space flow matching transports protein embeddings toward the binder manifold. On the SHS148k benchmark, Protein Thoughts achieves mean best-binder rank of 11.2 versus 47.7 for an entropic tree search baseline, a 76% improvement, and for binding prediction the trained value function achieves $91.08 \pm 0.19$ Micro-F1, outperforming existing PPI methods on the same dataset.

Generating stable molecular conformations typically forces a tradeoff between the physical realism of energy-based relaxation and the sampling efficiency of data-driven generative models. While machine learning force fields (MLFFs) can sample stable conformations by relaxing molecular geometries according to physical forces, they require costly ab-initio training data. Conversely, diffusion models (DMs) learn from equilibrium data alone but are dependent on noise schedules and time-step conditioning. In this work, we propose generative pseudo-force fields (GPFFs) to bridge these paradigms by training an MLFF on a quadratic pseudo-potential energy surface relative to reference equilibrium structures. Because no ab-initio calculations are required for the perturbed geometries, non-equilibrium training data can be generated on the fly by perturbing the equilibria with Gaussian noise. We show that GPFFs constitute a time-step-agnostic variant of variance exploding DMs: the score comes from the predicted pseudo-forces but because force magnitudes implicitly encode the noise level, no time-step conditioning is needed. Our GPFF can hence be used as a drop-in replacement in standard diffusion sampling (ancestral, Heun) but also facilitates more efficient, adaptive variants and an MLFF inspired direct denoising scheme. Our proposed sampling algorithms support arbitrary structural priors and geometric constraints. On QM9, GPFF has 100 % validity at 256 neural function evaluations (NFE) and over 50 % at just 6 NFE, outperforming diffusion baselines across all samplers. Combined with custom priors, we showcase the fast and accurate generation process of our method in a molecular editor for a drug design setting, where a molecule is generated in real time.

Classifying protein topology is essential for deciphering biological function, but progress is held back by the lack of large-scale benchmarks that avoid duplicates and by models that do not scale well. We introduce TEDBench, a large-scale, non-redundant benchmark for protein fold classification constructed from the Encyclopedia of Domains (TED) and Foldseek-clustered AlphaFold structures. We show that on TEDBench, current protein representation learning methods either require very large models or fail to deliver strong performance. To address this challenge, we propose Masked Invariant Autoencoders (MiAE), a self-supervised framework for protein structure representation learning. MiAE uses an extremely high masking ratio of up to 90% with an $\mathrm{SE(3)}$-invariant encoder and a lightweight decoder that reconstructs backbone coordinates from the latent representation and mask tokens. MiAE scales well and outperforms supervised counterparts and state-of-the-art baselines on TEDBench, establishing a strong recipe for protein fold classification. To test transfer beyond AlphaFold structures, we further benchmark on a curated dataset from experimental structures of CATH v4.4. TEDBench is available at https://github.com/BorgwardtLab/TEDBench.

Molecules in equilibrium follow a Boltzmann distribution, making the underlying energy landscape a physically grounded modeling objective. However, such landscapes are difficult to learn from data and, once learned, hard to sample from. Diffusion and flow-matching models sidestep these difficulties by learning a time-conditional score or transport field between noise and data, losing the energy inductive bias in exchange for a more tractable training objective. We introduce EBMol, an energy-based model (EBM) that restores this inductive bias by learning an atom-additive scalar potential without explicit simulation during training. Our method employs a flow-inspired Restoring Field Matching objective to approximate the energy landscape. We adopt the Mirror-Langevin algorithm for sampling, enabling unified updates of atomic positions and types, and incorporate parallel tempering for inference-time compute scaling. EBMol is the first EBM for 3D molecular generation to achieve state-of-the-art performance on QM9 and GEOM-Drugs. Moreover, we show that the learned energy landscape serves as a principled quality metric for ranking and filtering configurations, and demonstrate controllable generation without retraining through shape-steered sampling via potential composition and zero-shot linker design.

AlphaFold3 introduces a diffusion-based architecture that elevates protein structure prediction to all-atom resolution with improved accuracy. This state-of-the-art performance has established AlphaFold3 as a foundation model for diverse generation and design tasks. However, its iterative design substantially increases inference time, limiting practical deployment in downstream settings such as virtual screening and protein design. We propose DCFold, a single-step generative model that attains AlphaFold3-level accuracy. Our Dual Consistency training framework, which incorporates a novel Temporal Geodesic Matching (TGM) scheduler, enables DCFold to achieve a 15x acceleration in inference while maintaining predictive fidelity. We validate its effectiveness across both structure prediction and binder design benchmarks.

Efficient discovery of precursor additives is essential for improving the performance of perovskite solar cells, yet the large chemical space makes conventional trial-and-error screening inefficient. We develop LEAP(LLM-driven Exploration via Active Learning for Perovskites), an expert-in-the-loop closed framework that couples a domain-specialized large language model(LLM) with active learning for iterative additive prioritization. The LLM is trained to extract mechanism-relevant knowledge from the perovskite additive literature and to represent candidate molecules through interpretable descriptors, which are further integrated into a Bayesian optimization workflow for uncertainty-aware prioritization under low-data conditions. Benchmark results on unseen literature show that the domain-specialized model outperforms general-purpose models in mechanism-consistent reasoning. Experimental validation in an expert-in-the-loop proof-of-concept study suggests improved additive prioritization across three screening rounds, leading to average device PCEs of 20.13% and 20.87% for the later-round 6-CDQ- and 2-CNA-treated devices, respectively, compared with 19.25% for the control, with a champion PCE of 21.32%. These results provide preliminary evidence that literature-grounded mechanistic descriptors, when coupled with Bayesian optimization and expert feasibility review, can support mechanism-aware additive prioritization in perovskite photovoltaics.

Structure-based drug design has been accelerated by pocket-aware 3D generative models, yet most methods primarily fit the training distribution and may fall short of satisfying multiple properties required in real-world therapeutic drug discovery. Recently, increasing attention has focused on structure-based molecule optimization (SBMO), which targets fine-grained control over multiple specified molecular properties. In this paper, we present DEPPA, a novel SBMO approach building upon Denoising Diffusion Policy Optimization for fine-tuning a pre-trained pocket-aware diffusion model via reinforcement learning. DEPPA enables optimization over multiple properties, including binding affinity, drug-likeness, synthesizability and diversity. We formulate the reverse denoising process of the pretrained pocket-aware diffusion model as a multi-step Markov Decision Process, where the desired properties that serve as reward signals are evaluated on the final generated ligand molecules. DEPPA incorporates a coarse denoising scheduler during the RL fine-tuning to achieve efficient and effective molecule optimization. Experimental results on the CrossDocked2020 benchmark demonstrate that DEPPA outperforms baselines in binding affinity (Vina Score -8.5 kcal/mol), drug-likeness and diversity while exhibiting competitive performance in synthesizability. The source code is available at https://github.com/xy9485/DePPA .

Accurate prediction of molecular properties underpins drug discovery and material design, yet even state-of-the-art models remain vulnerable to localized failure modes that aggregate metrics cannot detect. The places where molecular similarity should be most helpful are also places where standard evaluation can be most misleading. Property cliffs expose this gap: structurally similar molecules can still differ sharply in target property, so models with competitive overall performance may fail in high-risk local neighborhoods. To expose and mitigate this failure mode, CliffSplit, a cliff-aware evaluation protocol that constructs locally supported, cliff-exposed test cases, and CliffLoss, a model-agnostic train-only mitigation mechanism for cliff-sensitive errors, are introduced. Experiments on three QM9 targets and three MoleculeNet tasks across five backbones show that CliffSplit reveals at least 15% higher error in cliff-heavy QM9 regions, while CliffLoss reduces the cliff-to-smooth error gap by up to 30% on Lipophilicity and improves overall MAE by 9.7%. Together, these results turn molecular similarity failure from a descriptive anomaly into a benchmarked evaluation problem for molecular machine learning. The code is available at https://anonymous.4open.science/r/Cliff_Loss.

While Large Language Models (LLMs) have revolutionized scientific text processing, they exhibit a significant capability gap when interpreting chemical reaction diagrams. We identify two fundamental bottlenecks restricting current systems: a Visual Deficit, where generic vision encoders struggle to resolve the strict topological connectivity of dense molecular graphs, and a Semantic Disconnect, where standard linear strings, such as SMILES, fail to effectively activate the model's latent chemical reasoning. To bridge these gaps, we propose the Chemical Visual Activation (ChemVA) framework, which employs a Visual Anchor mechanism to ground functional groups via hybrid-granularity detection, followed by a semantic alignment approach that translates visual features into entity names to maximize knowledge activation in LLMs. We evaluate our approach on OCRD-Bench, a newly constructed dataset featuring dense visual-semantic contexts and comprehensive reaction coverage to evaluate the full spectrum from recognition to reasoning. Extensive experiments on OCRD-Bench demonstrate that ChemVA achieves 92.0% structural recognition accuracy. By bridging visual and semantic bottlenecks, our framework delivers a consistent performance gain of approximately 20 percentage points across 9 diverse LLMs, enabling open-weight models to rival proprietary SOTA systems in complex chemical reasoning tasks.

Diffusion models generate high-dimensional data with remarkable quality, yet how their training efficiently learns the score function, bypassing the curse of dimensionality when data is supported on low-dimensional manifolds, remains theoretically unexplained. We identify a collapse-and-refine mechanism driven by the geometry of the score function itself: at small noise scales, the diverging singularity of the score drives a rapid dimensional collapse of the induced denoising map onto the data manifold projection; at moderate noise scales, training refines the intrinsic density on the learned manifold. We instantiate this principle as Score-induced Latent Diffusion (SiLD), a two-stage framework in which both manifold learning and density estimation emerge from a single denoising score matching objective, replacing the heuristic KL regularization of VAE-based latent diffusion models. We prove that the resulting sample complexity depends on the intrinsic dimension rather than the ambient dimension. Experiments on Stacked MNIST, CelebA variants, and molecular generation benchmarks show that SiLD matches or outperforms VAE-based LDMs in generation quality and consistently improves reconstruction, validating our theoretical predictions.

We introduce a tensor-channel equivariant graph neural network for direct prediction of molecular polarizability tensors. Building on the efficient PaiNN architecture, we augment the hidden representation with explicit symmetric rank-2 tensor channels aligned with the decomposition of polarizability into isotropic and anisotropic components. In contrast to approaches that construct tensor outputs only at readout, our model propagates tensor structure throughout message passing using geometrically motivated tensor bases. This yields a target-aligned architecture for tensor-valued molecular prediction. On optimized QM7-X geometries, the proposed model achieves lower full-tensor and anisotropic error than both a PaiNN-style readout baseline and a dielectric MACE baseline under matched training conditions and at nearly identical parameter count. In this controlled setting, it also outperforms MACE while remaining substantially faster at inference. Ablation studies show that the gain does not arise from increased capacity alone, but from the combination of explicit tensor propagation and a traceless target parameterization matched to the anisotropic part of the polarizability tensor. Among the tensor bases considered, the strongest results are obtained from interactions between learned directional features, indicating that these are particularly effective for modeling molecular polarizability. Rotational equivariance tests further confirm that all compared models are numerically equivariant, so the observed improvements are attributable to better learning of the target tensor itself. Overall, our results show that for structured tensor-valued targets, propagating target-aligned tensor features can outperform both readout-only tensor construction and a more general higher-order equivariant model in the present training setting.

Recent advances in molecular representation integrates molecular topological and visual modalities, opening new avenues for precise Molecular Relational Learning (MRL). Existing MRL methods focus on intra-domain modeling, and their inherent domain-closed effect limits applicability to molecular science, particularly in elucidating cross-domain interaction mechanisms. Consequently, the imperative for Cross-Domain Molecular Relational Learning has become increasingly pressing. Benefiting from structure-activity analysis, we propose the Domain Adversarial Training Network with Structural-Semantic Transfer Discrepancy (DisTrans) to optimize cross-domain adaptive representation for molecular structures and visual images. 1) We employ the gradient reversal strategy based on substructure topological discrepancies between domains to learn the domain dependence of molecular structures. This strategy guides the model to adapt to the structural adjacency patterns in the target domain, generating domain-separable structural representations. 2) We apply the cross-domain representation guidance mechanism to align the functional-group semantic information between the source and target domains, learning cross-domain consistency information. The experimental results in two typical cross-domain strategies demonstrate that DisTrans outperforms 16 baseline methods, maintaining satisfactory performance even under pronounced inter-domain discrepancy.

Masked language modeling (MLM) is the standard objective for training protein language models, typically implemented by randomly masking individual residues at a fixed rate (e.g., 15%). This practice implicitly assumes that all sequence positions contribute equally to representation learning. In downstream fitness prediction tasks, however, protein sequences are governed by three-dimensional structural dependencies and long-range residue contacts that induce strong nonlocal couplings between residues. We introduce Bucket Masking, a structure-aware masking strategy that selects groups of residues based on their proximity in three-dimensional space, preferentially masking structurally coupled regions during training. By conditioning the masking distribution on residue contacts, Bucket Masking shifts the learning objective toward modeling long-range interactions that are critical for protein function. Across four downstream protein fitness prediction tasks, Bucket Masking enables up to a 14% improvement over standard random masking, excelling at predicting higher-order mutational interactions. Through controlled ablations, we show that these improvements arise from mask placement rather than span size, establishing masking as a positional inductive bias.

Hypergraphs model higher-order relations that drive real-world decisions, from drug prescriptions to recommendations. A central structural signal in such data, beyond what pairwise relations can express, is interaction compositionality: whether a higher-order relation is compositional, emergent, or inhibitory with respect to its observed or unobserved sets. In polypharmacy, the regime decides whether a drug should be dropped, kept, or excluded: a compositional drug triple can be safely simplified, an emergent triple requires all drugs jointly, and an inhibitory triple flags a drug that disrupts an existing interaction. However, existing hypergraph learning methods, which merely propagate messages over observed hyperedges, leave this compositional signal unmodeled, allowing dangerous drug combinations to slip through and be misclassified. To this end, we propose the Hypergraph Pattern Machine (HGPM), shifting the paradigm from message passing to learning the compositional pattern of subsets. It tokenizes compositional subsets, organizes them in an inclusion DAG, and trains an inclusion-aware Transformer under masked reconstruction. On ten hypergraph benchmarks, HGPM matches or exceeds state-of-the-art methods. Notably, in a real adverse-event prediction case, HGPM correctly identifies the drug addition that inhibits the side effect among feature-identical candidates, a discrimination existing methods cannot make. The code and data are in https://github.com/KryieZhao/HGPM.git.

Molecules are graphs, but large language models~(LLMs) are usually asked to reason about them through linear strings. The most popular molecular representation, SMILES, compresses atoms, bonds, branches and rings into a compact sequence in which topology is implicit, forcing LLMs to reconstruct molecular structure before performing the requested chemical operation. Here we introduce MoleCode, an LLM-native, training-free, graph-explicit molecular language in which all molecular components are represented as typed entities with persistent identifiers and explicit relations. MoleCode makes molecular topology directly readable, editable and auditable within the language context, allowing an LLM to operate on structure rather than recover it from syntax. Across molecular reasoning, editing, generation and analysis tasks, this representational shift improves frontier LLMs most strongly when structural access is limiting: unfamiliar molecules, topology-sensitive operations, larger structures and repetitive polymers. It also changes how inference is allocated, replacing long reasoning traces devoted to implicit structural reconstruction with shorter, more chemically directed reasoning over explicit atoms and bonds. In molecular optimization, this enables localized, property-aligned edits that preserve structural similarity to the starting compounds. The same Subgraph--Node--Edge grammar extends beyond small molecules to polymers, Markush structures, mechanism-style transformations and interleaved scientific documents, including research articles and patent disclosures in which chemical information is distributed across text and images. These results suggest that the interface between scientific objects and LLMs should not treat structure as something to be decoded from text. When the object of reasoning is relational, the structure itself should be part of the language.

Self-supervised pretraining on molecular graphs has emerged as a promising approach for molecular property prediction, yet most existing methods operate at a single structural granularity and treat bond information as auxiliary edge attributes rather than as an independent semantic layer. In this work, we propose MolCHG, a multi-level self-supervised pretraining framework built upon a novel Compositional Hierarchical Graph that organizes molecular structure into four types of nodes across three semantic levels. By introducing a bond graph that operates in parallel with the atom graph, our architecture elevates bond-level information to independently evolving node representations, enabling fragment nodes to aggregate atom-level and bond-level semantics on an equal footing. We design three level-specific pretraining objectives: an atom-bond cross-view contrastive task that aligns the atom-view and bond-view representations within each fragment, a fragment-level functional group prediction task to inject domain-relevant chemical knowledge, and graph-level structure prediction tasks to encode global molecular topology. Experiments on nine MoleculeNet benchmarks demonstrate that MolCHG achieves the best performance on seven datasets across both classification and regression tasks, remaining competitive with the strongest baselines on the rest. Ablation studies further confirm that the multi-level supervision signals are complementary and that each component contributes to the overall performance.

Proteins perform their biological functions through three-dimensional structures encoded by amino acid sequences, and ligand-binding protein co-design requires models that generate sequence-structure compatible proteins under explicit ligand constraints. Although continuous diffusion and flow-based models support ligand-aware design in coordinate or latent spaces, existing discrete diffusion protein language models mainly operate over sequence or structure tokens without direct small-molecule conditioning. We introduce \textbf{ProtLiD$^2$}, a \textbf{Prot}ein \textbf{L}igand-conditioned \textbf{D}iscrete \textbf{D}iffusion model for protein sequence-structure co-design. ProtLiD$^2$ jointly generates amino-acid sequence and discrete structure tokens while incorporating ligand chemical and geometric information through geometry-aware cross-attention. Trained on over one million ligand-protein complexes, ProtLiD$^2$ extends masked discrete diffusion to ligand-aware functional protein design. We further propose maximum confidence-margin guided ReMask decoding, an inference-time self-correction strategy that retains confident predictions and remasks uncertain tokens. ProtLiD$^2$ improves global fold confidence over Complexa in whole-protein design, increasing TM-score from 0.672 to 0.802 and pLDDT from 64.55 to 73.00. In pocket co-design, ProtLiD$^2$ reduces active-site BB-RMSD from 3.46/3.40Å for FAIR/PocketGen to 1.97Å, and improves ligand-aware pass rates over PocketGen from 14.86% to 59.73% and from 6.08% to 23.49% under stricter docking thresholds. These results support ligand-conditioned discrete diffusion as an effective token-space framework for functional protein co-design. Code will be available at https://github.com/auroua/ProtLiD.

Generative models trained on public databases of protein structures, most of which have been determined by X-ray crystallography, now provide powerful priors for structure prediction. However, they are not readily conditioned on the measurements from a new crystallographic experiment, limiting their use for X-ray structure determination. In crystallography, the measured structure-factor amplitudes do not by themselves determine an electron density map or atomic structure because the associated phases are unobserved and must be inferred. Structure determination therefore remains an inverse problem in which candidate models must be both structurally plausible and consistent with measured diffraction data, often requiring substantial manual refinement by human experts. Emerging methods aim to incorporate experimental information more directly into predictive and refinement workflows. We present CrystalBoltz, a generative framework that casts crystallographic refinement as Bayesian inference over atomic structures and operates directly on structure-factor amplitudes. CrystalBoltz moves from unguided generation with a pre-trained prior over protein structures to experiment-guided posterior sampling, followed by atomic coordinate and B-factor refinement. Across multiple protein crystallography datasets, CrystalBoltz attains lower coordinate RMSD and lower R-factors than the strongest baselines considered, while reducing runtime by a factor of 33 relative to existing experimentally guided refinement.

Building state-of-the-art (SOTA) predictive models for drug discovery requires expensive search over tools, architectures, and training strategies. Current LLM-based agents can find SOTA solutions through extensive trial and error, but they do not retain the experience accumulated along the way and therefore pay the full search cost on every new task. We propose \method (Self-evolving Agent Experience), a framework that accumulates and reuses experience across tasks to build SOTA drug discovery models efficiently. \method maintains a cross-task memory of verified skills, statistical evidence about effective strategies, and a record of recurring errors and their fixes. In some cases, \method transfers a working solution directly without test-time search. In 33 molecular property prediction tasks, \method ranks first among nine SOTA agents in a single-task setting. With memory accumulated from 16 smaller tasks, \method achieves an averaged normalized score of 0.935 on 17 held-out tasks in a cross-task evaluation setting and outperforms all baseline agents by 10-30% in a zero-test-time search regime. In summary, our work shows the advantage of cross-task memory for efficient SOTA model development in drug discovery.

Despite the success of foundation models in language and vision, molecular graph generation still lacks a unified framework for heterogeneous design tasks with reliable controllability. While reinforcement learning (RL) offers a natural post-training mechanism for task-specific optimization, applying it to graph generative models is hindered by the vast atom-wise action spaces and chemically invalid intermediate states. We propose \textbf{Co}ntrollable \textbf{Mole}cular Generative Foundation Models (CoMole), built with a unified motif-aware graph diffusion pipeline. By learning a motif-aware graph space, CoMole transfers pretrained structural priors into controllable generation, where RL optimizes conditional reverse policies over chemically meaningful decisions. We theoretically characterize the bottleneck of atom-level RL and justify motif-aware policy optimization. Across three heterogeneous benchmarks spanning materials and drug discovery, CoMole ranks first in controllability on all nine targets, reduces MAE by up to 48.2% relative to the strongest baselines, and maintains validity above 0.94 without rule-based correction or post-hoc filtering. We further show that CoMole transfers controllability to unseen properties by optimizing only task embeddings with the generator frozen, achieving performance competitive with strong task-specific baselines.

Large language models (LLMs) still struggle with the rigorous reasoning demands of hard competitive programming. While recent multi-agent frameworks attempt to bridge this reliability gap, they remain fundamentally stateless: they rely on static retrieval and discard the valuable problem-solving and debugging experience gained from previous tasks. To address this, we present Solvita, an agentic evolution framework that enables continuous learning without requiring weight updates to the underlying LLM. Solvita reorganizes problem-solving into a closed-loop system of strategy selection, program synthesis, certified supervision, and targeted hacking, executed by four specialized agents: Planner, Solver, Oracle, and Hacker. Crucially, each agent is paired with a trainable, graph-structured knowledge network. As the system operates, outcome signals, such as pass/fail verdicts, test certification quality, and adversarial vulnerabilities discovered by the Hacker, are recast as reinforcement learning updates to these network weights. This allows the agents to dynamically route future queries based on past successes and failures, effectively accumulating transferable reasoning experience over time. Evaluated across CodeContests, APPS, AetherCode, and live Codeforces rounds, Solvita establishes a new state-of-the-art among code-generation agents, outperforming existing multi-agent pipelines and nearly doubling the accuracy of single-pass baselines.

De novo crystal generation, a central task in materials discovery, aims to generate crystals that are simultaneously valid, stable, unique, and novel. Existing methods mainly rely on black-box stochastic sampling, providing limited control over how generated structures move beyond the observed distribution. In this paper, we introduce a concept-based compositional framework for crystal generation. We train a vector-quantized variational autoencoder to automatically discover a shared set of reusable crystal concepts, which serve as building blocks for guided generation. These learned concepts naturally exhibit interpretability from both local atomic environments and global symmetry patterns, and generalize to crystals from different distributions. By recombining such concepts, our framework enables controllable exploration of novel crystals beyond the training distribution, rather than relying solely on unconstrained random sampling. To further improve composition efficiency, we introduce a composition generator and iteratively refine it using high-quality samples generated by the model itself. The resulting concept compositions are then used to condition downstream crystal generation. Numerical experiments on MP-20 and Alex-MP-20 show that compositing concepts separately increase base model up to 53.2% and 51.7% on V.S.U.N metric, with particular gains in novelty.

De novo crystal generation seeks to discover materials that are not merely realistic, but also stable and novel. However, most existing generative models are trained to maximize the likelihood of observed crystals, which encourages samples to stay close to known materials yet not necessarily align with the criteria that matter in discovery. Our empirical analysis shows that current crystal generative models exhibit a clear conflict between stability and novelty: samples near the observed distribution tend to retain stability but offer limited novelty, whereas samples farther from it often lose stability rapidly. This suggests that the useful region for discovering crystals that are both stable and novel is extremely narrow. To move beyond this limitation, we introduce Crys-JEPA, a joint embedding predictive architecture for crystals that learns an energy-aware latent space preserving formation-energy differences. In this space, stability assessment can be reformulated as an embedding-based comparison against accessible training crystals, reducing the reliance on expensive energy evaluation and task-specific external references. Building on Crys-JEPA, we further develop a screening-and-refinement pipeline that identifies promising generated crystals and reintroduces them to refine the generative model. On MP-20 and Alex-MP-20 datasets, we achieve improvements over baselines up to 53.8% and 72.7% on V.S.U.N. metric, respectively.

Implicit solvent models are widely used to decrease the number of solvent degrees of freedom and enable the calculation of solvation energetics without water molecules. However, its accuracy often falls short compared to explicit models. Recent advancements in neural potentials have shown promise in drug discovery, but transferability remains a persistent challenge. Here, we introduce the Protein Hydration Neural Network (PHNN), an implicit solvent model that extends analytical continuum solvation by learning transferable corrections to model parameters instead of applying post hoc adjustments to final energies. The model is explicitly designed to maximize data efficiency by leveraging physical priors embedded in the data. We demonstrate that PHNN improves accuracy relative to traditional analytical methods and maintains predictive accuracy on out-of-domain protein systems.

When reliable target structures are unavailable at scale or phenotypes arise from dysregulated pathways, transcriptomic perturbations provide a system-level functional readout for drug action. In this work, we formalize \emph{Transcriptome-based Drug Design (TBDD)} as a generative inverse problem: designing drug molecules conditioned on desired transcriptomic state transitions. We analyze the inherently ill-posed nature of this task, which is further complicated by the profound domain gap between biology and chemistry and by the sparsity of transcriptomic signals. To address these challenges, we propose \textbf{\themodel{}} (A \textbf{C}ell\textbf{U}lar \textbf{R}esponse \textbf{E}ngine), a multi-resolution transcriptome-guided diffusion framework. \themodel{} features a specialized \textbf{Transcriptome Perturbation Functional Feature Extractor (TFE)} that (1) distills function-oriented perturbation embeddings from pre/post states, (2) aligns these signatures to dual chemical views to bridge the cross-modal gap, and (3) performs heterogeneity-aware aggregation to extract robust state-specific signals from noisy transcriptomic data. Extensive evaluations on both standard benchmarks and rigorous out-of-distribution protocols demonstrate that \themodel{} consistently outperforms strong baselines in structural quality and functional consistency. Furthermore, we validate its practical utility via a zero-shot gene-inhibitor design task, highlighting the potential of phenotype-driven generative discovery.

Generative modeling has emerged as a promising approach for crystal structure discovery. However, existing LLM-based generative models struggle with low-level atomic precision, while diffusion-based methods fall short in integrating high-level scientific knowledge. As a result, generated structures are often invalid, unstable, or do not possess desirable properties. To address this gap, we propose CrystalReasoner (CrysReas), an end-to-end LLM framework that generates crystal structures from natural language instructions through reasoning and alignment. CrysReas introduces physical priors as thinking tokens, which include crystallographic symmetry, local coordination environments and predicted physical properties before generating atomic coordinates. This bridges the gap between natural language and 3D structures. CrysReas then employs reinforcement learning (RL) with a multi-objective, dense reward function to align generation with physical validity, chemical consistency, and thermodynamic stability. For property-conditioned tasks, we design task-specific reward functions and train specialized models for discrete constraints (e.g., space group) and continuous properties (e.g., elasticity, thermal expansion). Empirical results demonstrate that compared to prior works and baselines without thinking traces or RL, CrysReas obtains better performance on diverse metrics, triples S.U.N. ratio, and achieves better performance for property conditioned generation. CrysReas also exhibits adaptive reasoning, increasing reasoning lengths as the number of atoms increases. Our work demonstrates the potential of leveraging thinking traces and RL for generating valid, stable, and property-conditioned crystal structures.

Drug-drug interaction (DDI) prediction is a critical task in computational biomedicine, as adverse interactions between co-administered drugs can cause severe side effects and clinical risks. A key challenge is unseen-drug generalization, where interactions must be predicted for drugs not observed during training. Although multimodal DDI models exploit diverse drug-related information, their fusion mechanisms are often tied to specific prediction architectures, limiting their reuse across models. To address this, we propose AIM-DDI, an architecture-independent multimodal integration module that represents heterogeneous modality information as tokens in a shared latent space. By modeling dependencies across modality tokens through a unified fusion module, AIM-DDI enables model-agnostic integration of structural, chemical, and semantic drug signals across different DDI prediction architectures. Extensive evaluations across diverse DDI models and DrugBank-based settings show that AIM-DDI consistently improves prediction performance, with the strongest gains under the most challenging both-unseen setting where neither drug in a test pair is observed during training. These results suggest that treating multimodal integration as a reusable module, rather than a model-specific fusion component, is an effective strategy for robust unseen-drug DDI prediction.

Scientific machine learning reports predictive performance. It does not report whether the same prediction would survive a different draw of training data. Across $9$ chemistry benchmarks, two classifiers trained on independent bootstraps of the same training set agree on aggregate accuracy to within $1.3\text{--}4.2$ percentage points but disagree on the class label of $8.0\text{--}21.8\%$ of test molecules. We call this gap \emph{cross-sample prediction churn}. The standard parameter-side techniques (deep ensembles, MC dropout, stochastic weight averaging) do not reduce this gap; two data-side methods do. The first is $K$-bootstrap bagging, which cuts the rate $40\text{--}54\%$ on every dataset at no accuracy cost ($K{\times}$-ERM compute). The second is \emph{twin-bootstrap}, our proposal: two networks trained jointly on independent bootstraps with a sym-KL consistency loss between their predictions, which at matched $2{\times}$-ERM compute reduces churn a further median $45\%$ beyond bagging-$K{=}2$. Cross-sample prediction churn deserves a column alongside predictive performance in scientific-ML benchmark reports, because without it the parameter-side and data-side methods are indistinguishable on the metric they actually differ on.

Protein structure tokenizers (PSTs) are workhorses in protein language modeling, function prediction, and evolutionary analysis. However, existing PSTs only capture local geometry of static structures, and miss the correlated motions and alternative conformational states revealed by protein ensembles. Here we introduce Ensembits, the first tokenizer of protein conformational ensembles. Ensembits address challenges inherent to tokenizing dynamics: deriving informative geometric descriptors across conformations, permutation-invariance encoding of variable-size ensembles, and conquering sparsity in dynamics data. Trained with a Residual VQ-VAE using a frame distillation objective on a large molecular dynamics corpus, Ensembits outperforms all related methods on RMSF prediction, and is the strongest standalone structural tokenizer on an token-conditioned ANOVA test on per-residue motion amplitude. Ensembits further matches or exceeds static tokenizers on EC, GO, binding site/affinity prediction, and zero-shot mutation-effect prediction despite using far less pretraining data. Notably, the distillation objective enables Ensembits to predict dynamics token from one single predicted structure, which alleviates dynamics data sparsity. As the field moves from static structure prediction toward ensemble generation, Ensembits offer the discrete vocabulary needed to bring dynamics into protein language modeling and design.

Robust prediction of molecular properties under extreme out-of-distribution (OOD) scenarios is a pivotal bottleneck in AI-driven drug discovery. Current scaffold-splitting protocols fail to obstruct microscopic semantic overlap, predisposing models to shortcut learning and overestimating their true extrapolation capability; meanwhile, conventional domain adaptation paradigms suffer under extreme structural shifts, as blindly aligning heterogeneous source libraries injects topological noise and triggers negative transfer. To address these two challenges, scaffold-cluster out-of-distribution performance evaluation benchmark (SCOPE-BENCH), a benchmark built on cluster-level partitioning in an explicit physicochemical descriptor space, is proposed alongside policy optimization for multi-source adaptation (POMA), a framework that formulates knowledge transfer as a retrieve-compose-adapt pipeline: labeled source scaffolds structurally close to the unlabeled target are first identified as proxy targets; a reinforcement learning policy then adaptively selects the optimal source subset from an exponentially large candidate pool; and dual-scale domain adaptation is finally performed at macroscopic topological and microscopic pharmacophore scales. Evaluations show that prediction errors of state-of-the-art 3D molecular models surge by up to 8.0x on SCOPE-BENCH with a mean of 5.9x, while POMA achieves up to an 11.2% reduction in mean absolute error with an average relative improvement of 6.2% across diverse backbone architectures. Code is available at https://anonymous.4open.science/r/Molecular-OOD-Code-73F6.

Modern SMILES-based chemical language models obtain strong MoleculeNet performance by treating SMILES as generic text and compensating with multi-million-molecule self-supervised pretraining. We ask: when a domain carries structural priors as rich as chemistry's, does it warrant a domain-native transformer rather than a generic one rescued by scale? We answer affirmatively with \textbf{GM-Net} (Geometric Measure Network), a transformer family in which every module is replaced by a sphere-native counterpart, and instantiate it as \textbf{Chem-GMNet}. Three blocks follow: SH-Embedding (tokens as learnable directions on $S^{k-1}$ lifted through a Gegenbauer feature map); DualSKA (a per-head fusion of a linear-time gated Sphere-Flow recurrence whose persistent state we prove is the truncated multipole expansion of the input distribution, and a softmax Sphere-Kernel branch over the same Schoenberg-valid kernel); and SH-FFN (sphere projection $\to$ Gegenbauer lift $\to$ moment readout). On canonical DeepChem scaffold splits, against same-shape ChemBERTa-2 baselines under the chemberta3-faithful protocol: (i) random-initialised, Chem-GMNet wins on 7 of 10 MoleculeNet endpoints at $\sim\!35\%$ fewer parameters; (ii) pretrained on the same 10M-SMILES ZINC corpus as ChemBERTa-2 MLM-10M, it matches or beats the public release on 6 of 8 shared endpoints (5/7 excluding a known ClinTox release anomaly). A $(k,L)$ ablation shows that increasing the sphere dimension from $k\!=\!8$ to $k\!=\!10$ at fixed $L\!=\!3$ lowers ESOL RMSE to $0.938$ at scratch, beating pretrained ChemBERTa-2 MLM-10M on this endpoint without any pretraining at all.

Molecular structure elucidation from tandem mass spectra (MS/MS) remains challenging, particularly for de novo generation beyond database coverage. A common approach decomposes the task into spectrum-to-fingerprint prediction followed by fingerprint-to-structure decoding, enabling the use of large-scale molecular corpora. However, at deployment, the decoder relies on predicted rather than oracle fingerprints, introducing structured errors that propagate into generation. This results in a fundamental condition mismatch, where models trained on clean inputs must operate under noisy, biased predictions, especially for long-tail substructures. We present CoRe-Gen that explicitly addresses this gap. CoRe-Gen improves the intermediate condition via synthetic-spectrum pretraining of the encoder, matches deployment-time noise through frequency-aware fingerprint corruption during decoder training, and mitigates residual errors using structure-aware autoregressive decoding with compositional SELFIES representations, auxiliary structural supervision, and lightweight chemical constraints. Experiments on standard benchmarks show that CoRe-Gen establishes a new state of the art on NPLIB1, achieving 19.54% Top-1 and 29.92% Top-10 exact-match accuracy, while remaining competitive on the more challenging MassSpecGym benchmark. Importantly, CoRe-Gen preserves the efficiency advantages of autoregressive decoding, providing a practical and scalable solution for robust spectrum-to-structure generation under realistic conditions.

Drug development and pharmacovigilance are frequently bottlenecked by legacy clinical reporting pipelines. These monolithic systems encode regulatory-grade logic but resist AI integration by producing opaque output with no machine-readable intermediate layer. Existing modernization approaches force a choice between full rewrites and incremental refactoring that preserves structural barriers. We present a non-destructive methodological framework achieving AI-driven pharmacoinformatics readiness without altering legacy source code. A metadata layer--comprising a bridge map, a typed Intermediate Representation (IR), and an orchestrator--wraps existing components and re-exposes their outputs as structured data consumable by LLMs. It enables optional incremental consolidation, replacing selected legacy components with metadata-configured core routines while the remainder operates unchanged. Validated on a 558-component SAS reporting library (373,000 lines of code), the framework demonstrated immediate AI-readiness under coexistence mode, yielding machine-readable output. Where consolidation was elected, the modernized core achieved a 92% reduction in proprietary code. Parity validation on 14 report types from a Phase III study achieved cell-level parity of 80% or above on 11 reports (mean 82.7%, best 99.2%). A benchmark using CDISC CDISCPilot01 data achieved 100% parity across 5 reports. LLM experiments confirmed the IR enables automated pharmacovigilance, table summarization, and trial configuration generation. The framework offers a regulation-aware path to AI-integrated clinical reporting, accelerating drug development without interrupting regulatory submissions.