Vast Chemical Space

Structure-property relationships are foundational to biology, chemistry and materials science, where function, reactivity and physical response emerge from spatial, chemical and periodic organization. Mechanistically explaining these relationships requires interpreting structural evidence through scientific principles and physical constraints, from stereochemistry and bonding to symmetry, energetics and periodic order. However, applying artificial intelligence to this process presents a joint challenge of representation and reasoning: models must preserve domain-native structural information while showing how specific evidence supports predictions under these constraints. Here we introduce SciReasoner, a multimodal scientific foundation model for native structural reasoning across proteins, small molecules and inorganic crystals. SciReasoner discretizes coordinates, topologies and periodic connectivities into a unified structure-aware vocabulary, treating structural tokens as addressable evidence units during reasoning. In homology-controlled Gene Ontology prediction, SciReasoner improves Cellular Component annotation for low-homology and orphan-like proteins, increasing $F_{\max}$ from 0.42 to 0.55. In chemistry, it raises single-step retrosynthesis accuracy from 0.63 to 0.72 while generating fragment-level disconnection and precursor-verification traces. In materials science, its representations separate elemental and compound phases and resolve high- and low-band-gap regimes. Across 86 benchmarks, SciReasoner achieves state-of-the-art performance on 67 tasks. Double-blind expert evaluation rates its reasoning traces as preferred or at least comparable to those of a frontier large language model in 98% of cases. By making structure an inspectable substrate for reasoning under scientific constraints, SciReasoner connects accurate prediction with interpretable scientific inference.

Large language models (LLMs) demonstrate remarkable reasoning capabilities, yet their stateless architecture fundamentally limits deployment in long-horizon research workflows requiring multi-session continuity and quantitative rigor. Here we present Ensemble QSP, a multi-agent framework featuring a three-layer hierarchical memory architecture that keeps injected context bounded and constant in project duration (mid-term project state: median 301 tokens, max 4,050, across 104 runs) by capping each state category and evicting completed work, enabling continuous autonomous operation without context degradation. The system orchestrates five specialist worker agents under domain-expert principal investigators, enforcing physical constraints through physics-based checklists and structured-domain knowledge. Comprehensive benchmarking demonstrates robust autonomous pharmacokinetic-pharmacodynamic model selection without human intervention, consistent result quality across both lower-cost and frontier LLMs, improved PK parameter recovery relative to single-agent baselines, and stable model selection across linguistically diverse prompts of the same task. Feature-level ablation across physiologically based pharmacokinetic (PBPK) models spanning a broad complexity range shows that PI-agent oversight improves debugging efficiency while preserving final accuracy across conditions. The architecture is structurally domain-agnostic, adding a new scientific domain requires only a new PI agent configuration.

Background: Graph neural networks improve computational prediction of polypharmacy side effects, but standard binary cross-entropy training allocates equal capacity to well-classified and difficult examples, potentially missing clinically significant interactions. We evaluated whether an asymmetric focal objective could improve multi-relational drug-drug interaction (DDI) prediction by emphasizing difficult positive interactions. Methods: ClinicalFocal loss was integrated into a relation-aware graph convolutional network using molecular fingerprints, physicochemical descriptors, and learned embeddings. The model was evaluated on TWOSIDES using five-fold cross-validation with identical experimental conditions (architecture, features, data partitions, hyperparameters, and random seeds) for ClinicalFocal loss and binary cross-entropy baseline. Results: ClinicalFocal loss increased accuracy from 0.699 to 0.892 (+19.3 percentage points) and F1 score from 0.700 to 0.894 (+19.4 percentage points). AUROC increased from 0.766 to 0.914, and AUCPR increased from 0.714 to 0.860. The false-negative rate decreased from 29.8% to 9.1%, while specificity increased from 69.6% to 87.5%. Overall classification error decreased from 30.1% to 10.8%, corresponding to a 64.1% relative reduction. Improvements were consistent across all five folds. Conclusions: Asymmetric focal optimization improved classification and ranking performance while achieving 90.9% recall for observed interaction triples, without modifying the underlying architecture. Loss-function design is a direct, tunable lever for improving graph-based DDI prediction.

Accurate ranking of antibody candidates according to their binding affinity is essential for therapeutic antibody discovery. However, existing methods treat affinity comparisons independently and ignore the contextual information encoded in other labeled comparisons, limiting their ability to capture antigen-specific binding landscapes. For many target antigens, a small number of experimentally characterized affinity comparisons are often available. An important question is whether the model can exploit these existing comparisons to infer antigen-specific ranking patterns that facilitate subsequent affinity ranking. This form of learning from labeled demonstrations closely resembles the paradigm of In-Context Learning, motivating us to revisit antibody affinity ranking from an ICL perspective. To this end, we propose AbICL, an ICL framework for antigen-specific antibody affinity ranking. AbICL combines a pretrained structural encoder with a context ranking head and is trained with an episodic meta-training strategy that enables the model to leverage support demonstrations for test-time adaptation without gradient updates. Experiments on the AbRank benchmark demonstrate that AbICL consistently outperforms existing ranking baselines across almost all data splits and evaluation benchmarks. Further analysis shows that the value of contextual demonstrations depends on how well they match the target inference task, and becomes increasingly pronounced under distribution shift and fine-grained affinity discrimination. These findings highlight the potential of ICL as an effective paradigm for antigen-specific antibody affinity ranking, particularly in challenging settings where a single global ranking function is insufficient.

Conformal prediction is being adopted in drug discovery to put an honest number on model reliability: pick an error rate alpha, and the method returns prediction sets containing the true label with probability at least 1 - alpha. We show this guarantee can be dangerous on imbalanced datasets. Across four datasets, standard (marginal) conformal prediction hits its global 90% coverage target while leaving the minority class badly exposed: realized minority coverage falls to 64.8% on blood-brain-barrier penetration and to 4.2% on clinical-trial toxicity, where the rare class is nearly abandoned. The failure is not tied to one model: a random forest, a graph network, and a frozen chemical language model all reproduce it (p < 0.001 in every case), with severity tracking baseline calibration on rare labels rather than architecture. A conservation identity explains the effect: the minority's shortfall equals the majority's surplus amplified by the imbalance ratio, predicting the measured gap to within one point and ordering severity across datasets. The failure survives realistic scaffold splits and a second conformal score, while aggregate accuracy and overall coverage stay reassuringly high, which is exactly why it is easy to miss. Class-conditional (Mondrian) conformal prediction closes the gap on every dataset, restoring minority coverage to target for a modest increase in prediction-set size. We localize the failures to generic molecular scaffolds - plain benzene and pyridine cores occurring in both classes - propose a one-number diagnostic, and show with a cost model that abstaining on affected compounds flips a screening campaign from net-negative to net-positive utility. Our contribution is demonstrating on real chemistry how severe and invisible this known conformal-theory gap becomes under imbalance, and laying out a practical protocol restoring per-class reliability.

Untargeted tandem mass spectrometry (MS/MS) detects thousands of small molecules per biological sample, yet most go unidentified because they are absent from spectral libraries. These uncharacterized metabolites and natural products are precisely the compounds that matter for drug discovery, biomarker research, and exposomics. Computational de novo structure elucidation could close this gap, but almost all state-of-the-art methods assume the ground-truth molecular formula is known, an oracle that does not exist for genuinely novel compounds and is itself predicted with substantial error. We present MARLIN, a de novo method that elucidates structures directly from a spectrum with no molecular formula at any stage. A self-supervised encoder predicts a molecular fingerprint from the raw peaks, and a block-diffusion language model generates candidate structures conditioned only on the fingerprint and the instrument-measured precursor mass. A provably safe mass-shell constraint keeps every candidate consistent with the measured mass without fixing the atom inventory, and candidates are accepted by exact parts-per-million mass agreement. A symmetric noise objective absorbs encoder error, and a candidate-diversity mechanism keeps the candidates from collapsing to a single structure. On the NPLIB1 benchmark, MARLIN is the strongest method evaluated without a ground-truth formula across exact-match accuracy, structural distance, and fingerprint similarity, and it recovers the correct molecular formula as a byproduct about as often as a dedicated predictor without ever using one. MARLIN enables reliable de novo structure elucidation in the realistic discovery regime where the molecular formula is unavailable.

Synthesis planning aiming to find pathways of reactions for a target molecule is one of the most important and challenging tasks in drug discovery. Recent progress has produced both specialized deep-learning retrosynthesis systems and general-purpose large language models, but objective comparison remains difficult due to the lack of flexible, chemically interpretable benchmarking protocols. In the current study, we are introducing the URSA (Utilitarian RetroSynthesis Assessment) evaluation framework that provides the opportunity to benchmark the synthetic routes not only from a formal perspective, such as convergence to commercially available starting materials, but also from a chemical plausibility perspective, mimicking the way expert chemists evaluate the reactions and routes. The study covers a comprehensive evaluation of both conventional end-to-end retrosynthesis solutions and LLMs for the synthesis planning task on a set of novel, diverse target molecules with undisclosed synthetic routes, which represent realistic tasks in the daily drug design routine. We find that while LLMs can support high-level strategic planning, they currently underperform specialized retrosynthesis models in reliably solving synthesis planning tasks.

Accurately modeling biomolecular interactions is a central bottleneck in biology and therapeutic discovery. Here, we introduce Open Drug Discovery Engine (OpenDDE), an open-source, all-atom biomolecular foundation model that uses co-folding as the entry point to a scalable AI-driven drug discovery engine. Rather than treating structure prediction as an isolated endpoint, OpenDDE is designed as a shared structural reasoning layer for modeling sequence-structure-function relationships across biomolecular complexes, enabling complex structure prediction today while providing a foundation for de novo design, affinity estimation, structure-conditioned optimization, and more. OpenDDE integrates advances in all-atom architecture, atomic latent reasoning, inference optimization, and large-scale data processing to achieve IsoDDE-level co-folding accuracy within a reproducible and openly accessible framework. We also identify two scaling-law directions for co-folding models, revealing practical routes for continued improvement through data, model, inference, and training scaling. By releasing training code, inference pipelines, checkpoints, and benchmarks, OpenDDE aims to democratize access to frontier biomolecular intelligence, accelerate global collaboration, and lay an open foundation for next-generation drug discovery systems that can move from predicting molecular structures toward designing, scoring, and optimizing therapeutic candidates for human health.

We present AquaGen, the first all-atom, explicit solvent, periodic-boundary-condition-aware generative model that produces molecular configurations from the Boltzmann distribution at a fraction of the cost of molecular dynamics (MD). This is in contrast with existing generative models that remove degrees of freedom by operating on coarse-grained, vacuum, or implicit solvent systems. Operating at this resolution allows for post-processing through force field energy evaluations and MD simulations, and enables the prediction of relevant properties in a gray-box manner (as ensemble averages of potential energy evaluations over generated samples). We demonstrate the utility of this paradigm on absolute hydration free energy (AHFE), producing estimates 4-10x faster and with comparable accuracy to standard GPU-based MD. By generating uncorrelated samples from alchemical Boltzmann distributions, we create more accurate, interpretable, and refinable ensemble predictions with calibrated uncertainty estimates, unlike regression methods which are entirely black-box predictors. Our approach also yields predictable benefits from increasing train- and test-time compute, realized by scaling model size and generating more samples, respectively. We believe that this approach demonstrates the utility of high-resolution ensemble generation for free energy estimation, with future potential to replace MD in tasks such as the prediction of lipophilicity, membrane permeability, or absolute binding free energy (ABFE) -- whose grounding and interpretability may be critical for the development of new drugs and materials.

Many all-atom generative protein models can in principle design large multimeric complexes by jointly modelling all chains, but their quadratic token- and atom-pair representations quickly exceed single-GPU memory as the number of chains and residues modelled grows. We introduce Design-CP, two context-parallel (CP) inference strategies for RFdiffusion 3 (1D row-sharding and 2D grid sharding with ring attention) that distribute the quadratic activations across a multi-GPU mesh while preserving pretrained weights. We characterise their scaling when sampling icosahedral assemblies, showing that the maximum feasible asymmetric subunit (ASU) size grows with the expected square-root trend in GPU count and that 2D sharding achieves better wall-clock scaling. Moreover, we show how strong point-group symmetry constraints make CP usable out of the box for end-to-end, all-atom design of icosahedral nanoparticles, yielding favourable in silico structural and interface metrics. Finally, we demonstrate octahedral nanoparticle design on a small cluster of workstation-grade 16GB GPUs, illustrating how Design-CP can be a practical path towards democratising large-assembly protein design.

Recent advances in molecular large language models have led to strong performance on molecular understanding and generation tasks, yet these gains often come without reliable structural grounding. In particular, existing approaches conflict with the chemistry principle that structure determines function: despite their downstream success, current molecular LLMs perform poorly on basic structure recognition, suggesting that they fail to capture molecular graphs from canonical SMILES. To remedy this, we propose MolBasic, a structure-first framework that strengthens structural comprehension via SMILES-Graph translation. MolBasic is built around a multi-level structure perception benchmark, where bidirectional SMILES-Graph conversion serves as the core task to align sequential and topological representations. On top of this foundation, we employ a progressive learning scheme with a standardized Chain-of-Thought (CoT) to steer models from structure acquisition toward higher-level molecular reasoning. Experiments show that MolBasic substantially improves structural understanding and yields robust gains on downstream tasks, including property prediction and objective optimization, supporting our structure-first paradigm.

We propose PRECEDE, a precedent-guided co-scientist for side-effect-aware drug redesign that revises a parent compound to mitigate a specified side effect while preserving therapeutic function. Rather than isolated molecular generation, PRECEDE frames redesign as evidence-grounded reasoning over drug--side-effect associations, biomedical knowledge graphs, and precedents of safety-driven optimization, coordinated by an LLM orchestrator with explicit policies and human-review checkpoints. We position PRECEDE as a human-supervised AI-for-science workflow in which hypotheses remain auditable, falsifiable, and bounded by prior pharmacology.

Cold-start drug-drug interaction (DDI) prediction for new drugs is critical for minimizing unexpected adverse drug reactions. The key challenge is to capture similarity between new and known drugs. However, such similarity is closely associated with complex relationships and mechanisms among drugs, enzymes, transporters, molecular structures, and other biomedical entities. Existing methods have three limitations in capturing such similarity: (1) only partial relationships and mechanisms are considered, which overlooks cross-modal information and yields incomplete or biased similarity modeling; (2) similarity computation between new and known drugs is conducted separately across modalities and performed offline for cold-start DDI prediction, leading to misalignment between similarity computation and DDI prediction; and (3) existing interpretability analyses are typically single-modality and focus primarily on key determinants of the perpetrator drug, while the underlying causes of susceptibility for the victim drug are seldom investigated. To address these issues, this paper proposes a novel Cross-Modal-Fused End-to-End Learning Network (CMF-ELN) with three components. First, diverse multimodal information is leveraged to construct four types of drug-centered knowledge graphs, enabling comprehensive similarity modeling under reconstruction-based supervision. Second, a four-channel graph autoencoder is designed to fuse cross-modal similarity within an end-to-end learning framework. Finally, a two-stage interpretability scheme is devised to precisely localize key factors for both perpetrator and victim drugs. Extensive experiments on two real datasets demonstrate that CMF-ELN achieves significantly higher prediction accuracy and more comprehensive interpretability of mechanisms than its peers.

We study how to recover candidate circadian-clock regulators of pituitary hormone genes that are important for women's health but do not show a clear 24-hour rhythm in bulk tissue, aiming to nominate clock-linked regulatory targets that could inform future chronopharmacologic and chronotherapeutic strategies. We propose \textbf{rwMagLap}, which builds a graph on rhythmic backbone genes. For each edge, we combine 24-hour fit quality with peak-time phase, represented as a complex unit-circle value, yielding a Hermitian adjacency matrix and a magnetic Laplacian. We insert arrhythmic hormone genes, treated as anchors, by a reliability-weighted nearest-neighbor projection. The projected anchor-neighbor weights are pooled into a soft teleport distribution, and complex personalized PageRank then ranks rhythmic backbone genes by the magnitude of their PageRank scores. In pituitary data, we find that all 11 women's-health anchors are arrhythmic. Even so, we find that the top-50 list is $7.95\times$ enriched for the 13-gene KEGG circadian set (7 of the 8 set genes in the 454-gene backbone; corrected Benjamini-Hochberg (BH) $p_{\mathrm{BH}}=4\times10^{-6}$) and $4.54\times$ enriched for the 111-gene Reactome set (8 of 16 genes; $p_{\mathrm{BH}}=1.6\times10^{-4}$), while a phase-blind real-valued baseline recovers none. We recover candidates through reliability weighting and phase-aware seeding rather than through magnetic propagation. The magnetic phase adds a different capability: it represents temporal order. On pituitary backbone, the magnetic embedding recovers measured peak-time order of connected pituitary genes with accuracy $0.971$, while $q{=}0$, i.e., no magnetic charge, is at chance.

Molecular optimization often starts from a pretrained generative model that captures a broad prior over valid molecular structures. At test time, however, the goal is not to sample from this prior, but to use a limited oracle budget to shift generation toward task-specific high-reward molecules. We study this adaptation problem for discrete diffusion models. Each online round couples several choices. The loop must decide which candidates to evaluate, how rewards become model updates, which feedback to reuse, and how far to move beyond the pretrained prior. These choices have mostly been studied in isolation, leaving open whether they complement one another, become redundant, or interfere inside a full online adaptation loop. We conduct controlled studies across six small-molecule binding-affinity tasks and three protein-fitness tasks. We find that acquisition, reward shaping, and model debiasing provide complementary routes to higher reward, especially for small molecules. Replay further stabilizes learning, while validity penalties keep small-molecule exploration on the valid molecular manifold. Together, these findings point to a practical recipe for feedback-efficient molecular optimization: online fine-tuning with acquisition, reward shaping, debiasing, replay, and validity control. This recipe outperforms offline fine-tuning and inference-time search baselines under matched oracle-call budgets and GPU-hour accounting. The gains are largest when high-reward candidates require larger shifts from the pretrained prior.

Molecular docking predicts how a small molecule binds to a protein and is a key bottleneck in drug discovery. Classical scoring functions sum empirical pairwise contacts, blind to quantum-mechanical effects like orbital charge transfer that govern binding specificity. We introduce Q-Score, encoding GNN-predicted orbital donor-acceptor energies into a weighted graph and scoring binding by solving a maximum-weight vertex clique problem via Digitized-Counterdiabatic QAOA. Each interaction anchor maps to one qubit and compatibility constraints become edges. Across 11 protein targets, DC-QAOA recovers the exact optimum on 8 at 10 qubits. On 1000 AI-generated molecules, Q-Score is orthogonal to classical scoring with Spearman rho of 0.05, driven by orbital quality with rho of 0.90, and free of molecular-weight bias, enriching for strong orbital interactions at twice the random rate. DC-QAOA achieves a mean approximation ratio of 0.94 with 52 percent exact. Execution of 1000 circuits on IBM Eagle confirms 6-qubit solvability on NISQ hardware.

Aqueous solubility is a key property in early-stage drug discovery, but most predictive models merge physicochemical descriptors and molecular graph information into a single representation, obscuring whether a prediction is driven by global chemistry, molecular structure, or both. We present an additive deep-learning framework that keeps these two sources of information separate throughout training: physicochemical descriptors are encoded by a multilayer perceptron (the chemical branch) and molecular graph topology by a graph neural network (the structural branch), with the two outputs combined only at the prediction stage through an additive model with an optional multiplicative interaction. This design provides a direct decomposition of chemical and structural components that can be examined separately after training. Furthermore, pretraining on the larger AqSolDB dataset and fine-tuning on the smaller BigSolDB2 dataset substantially improve accuracy and reduce run-to-run variations, indicating generalizability of the learned features from the data-rich settings. We further interpret the fitted model using best linear projections of the branch outputs, molecule-level embedding summaries across solubility classes, and atom-level GNNExplainer masks aggregated over functional groups. These analyses show that the chemical branch aligns with familiar physicochemical descriptors, while the structural branch captures graph-topological and functional-group patterns associated with solubility. Across both datasets, the framework attains competitive predictive performance while making the distinct roles of chemical and structural information more transparent.

Chemical language models (CLMs) are trained with linearized representations such as SMILES, yet it remains unclear which chemically meaningful substructures they encode. To foster a better understanding of CLMs, we conduct a systematic study and probe for 78 molecular substructures across eight pre-trained and six randomly initialized models. We furthermore study how fine-tuning on chemical downstream tasks affects the learned representations of molecular substructures. Our results show that pre-training generally improves molecular structure awareness of CLMs, particularly in the upper layers. Moreover, randomly initialized models already encode ring structures well in the first layer. Our analysis on two chemical downstream tasks further reveals that, interestingly, fine-tuning affects task-relevant molecular substructures more than others, indicating that the changes in the representations follow chemical theory.

Using molecular large language models (LLMs) as a unified framework for understanding molecular structures and functions is emerging as a new trend in tasks such as molecular design and drug discovery. However, these models struggle to fully capture the visual representation of molecular structures, limiting their potential. While existing molecular vision-language models (VLMs) show promise, they still face challenges in structural alignment and lack the necessary topological modeling for accurate molecular understanding. To address this, we propose MolSight, a graph-aware vision-language model framework designed to enhance the understanding of molecular images by VLMs. MolSight integrates a Molecular Topology Module to inject chemical-bond adjacency information into vision tokens, and a Molecular Grounding Module to align visual features with chemical symbolic semantics. Our experiments demonstrate that MolSight significantly outperforms existing VLMs, molecular LLMs, and specialized tools across multiple chemical visual understanding tasks, achieving a new level of molecular image reasoning.

Accurate protein-protein interaction (PPI) prediction is central to functional genomics, disease mechanism discovery, and drug development. A difficult setting arises when candidate interactions include proteins that have no observed PPI edges during training, where models relying on network topology alone often lose useful context. This paper presents \method, a multimodal representation framework for cold-start PPI prediction. \method\ combines region-aware protein sequence encoding with four protein-centered biomedical knowledge graphs, including protein-drug, protein-disease, protein-miRNA, and protein-lncRNA associations. The sequence branch extracts contextual representations from structurally informed sequence regions, while graph attention encoders learn modality-specific protein embeddings from sparse biomedical associations. A bridge reconstruction objective regularizes graph learning by recovering shared protein-entity associations, and a pair-level gating module adaptively integrates sequence and graph evidence for each candidate protein pair. Experiments on two benchmark datasets under novel-old and novel-novel cold-start settings show that \method\ consistently outperforms competitive sequence, network, and knowledge-graph baselines across ACC, F1, AUC, AUPR, and MCC.

Recent advances in automatic speech recognition (ASR) have explored different sequence models, including Conformer-based models and newer state space models such as Mamba. Although prior work has evaluated these architectures in multiple languages, their effectiveness in African languages remains underexplored. In this work, we evaluate Mamba for ASR on seven South African languages. In monolingual experiments, each model is trained on 50 hours of speech per language, and we compare Mamba to a Conformer baseline of similar parameter scale. Mamba achieves similar recognition accuracy to Conformer while using fewer computational resources and training faster. We further evaluate generalization in this setting and find that both models struggle to generalize to speech that is much longer than what they were trained on. We then study multilingual ASR using Mamba models, where the baseline is pooling all languages together. On top of this, we tested three extensions: training with language-family information by adding both language and language-family embeddings as biases to the downsampled acoustic representations, and multitask learning with a CTC ASR objective and a language identification (LID) head. We find that multilingual training consistently improves performance over monolingual training. However, adding explicit language information does not improve in-domain performance but does improve cross-corpus robustness. We conducted ablation studies in low-resource multilingual settings using 5-hour and 10-hour per-language training data, where we observed gains from using language embeddings and further demonstrated that removing or altering them hurt model performance. Lastly, we analysed these embeddings and find that they do not capture linguistic similarity in a typological sense, but instead act as task-specific control vectors.

Computer-assisted synthesis planning breaks target molecules into accessible precursors using large libraries of reaction rules that assign each transformation a deterministic, interpretable label. But chemistry is long-tailed, making manual encoding intractable, and existing tools rely on fixed rulesets that cannot adapt to new chemistries. Here we present a fully automated pipeline in which a multi-agent framework of large language models (LLMs) classifies reactions and writes the rules themselves across 665,901 US patent reactions, generating each rule under a verification loop that tests it against the corpus. It expands a standard taxonomy from 68 to 14,073 classes without human curation. With a lightweight fingerprint classifier, it classifies 97.7% of unseen reactions, matching a leading proprietary classifier while resolving chemistry more finely and extending on demand to chemistry outside its training distribution. The result is a living reactivity database and a general route to turning generative models into reliable, self-expanding symbolic systems.

Generative models learn data distributions that reside on a low-dimensional manifold within a higher-dimensional ambient space. Optimizing differentiable objectives on this manifold is challenging: the ambient loss landscape is high-dimensional, rugged, and non-convex. Direct gradient descent, blind to the manifold's geometry, quickly drifts off it. Diffeomorphic optimization starts from the observation that diffusion and flow models provide a map from the data manifold to a much simpler base space in which we perform gradient descent. Using differential geometry, we show this is equivalent to Riemannian gradient descent on the data manifold up to $\mathcal{O}(λ^2)$ corrections, keeping trajectories on-manifold by construction and yielding a smoother optimization surface. For protein design, we extend diffeomorphic optimization to the matrix Lie groups $\mathrm{SO}(3)$ and $\mathrm{SE}(3)$, deriving an autograd-compatible $\mathrm{SO}(3)$ gradient and a generalized adjoint-state method for backpropagation through Lie-group ODE solvers. Diffeomorphic optimization improves over tuned guidance on secondary-structure targeting with FrameFlow ($91.3\%$ vs. $63.3\%$ of residues in the Ramachandran target), outperforms OC-Flow on peptide binding affinity at $2\times$ the speed, and reduces Rosetta energies by thousands of units across the PDB test set for structures with hundreds of residues.

Scientific reasoning is an increasingly important capability of large language models, yet improving the robustness and efficiency of training such reasoning remains a key open challenge. We study this problem in instruction-based molecular optimization, where answer-only supervised fine-tuning (SFT) collapses multi-step reasoning and reinforcement learning with verifiable rewards (RLVR) suffers from sparse feedback. Reference-guided Policy Optimization mitigates both by anchoring policy updates to dataset-provided references, but its effectiveness is tightly coupled to reference quality: weak or misaligned references impose a performance ceiling. To overcome this ceiling, we propose active reasoning, a paradigm in which the policy actively decides, on a per-instance basis, when to imitate a reference and when to reinforce its own discoveries, while continuously upgrading what it imitates. We instantiate this paradigm as Active Group Relative Policy Optimization (Active-GRPO), realized through two coupled mechanisms: active imitate-reinforce and active referencing. The former performs imitation learning when the reference still outperforms the policy's own candidates, and shifts to self-improvement via reinforcement learning once the policy has generated molecules that surpass the reference. The latter continuously upgrades the reference itself by replacing it with the best policy-generated candidate discovered so far, progressively raising the imitation target and ensuring that reference guidance remains informative-rather than restrictive-throughout training. Across TOMG-Bench MOLOPT, Active-GRPO improves average SRxSim from 0.0959 for GRPO and 0.1665 for RePO to 0.1773 under matched three-seed evaluation, with statistically significant gains on LogP, MR, and QED.

Current molecular generation benchmarks emphasize task complexity, molecule novelty, and property alignment; they largely overlook a critical concern: the potential safety risks of AI-generated molecules. In practice, many generative models may produce molecules with toxic, reactive, or otherwise hazardous characteristics - posing hidden dangers that remain insufficiently addressed. To address this gap, we introduce MolSafeEval, a benchmark dedicated to evaluating and analyzing the safety risks of molecular generation. Unlike prior approaches that rely on narrow toxicity predictors, MolSafeEval integrates heterogeneous safety knowledge - ranging from toxicological databases to hazard rules - into a structured molecular safety knowledge graph. This graph serves as a foundation for large language model-based reasoning, enabling systematic detection and explanation of unsafe features in generated compounds. We further categorize molecular generative models into four representative task types - unconditional generation, property optimization, target protein-based design, and text-based generation - and provide standardized datasets and safety evaluation protocols for each. By systematically revealing the safety vulnerabilities of current generative approaches, MolSafeEval offers a new lens for benchmarking molecular models and provides essential guidance toward safer, more trustworthy molecular design.

Protein automodeling from cryo-EM density maps faces unique challenges in enforcing physicochemical validity and managing conformational heterogeneity. Current solvers are often limited to static predictions or require computationally intensive heuristic searches. We present CryoACE, an end-to-end framework that reconstructs precise atomic graphs for both homogeneous and heterogeneous structures. Our method features two key innovations: an atom-centric reconstruction paradigm, where density features are sampled directly at atomic coordinates and iteratively recycled to refine structures, replacing expensive voxel convolutions for efficient multimodal fusion; and a training-free guidance mechanism that leverages predicted local resolution priors to resolve dynamic ambiguity. Validated on a newly constructed high-quality dataset, CryoACE significantly outperforms existing baselines on static benchmarks and, for the first time, unveils atomic-level dynamic conformations on complex real-world datasets like EMPIAR-10345 without relying on pre-built static structures.

Predicting biomolecular properties from limited labeled data is a central bottleneck in protein engineering and small-molecule design. As strong pretrained encoders now supply rich fixed-length representations, the difficulty has shifted from representation learning to building a data-efficient predictor for the few-shot regime. Tabular foundation models such as TabPFN and TabICL are unlikely candidates for this role: they are in-context learners pretrained on synthetic tables drawn from random causal graphs, a generative prior with no obvious correspondence to the processes that produce protein sequences or molecular graphs. That this tabular, causal inductive bias should transfer to biomolecular data at all is counter-intuitive, yet we find it does. Treating each method as a predictor-representation pair, we evaluate across two domains. We find that on protein fitness regression tasks these in-context learning models coupled with ESM Cambrian representations achieve or exceed state-of-the-art results on ProteinGym, and outperform task-specific supervised regressors on a diverse esterase catalytic activity dataset. For small-molecule classification with ECFP/RDKit descriptors, no single predictor-representation pairing dominates across TDC ADMET, MoleculeNet, FS-Mol, and DrugOOD, but they are competitive with the existing task-specific state-of-the-art. Crucially, on both protein and small-molecule few-shot tasks, these predictor-representation pairs offer strong performance. We conclude that tabular foundation models can be strong biomolecular predictors, but only when coupled with expressive representations.

Drug-drug interaction (DDI) prediction is essential for medication safety, yet it requires reasoning over heterogeneous biomedical evidence whose relevance changes across interaction mechanisms. We propose DDIAgents, a mechanism-conditioned multi-agent framework that performs DDI prediction through dynamic knowledge orchestration. Given a drug pair, a planner agent instantiates specialized expert agents, routes mechanism-relevant knowledge sources to each agent, and aggregates their analyses through a conclusion agent. By adapting context flow to the inferred interaction mechanism, DDIAgents reduces irrelevant information, supports complementary expert reasoning, and produces interpretable agent-level rationales. Extensive experiments on realistic DDI prediction benchmarks show that DDIAgents consistently outperforms existing feature-based, graph-based, LLM-based, and agent-based baselines. Beyond prediction performance, DDIAgents demonstrates how multi-agent systems can organize heterogeneous scientific knowledge for adaptive and interpretable AI4Science reasoning.

Advances in deep learning architectures and representations have enabled ML-driven chemical property prediction, but state-of-the-art (SOTA) models have remained largely confined to independent codebases and lack support for diverse chemical species. This work introduces ElemeNet, a unified, general-purpose software package for molecular machine learning. The ElemeNet software package enables the training of advanced ML models for diverse properties and datasets with an enlarged range of elemental compositions. We define molecular representations compatible with elements 1-100, supporting diverse organometallic and biological systems in addition to organic chemistry already well-served by the Chemprop ML toolkit. As well as more common atom-, bond-, and molecule-level predictions, we introduce moiety predictions. We also natively define optional conditioning on charge and spin states. Advanced E(3)-equivariant and transformer architectures are supported, as well as classical 2D models, with all classes including built-in uncertainty quantification through deterministic and statistical measures. We benchmark our protocols for ML model training against representative datasets from organic, inorganic, coordination, and biological chemistry, achieving competitive and SOTA performance relative to literature baselines and favorable scaling to millions of molecules. The entire workflow is exposed through a concise command-line interface, lowering the barrier to entry for non-expert users. We anticipate ElemeNet will empower non-computational researchers to leverage modern deep learning methods across the chemical and physical sciences.

Mapping a chemical reaction network, the graph of minima and transition states (TS) and the elementary reactions connecting them, is the natural language of chemistry, from catalysis to combustion to the origin of life. Constructing such a reaction network for a given chemistry has been impractical: it requires finding and characterizing tens of thousands of TS, a task for which traditional methods such as density functional theory (DFT) are typically prohibitively slow and require reactant and product as input. We introduce ReactionAtlas, which builds a reaction network $\textit{ab origine}$ from a handful of seed molecules and without hand-crafted rules. Specifically, our machine-learned generative model proposes reactions from kinetically sampled candidate compounds and a DFT-trained machine learned force field (MLFF) filters them to valid TS, the resulting products of which enter the search as new seeds. Starting from eight pre-biotic seeds (CH$_2$O, H$_2$O, OH$^-$, H$_3$O$^+$, CO$_2$, H$_2$CO$_3$, HCO$_3^-$, H), ReactionAtlas discovers $\sim$47,000 reactions among $\sim$12,000 compounds. The MLFF TSs match the PBE0 references within 0.5 Å RMSD in 85% of the cases and can be easily brought to the PBE0 level. Thus, ReactionAtlas maps small carbohydrate chemistry up to C$_4$H$_8$O$_4$ at unprecedented scale and accuracy, including charge and stereo information. It enables novel insights into many well-studied reaction paths, including the formose cycle, which we highlight for its centrality to the chemical origins of life. Notably, our framework also allows establishing alternative reaction pathways for formose chemistry.

Calculation of binding energies for protein-ligand molecular systems requires accurate treatment of the electronic structure, a quantum chemistry problem that scales exponentially on classical hardware, while current quantum hardware remains too noisy for the required circuit depths. This report presents a hybrid quantum-classical workflow performed on the Fujitsu FX700 ideal state-vector simulator using QARP that addresses two structural inefficiencies in quantum-sampling-based diagonalization workflows. First, we integrate the Linear Scaling CNOT UCCSD (LCNot-UCCSD) ansatz into the QSCI framework, replacing the $\mathcal{O}(N^6)$ CCSD parameter initialization of the competing LUCJ ansatz approach with $\mathcal{O}(N^4)$ MP2-amplitude initialization. Second, we introduce QSCI-RBM, a variant that replaces the configuration recovery of the SQD framework with a Restricted Boltzmann Machine (RBM) acting as a compact generative subspace expansion model. Both are evaluated on eight different molecules in STO-3G across 14 controlled artificial error levels with 100 independent runs each, validated on potential energy surface scans of the N$_2$ molecule in cc-pVDZ, and embedded within DMET to treat the FDA-approved antiviral Amantadine (C$_{10}$H$_{17}$N, 11 DMET fragments) and the active region of the SARS-CoV-2 main protease complexed with its covalent inhibitor Carmofur (PDB: 7BUY, C$_{15}$H$_{28}$N$_4$O$_5$S, 10 fragments). To our knowledge, this is the first deployment of LCNot-UCCSD within QSCI on a quantum computing simulator, and the first DMET-QSCI(LCNot-UCCSD)-RBM application to an industry-relevant protein-ligand system. By utilizing a fraction of the classical computing resources required by the current state-of-the-art work by Cleveland Clinic, RIKEN, and IBM Quantum, this approach enables more efficient and economical drug discovery simulations for the industry.

Generative molecular design is shaped by simple proxy benchmarks for drug-like properties and models pretrained on large pharmaceutical datasets. This combination yields strong benchmark metrics but limits transferability to domains structurally distinct from drug discovery. To overcome this limitation and drive discovery toward real, scientifically grounded targets, we introduce the Nanotechnology Molecular Optimization (NMO) Benchmark, which bridges machine learning (ML) and quantum materials science. NMO acts simultaneously as a rigorous testbed for the ML community and a discovery engine for nanotechnology research. The suite replaces proxy oracles with quantum simulations and introduces strict protocols that prioritize scientific utility over leaderboard-oriented overfitting. The physics-based NMO tasks impose hard structural constraints and rugged fitness landscapes, posing fundamentally new requirements on generative models. Notably, advanced molecular optimization methods underperform much simpler approaches on the NMO tasks. We develop a new baseline method identifying the critical components to solve the NMO tasks, including a novel representation for modeling structural constraints and a domain-agnostic pretraining strategy to eliminate pharmaceutical dataset bias. Our results surpass state-of-the-art physical properties and reveal previously unknown structural motifs, offering new insights for the nanotechnology community and demonstrating that ML can drive genuine scientific discovery.

Nuclear Magnetic Resonance (NMR) spectroscopy is the gold standard for molecular structure elucidation, yet interpreting complex spectra for unknown molecules remains a bottleneck reliant on human expertise. While artificial intelligence has advanced this field, current methods face a critical trade-off: database retrieval cannot identify novel scaffolds, while de novo molecular structure elucidation models operate as black boxes, lacking the atom-level interpretability required for rigorous scientific validation. Here, we present NMRAgent, an evidential reasoning agent powered by large language models (LLMs) that bridges this gap by integrating specialized spectral analysis tools with chemical knowledge graphs. Unlike previous approaches, NMRAgent mimics the deductive reasoning of human experts: it takes experimental NMR spectra and molecular formula as input, plans the elucidation process, proposes candidate structures, verifies peak-atom consistency, and refines misaligned substructure through formula-aware fragment optimization. Enabled by its evidential reasoning, NMRAgent outperforms state-of-the-art methods, improving top-1 accuracy by 46.5% and Tanimoto similarity by 0.502 on a scaffold-split benchmark with novel scaffolds in the test set. Besides, we demonstrate the agent's practical utility by elucidating the structures of two previously unknown natural products isolated from Hydrangea davidii and Vitex trifolia, and by correcting structural misassignments in established literature. By combining high-accuracy prediction with transparent and evidence-based reasoning, NMRAgent establishes a new paradigm for interpretable AI in analytical chemistry.

Single-cell drug perturbation models should capture transcriptional response magnitude and whether a treatment changes the proliferative state of the cell. This is difficult because cell-cycle variation is often treated as a nuisance factor, and benchmark processing rarely makes drug-induced phase changes a primary prediction target. We introduce scCycleMol, a cell-cycle-aware perturbation prediction framework built on a curated 24-hour SciPlex3 benchmark with standardized molecule identities, dose and cell-line metadata, modeled genes, and expression-derived cell-cycle supervision. scCycleMol derives cell-cycle supervision from the treated state and applies it to predicted treated expression without using phase as an input covariate. The model includes a learnable full-expression cell-cycle head with circular G1/S/G2M targets, and we evaluate readout-only supervision (with stop-gradient) versus closed-loop supervision (backpropagating through decoder, dose-response module, and drug representation). We also compare molecular representations and pretraining sources to isolate the effect of the cell-cycle objective. On a processed 24-hour SciPlex3 benchmark (635,541 cells, 186 perturbations, 188 compound embeddings, 3 cell lines, 4 doses plus DMSO, 5,080 genes), the best LINCS-pretrained circular variant reaches 0.9093 mean all-gene R-squared and 0.6843 mean DE-gene R-squared. Under matched preprocessing, closed-loop cell-cycle supervision improves phase accuracy by 0.54-0.62 points while keeping mean all-gene R-squared within 0.003 of matched chemCPA no-cell-cycle models; Tahoe-pretrained readout-only circular supervision achieves the strongest phase accuracy at 0.9609.

$\mathrm{Cl}(3,0)$ interatomic potentials, despite their algebraic elegance, predict force magnitudes accurately but force directions poorly. Across ten rMD17 molecules, every $L \leq 1$ baseline in our twelve-model study attains aggregate force-cosine similarity below $0.25$. The cause is structural. The geometric product of two vectors in $\mathbb{R}^3$ realises only the $L=0$ and $L=1$ components of its irreducible representation content, leaving the symmetric-traceless rank-2 component absent from the per-edge bilinear that drives each message-passing layer. We address this with CliffordSTF, which couples the Clifford multivector to closed-form symmetric-traceless tensor tracks at ranks two and three through bilinear cross-track contractions, using a single learned bilinear and no Clebsch--Gordan tables, Wigner-$D$ matrices, or e3nn calls. On rMD17, CliffordSTF raises aggregate force-cosine similarity from $0.055$ (base Clifford) to $0.551$, an order-of-magnitude relative directional gain, alongside improved magnitude accuracy (force MAE $15.8\%$ lower; energy MAE $10.9\%$ lower). It outperforms all CG-free or body-ordered baselines in our study (all $\leq 0.17$). On catalysis benchmarks, CliffordSTF achieves the best out-of-distribution S2EF energy MAE on OC22 in our experiments, and the best in-distribution energy MAE among $L \geq 2$ methods on OC22 IS2RE. An eleven-variant ablation shows the two tracks are complementary: neither alone matches the combined model.

Diffusion models are increasingly utilized for modeling molecular structures and conformational ensembles, yet the thermodynamic meaning of their learned representations and scores remains elusive. To resolve this ambiguity, we introduce a mathematically consistent action-operator framework natively compatible with diffusion models. By defining a fixed molecular environment as a base action $S_0(x)$ and an alchemical perturbation as an operator $O(x)$, standard diffusion noising induces effective noised actions and operators whose gradients and alchemical derivatives are directly represented by the model's learned fields. This rigorous self-consistency enables a ``noisy operator bridge'' capable of reading out free-energy differences ($ΔF$) from endpoint ensembles and per-frame evaluations. In controlled experiments on alanine dipeptide systems, we show that incorporating physical inductive biases enables partial recovery of the base action and perturbation operator. When applied to a challenging C6-H to C6-F ligand-pocket nonbonded perturbation (185L/IND) with negligible phase-space overlap, our supervised bridge estimates the alchemical $ΔF$ within approximately $1\ k_\mathrm{B}T$ of a stable 19-state MBAR reference. Finally, we demonstrate that endpoint coordinates and binary labels alone are sufficient to partially recover the operator shape and a centered free-energy scale without any force or action supervision. This work provides a rigorous path toward transforming generative molecular diffusion models from black-box coordinate samplers into auditable thermodynamic estimators.

Predicting tandem mass spectra (MS/MS) from molecular structures represents a central task in analytical chemistry with direct relevance to clinical metabolomics, systems biology, and adjacent disciplines. In this work, we revisit the problem through the lens of object detection on molecular graphs. Molecular fragmentation, a central step in MS/MS prediction, can be approximated as detecting a set of subgraphs (i.e., fragments) and their associated spectral contributions. Existing fragment-based models follow a two-stage paradigm -- first generating candidate fragments and then scoring them -- analogous to two-stage R-CNNs in computer vision. Towards higher accuracy and faster inference, we introduce GLACIER, a single-stage transformer-based fragment detection neural network for molecular graphs. This unified formulation eliminates the need for candidate enumeration, enabling scalable and globally consistent modeling of molecular fragmentation. GLACIER is faster and more accurate than existing state-of-the-art by a significant margin, achieving 70.0% and 69.7% Top-1 retrieval accuracy with and without contrastive finetuning on the MassSpecGym dataset (from the previous SOTA of 64.0%) and 52.5% and 38.5% respectively on the NIST'20 dataset (from 33.2%). Furthermore, GLACIER provides nearly 8-fold inference speedup over our prior two-stage model. Code is available at https://github.com/coleygroup/ms-pred

Recent progress in flow-based generative modeling has led to models that output high-quality samples while using only a small number of function evaluations. However, at present, there is a lack of similar advances in estimating the model likelihood. In particular, most existing methods either rely on restrictive architectures that enable exact calculations, or use stochastic approximations such as Hutchinson's trace estimator that introduce substantial variance. In this work, we introduce SCAlable LikeLihood distillation of flOw maPs (SCALLOP). SCALLOP builds on the recently proposed F2D2, a likelihood flow map model that can generate samples and their densities in a small number of function evaluations. While F2D2 uses Hutchinson's estimator during training, we introduce an alternative and more scalable likelihood distillation objective that is Hutchinson-free and admits a vectorized formulation. Empirically, we demonstrate the effectiveness of SCALLOP as a Boltzmann generator in molecular science, and further validate its benefit on image datasets. SCALLOP significantly reduces both training variance and training time while consistently improving performance compared to F2D2, and is competitive with the state-of-the-art while achieving up to 10x inference speedup over the fastest baseline.

High-fidelity molecular docking simulations can produce biologically relevant estimates of epitope-receptor binding affinity but are computationally expensive and therefore limit the number of candidates that can be screened for vaccine design. In this work, we evaluate machine learning (ML) approaches where variants of active learning are used to classify instances of high binding affinity between 9-mer epitopes and a well-conserved swine leukocyte antigen (SLA) receptor in the context of Porcine Reproductive and Respiratory Syndrome (PRRS). We use an internally generated dataset of 80 epitope-SLA docking affinities, each requiring more than 48 hours of high-performance computing (HPC). Multiple model families (linear, MLP, CNN, and a small transformer) are trained under strict low-data conditions within a pool-based active learning loop. In each case, optimal model configurations are identified by conducting large-scale hyperparameter optimization over the combined space of model architecture, training configuration, acquisition policy, and ensemble decision rules. To mitigate the effects of data subsample selection, each candidate configuration is evaluated by averaging performance over many randomized and balanced training and validation data subsets. Across experiments, transformer-based sequence models consistently emerged as the best-performing architecture, with active incremental learning yielding significant improvement over a baseline random sample acquisition strategy. Under moderate training data availability (N=30), the optimized ML-model configuration outperforms a standard baseline trained on twice the amount of data. Under higher training data availability (N=60), the same configuration achieves a peak accuracy of 86.8%, consistent with an upper bound of 85% classification accuracy based on two independent estimates of conformational noise.

Closed-loop materials discovery iterates between proposing candidate structures and evaluating their properties, and property evaluation dominates the cost. In the generative variant, a learned prior proposes candidate crystals and a property oracle scores them; we ask whether a cheap probabilistic surrogate can triage the generator's output, and what such a surrogate must do well. Across three architecturally distinct pretrained diffusion priors (MatterGen, CrystalFlow, ADiT) and two targets (room-temperature heat capacity and bulk modulus), we insert a Gaussian process acquisition gate between structure generation and the oracle in an RL-steered generative workflow. The gate matches or exceeds ungated fine-tuning of the generative model while capping oracle calls at a fixed per-cycle budget. Budget-matched ablations isolate the mechanism. At an identical four-call budget, ranking-based selection outperforms arbitrary selection, confirming that the gain comes from the surrogate's choice; the gate comes within $\sim$9% of exhaustive oracle spending at roughly one-fifth of the calls. A density-functional-theory check of the bulk-modulus discoveries confirms the learned oracle to within 2.5% on average and the surrogate's ranking of the generated structures at Spearman $ρ= 0.94$. A cross-factorial benchmark of surrogate performance spanning mechanical, electronic, and vibrational properties identifies pretrained ORB embeddings with a Gaussian process as the most reliable combination, which we adopt as the building blocks of the proposed workflow. The complete pipeline is released as open-source software.

Protein language models are standard priors for biological sequence generation, but steering them toward explicit distributional design targets remains largely unexplored. We study a constrained protein generation problem in which sequences must match a desired amino-acid (AA) composition profile while preserving plausible sequence statistics and diversity. The motivating application is synthetic feed protein design, where the AA composition of dietary proteins directly determines their nutritional value. We propose a two-stage pipeline in which domain-adaptive fine-tuning (FT) on an in-domain protein dataset is followed by iterative reward-weighted FT via reinforcement learning (RL) anchored against the FT model as a frozen reference. We evaluate the pipeline on two AA compositions and find that FT brings the average composition close to the target, while the subsequent RL enforces specific sequence constraints that FT alone cannot satisfy. We additionally evaluate the design choices of the proposed composition reward term against two baselines and an ablated variant, isolate the contribution of each training stage, and verify that AA composition alignment is achieved without degrading sequence quality.

Peptides are a promising therapeutic modality that combine the chemical tunability of small molecules with the target specificity of macromolecular therapeutics. However, designing antigen-specific binding peptides while avoiding toxicity remains a major challenge for therapeutic peptide discovery. Here, we present Pepti-drift, a toxicity-aware latent refinement framework that generates peptide candidates through a single antigen-conditioned drift step. In a peptide embedding space, Pepti-drift learns to attract generated peptide latents toward antigen-matched binding peptides while repelling them from toxicity-associated regions. This is challenging because binding-promoting physicochemical features often overlap with toxicity-associated features in peptide representation space. To address this, we introduce a warm-up strategy to stabilize this competing objective by first learning binding-oriented attraction and then increasing toxicity repulsion. Pepti-drift achieves highly efficient generation, running 16.2-fold faster than PepMLM and 1,092.0-fold faster than PepTune. Generated peptides show 100% validity, 98.1% uniqueness, the highest sequence diversity, and near-zero cross-antigen reuse. Further evaluation indicates consistently reduced toxicity and hemolysis risk across most peptide-length ranges while retaining target-related predictive binding signal. Pepti-drift thus provides a fast, scalable, and controllable framework for antigen-specific peptide design that directly encodes safe-and-active properties.

Programming adaptive behaviors at the cellular level is a long-standing goal that raises the question of how probabilistic computation can be implemented in biochemical systems. Chemical reaction networks (CRNs) provide such a substrate and have been shown to realize probabilistic models, including hidden Markov models and factor graphs, with dynamics reproducing Bayesian inference and belief propagation. However, encoding these algorithms typically requires prohibitively large reaction networks, and classical CRN reduction techniques do not directly apply. By recovering the factor graph structure encoded in Napp--Adams-compiled CRNs, we transport recent factor-graph reduction results to their chemical implementations, obtaining significantly smaller CRNs while preserving the belief-propagation fixed points on surviving variables.

Molecule generation methods that leverage generative models have been successfully applied to drug discovery. However, they often require extensive pre-training, suffer statistical biases in the training data, and might suffer from limited interpretability of generated chemical structures. In this work, we introduce SpectralMol, an algorithm based on evolutionary computation that processes chemical structures as a compact matrix of Fourier coefficients, projected onto a fixed basis to generate position-wise latent vectors for SELFIES decoding. The NSGA-II algorithm enforces diversity and enable separate objective functions rather than collapsed objectives into a scalar reward. The quality of the algorithm was tested against standardized benchmarks. The results show comparable aggregate benchmark performance with a task-dependent profile: SpectralMol is strongest on several multi-parameter optimization tasks. The same benchmark was used to perform an ablation study to demonstrate the advantages of a structured latent matrix. Finally, method was tested on a realistic ClpP-targeted drug-discovery benchmark, comparing it with the reinforcement-learning-based model under a fixed oracle-call budget. SpectralMol generates more docking hits and more diverse scaffolds while maintaining competitive physicochemical properties. The representation adopted in this work can cleanly separates scaffold-level modifications from localized substructure variations, as the former occur with perturbations of low-frequency Fourier modes and the latter with perturbations of high-frequency Fourier modes. The results support the evidence that frequency-controlled evolutionary dynamics provide an interpretable, efficient, and training-free route to multi-objective molecular design.

Foundation models for structural biology have achieved remarkable performance in predicting biomolecular structure and show promise for the design of proteins and small molecules. Yet understanding which internal features drive their outputs remains challenging. Standard sparse autoencoders (SAEs), effective on transformer-style sequence embeddings, do not transfer cleanly to pairformer-like architectures: naively operating on pairwise representations yields a quadratic blow-up of features and obscures concepts distributed jointly across sequence and pair representations. We introduce PairSAE, which summarizes pairwise tensors via an N-mode SVD into token-wise interaction roles, then uses a sparse autoencoder to learn a shared set of token-level features that decode into both sequence and pair representations. Evaluated on Boltz-2 activations for PLINDER protein-ligand complexes, PairSAE yields interpretable features that align with UniProt annotations and predict Boltz-2 affinity values. These results indicate that PairSAE links the latent space of foundation models for structural biology to interpretable structural concepts, clarifying what the model "knows" while avoiding pairformer-induced pitfalls that limit conventional SAEs.

Efficient sampling of molecular systems at thermodynamic equilibrium is a hallmark challenge in statistical physics. This challenge has driven the development of Boltzmann Generators (BGs), which allow rapid generation of uncorrelated equilibrium samples by combining a generative model with exact likelihoods and an importance sampling correction. However, modern BGs predominantly rely on normalizing flows (NFs), which either suffer from limited expressivity due to strict invertibility constraints (discrete time) or computationally expensive likelihoods (continuous time). In this paper, we propose Autoregressive Boltzmann Generators (ArBG) -- a novel autoregressive modelling framework -- that overcomes these limitations by departing from the flow-based BG paradigm. ArBG circumvents the topological constraints of flows and enables sequential inference-time interventions, while offering enhanced scalability by leveraging architectures effective in Large Language Models. We empirically demonstrate that ArBG leads to significant improvements over flow-based models across all benchmarks, but particularly in larger peptide systems such as the 10-residue Chignolin. Furthermore, we introduce Robin, a 132 million parameter transferable model trained with the ArBG framework which improves over the previous state-of-the-art, reducing the zero-shot energy error, E-W$_2$, on 8-residue systems by over 60$\%$. The code can be found at the following link: https://github.com/danyalrehman/autobg.

Identifying high-utility candidates from massive discrete spaces under expensive evaluations is a recurring challenge across the sciences, with structure-based drug discovery as a prominent example. While surrogate-based optimization can increase sample efficiency by reducing the number of expensive evaluations, modern molecular libraries have reached billions to trillions of compounds, making full-library surrogate inference itself a major computational bottleneck. We introduce BOBa, a bandit-guided surrogate optimization framework that eliminates full-library inference by adaptively allocating computation across partitions of the action space. By treating partitions as arms in a multi-armed bandit, BOBa concentrates inference and evaluations on empirically promising partitions while maintaining principled exploration. Experiments on real-world synthesis-on-demand libraries demonstrate that optimism-under-uncertainty bandits, combined with meaningful action space partitioning, are essential for effective allocation of inference and evaluations. Our findings reveal a tunable tradeoff between screening performance and surrogate inference cost, which supports practical optimization over current libraries, and establishes a viable route to ultra-large library virtual screening.

Living systems navigate environments using noisy and incomplete sensory signals. In unicellular algae, phototaxis is often modeled as a mechanistic run--tumble process driven by stimulus--response rules. However, such descriptions overlook how organisms actively sample their environment to reduce sensory ambiguity. From a minimal cognition perspective, we reframe this navigation as a subjective, information-driven sensorimotor process. To this end, we propose a framework linking a Partially Observable Markov Decision Process (POMDP) with biochemical reaction dynamics. Environmental variables are hidden, while the cell updates a minimal internal state from each observation through a memoryless Bayesian step. These internal dynamics balance orienting toward light with exploratory reorientation and can be implemented through Chemical-Reaction-Network Ordinary Differential Equations (CRN--ODEs). Our model includes a biophysical observation process for photoreception and a chemically computable polynomial bound on information gain. Using Inverse Reinforcement Learning (IRL) on 30 experimentally recorded Chlamydomonas trajectories, we infer the behavioral objective consistent with observed phototactic motion and benchmark the resulting dynamics with standard Stochastic Simulation Algorithm (SSA) baselines. Our model reproduces the empirical alignment-to-light distribution, comparable to objective SSA baselines on this dataset. Within this framework, run--tumble alternation emerges as an information-acquisition strategy: tumbling reorients the cell to sample new sensory configurations and resolve sensor ambiguity, demonstrating how intracellular biochemical networks can support adaptive information-seeking behavior in cellular navigation.

Target-specific peptide design requires sequence and structure co-design under full atom geometric constraints. Latent generative frameworks offer an effective route for this problem by compressing fine grained atomic structures into block level latent representations and performing conditional generation in a compact latent space. However, the scalability of such systems depends heavily on the geometric backbone used throughout their encoding, decoding, and denoising components. We introduce MEET (Memory Efficient Equivariant Transformer), an E(3) equivariant backbone for scalable atomistic peptide modeling. MEET maintains coupled invariant scalar and equivariant vector feature streams, while reformulating geometric computation around memory efficient attention. It initializes vector features through global coordinate aggregation, incorporates pairwise distances through augmented query and key dot products, and injects covalent bond information through sparse bond adaptation. Integrated into a VAE and latent diffusion pipeline for full atom peptide generation, MEET achieves linear memory scaling with atom count and improves generation quality over existing peptide design methods. Experiments on large scale AFDB derived datasets further show that the proposed backbone supports systematic model and data scaling, leading to better binding affinity, physical validity, and sample diversity.

Reinforcement Learning (RL) has become a powerful paradigm for de novo molecular design, enabling Chemical Language Models (CLMs) to navigate and explore the chemical space while optimizing specific desired properties. However, the existing RL frameworks treat all scoring functions as deterministic oracles, neglecting the inherent uncertainty attached to the predictions of the different molecular properties. This can lead to the exploration of highly-uncertain regions of the chemical space, focusing on the generation of highly scored molecules which are poorly supported by the training data. This can destabilize the optimization process, yielding predictions that are far from their true values. We propose and compare two complementary ways of incorporating predictive uncertainty into RL. In the first one, uncertainty is treated as an additional optimization objective and incorporated along with the rest of the scoring functions, allowing the policy to trade off exploitation against reliability. Secondly, uncertainty is used to modulate policy updates, reducing the influence of molecules whose properties lie far outside the scoring function confidence domain. Both approaches were evaluated across three different settings: (i) a controlled model system, in which the prediction error is modeled as a Gaussian distribution, with a variance proportional to the distance to the training data; and two real-world tasks, making use of (ii) ChemProp models and (iii) a Conformal Prediction wrapper applied to a Random forest classifier. We show that uncertainty-aware RL enables CLMs to explore chemical space more robustly by favoring lower-uncertainty regions. This leads to more reliable hit discovery without compromising molecular score, increasing the true hit rate by 0.25 (from 0.5 to 0.75), and nearly doubling the total number of true hits.

Implicit solvent machine learning potentials (MLPs) offer a powerful route to bridging the gap between accuracy and efficiency in molecular simulations. However, existing models have largely focused on aqueous environments, overlooking the diverse and important roles of non-aqueous solvents in areas such as organic synthesis and battery technology. Here, we present ConSolv, a solvent-conditional MLP architecture that explicitly incorporates solvent effects on solute interactions through an attention-based solvent-embedding block. By combining experimental solvation free energy data with ab initio data, we train a single implicit solvent MLP that is transferable across 66 common organic solvents. ConSolv outperforms classical explicit solvent methods and selected ab initio implicit solvent approaches across multiple solvation free energy benchmarks, and demonstrates generalization to unseen solvents. Beyond solvation free energies, the model shows close agreement with experimental nuclear magnetic resonance (NMR) data for $γ$-fluorohydrin molecules in chloroform. ConSolv's architecture is readily extensible to broader chemical spaces and alternative training strategies, while its attention-based design supports explainable artificial intelligence (AI) analysis that can help elucidate complex, solvent-dependent molecular interactions.

Generative molecular models for drug design are a promising direction with much active research. In the next phase of computational drug design, such models will need to understand small molecule structure and protein-ligand interactions, and they will need to possess the machinery to generate molecules de novo. Incorporating each feature poses a critical challenge. Equally important, yet often treated as secondary, is the ability to grow a molecule from a partial starting point -- a scaffold or fragment supplied by a chemist -- which is the central operation of lead optimization. We present Sesame (Spatial Evoformer for a Structure-Aware Molecular Engine), a diffusion-based molecular generation model that leverages a novel spatial pairformer module to condition on partial molecular structure and the surrounding protein pocket, both expressed as continuous spatial density maps. This single conditioning mechanism supports both de novo generation and fragment-conditioned lead optimization, letting a medicinal chemist prune a hit to a scaffold and have Sesame grow it in productive ways. In addition to this module, we also introduce a diffusion framework for joint denoising of atom types, bond types, and positions, along with a trajectory finetuning scheme that trains on the model's own sampling rollouts to improve generation quality. Sesame is trained on a large corpus of ligand-only and protein-ligand datasets.

Backdoor attacks on molecular graph neural networks (GNNs) are typically evaluated as abstract graph edits, but real molecular learning pipelines do not train on arbitrary graphs. Molecular records must first survive parsing, sanitization, canonicalization, and graph-string consistency checks. We formalize this overlooked admission stage as ChemGuard, an operational protocol for testing whether a submitted molecular record can enter a realistic learning pipeline, while complementing existing defenses. ChemGuard admits a record only when its molecular string is sanitizable and the graph reconstructed from that string matches the submitted molecular graph. Under this operational view, many existing graph-based backdoors lose much of their apparent efficacy because their poisons are chemically invalid or representation-inconsistent. We then show that admission checks alone are insufficient to rule out molecular backdoors. We propose ChemBack, an admission-aware molecular backdoor attack that constructs chemically feasible motif-anchor attachments and ranks admitted candidates by fingerprint-based Tanimoto similarity to clean target-class molecules. ChemBack is model-free during trigger selection, using molecular structures, target labels, fingerprints, and public validity checks, but no victim model, surrogate GNN, learned embedding, gradient, logit, or training-code access. Across molecular benchmarks, validators, architectures, and defenses, \textbf{ChemBack} achieves high attack success with fully admitted poisons while preserving clean accuracy. Our results reveal a two-sided lesson, chemistry-aware admission suppresses many graph-only backdoors, yet chemically valid and target-aligned molecular backdoors remain a practical threat.

There has been rapid progress in generative artificial intelligence (AI) models for inorganic crystal design, which can efficiently generate large numbers of candidate compounds after being trained on databases of known crystals. However, it remains unclear whether they genuinely expand the accessible materials search space beyond conventional strategies such as elemental substitution within known structure types. We address this question by developing a workflow to assess whether AI-generated crystals are duplicates of training structures, reproducible by elemental substitution, or unmatched by either criterion. Applying this workflow to representative generative models reveals that 81-92% of chemically valid and metastable generated crystals are either training duplicates or substitution-derived structures. This tendency is particularly strong in high-symmetry crystal systems, even though many possible structural prototypes remain unexplored. Further analysis of the underlying structural fingerprints shows that low-symmetry structures beyond duplication or substitution can be interpreted as interpolation in training-data-rich regions, while high-symmetry duplicates appear to result from memorisation in training-sparse regions. Our findings highlight a limitation in the current generation of models that exhibit a bias towards known structural prototypes in the high symmetry regions, but enable wider exploration of the low-symmetry structural space.

Closed-loop Auto Research extends automated machine learning from fixed-dataset fitting to changing the research workflow, with language-model agents editing representations and model code and acquiring external evidence. Molecular property prediction spans many small endpoints. We ask whether this action space yields improvements generalizing beyond the validation signal selecting them. We isolate three Auto Research axes, features, models, and external evidence, under a file-level ablation lock attributing each gain to one axis over a strong baseline. Across 36 endpoints in three benchmark suites we score each selected configuration once on a held-out test whose labels the search never read. A routed pipeline taking each endpoint's best validation axis reaches positive held-out gains of 0.013, 0.011, and 0.042, the transferable axis differing by suite, data on TDC, model on Polaris, feature and model on MoleculeNet. The largest model-search gain falls from 0.041 on validation to 0.003 on test, while curated data reaches 0.022 but negative 0.019 on test, two non-transfer signatures. Curated external data raises held-out CYP2C9-substrate performance by 0.17 and half-life by 0.08, admitted through a contamination filter rejecting same-source files overlapping 64 to 89 percent of test structures, necessary but not sufficient for transfer. A matched-trial automated machine learning control did not reproduce the agent's code-level model intervention, reaching 0.006 against 0.042, and the pipeline stays competitive with an 84M-parameter pretrained 3D model on the shared training split. The experiments stay within molecular property prediction, but separating discovery from held-out certification is a domain-agnostic lesson for any closed-loop system optimising a proxy for a held-out quantity.

We present JEDEL, a framework for generating synthesis-ready DNA-encoded libraries (DELs) directly from three-dimensional pharmacophore representations of active ligands. JEDEL is the first model to map pharmacophore interaction patterns to actionable, scalable synthesis instructions, enabling the design of targeted libraries comprising potentially millions of molecules. Unlike existing generative approaches that produce virtual compounds requiring downstream synthesis planning, JEDEL operates within the space of purchasable building blocks and validated reactions, ensuring that every output is experimentally realizable by construction. JEDEL learns a predictive alignment between pharmacophore geometry and molecular structure and decodes this into combinatorial synthesis routes at scale. Across 18 protein targets, it generates focused libraries that outperform random and diversity-based baselines in predicted binding affinity, pharmacophore recovery, and sample efficiency, without target-specific retraining. JEDEL enables a shift from virtual molecule generation to experimentally deployable library design.

Hybrid Quantum Neural Network (QNN) classifiers produce logits as expectation values of quantum measurement operators. For standard Pauli measurements, these outputs are intrinsically bounded to the interval [-1,1]. When such bounded logits are used directly with the cross-entropy loss applied to softmax-normalized logits for multi-class classification, the loss function operates in a regime of weak sensitivity to logit differences. As a consequence, parameter gradients are suppressed, leading to unstable optimization in variational quantum classifiers (VQCs). In this work, we identify this effect as measurement-induced logit contraction, a previously uncharacterized source of trainability degradation in hybrid QNNs. To address this limitation, we introduce a learnable scaling parameter, termed Quantum Measurement Temperature (QMT), which rescales quantum measurement outputs prior to the loss. Unlike post-hoc calibration, QMT acts during training and compensates for the physically imposed bounds on quantum measurement outputs. This rescaling increases gradient magnitude and variance, thereby improving loss sensitivity. The proposed mechanism is architecture-agnostic and does not modify the quantum ansatz, circuit depth, or measurement operators. Experiments on fluorescence microscopy images and a six-class variant of Fashion MNIST demonstrate that QMT consistently enhances logit separation, strengthens gradients, stabilizes training across random initializations, and improves classification accuracy, relative to unscaled measurement readouts. These results demonstrate that QMT enables stable and reliable training of hybrid QNNs for practical applications.

Deep learning has demonstrated significant success for modeling biochemical molecular systems, where inputs are commonly represented as graphs or 3D grids. A major challenge is that computational cost scales with resolution, making full graph/grid computation of molecular densities expensive and often unstable. We introduce a multigrid training strategy that leverages low-resolution optimization to accelerate learning at higher resolution through parameter transfer across discretizations. For graph molecular representations, we progressively transfer parameters learned from a coarse graph to a sequence of increasingly finer graphs via biased random walk upsampling. For 3D molecular generation, we voxelize the molecular structures at multiple resolutions, pretrain a coarse-resolution conditional Variational Autoencoder (CVAE), and initialize a fine-resolution CVAE by transferring shape compatible convolutional parameters from the coarse model. Numerical experiments on receptor-conditioned 3D Ligand generation show that multigrid training accelerates convergence and improves generalization compared to training from scratch.

Data augmentation (DA) has been proven to be an effective means for improving protein representation learning (PRL) by generating additional training samples. Although mainstream perturbation- and sampling-based augmentation methods can produce data containing sufficient variations, they carry the risk of disrupting the protein structure and function. Some crafted protein homology modeling tools can generate conformations, but reduce structural diversity. The above dilemmas lead us to a question: Can we restore the disrupted structure caused by DA operations, providing data with both the original structure and diverse variations? In this work, we first analyze and empirically reveal the structure defect and performance degradation issues of existing DA methods. Based on the findings, we propose a simple yet effective DA method, Manifold Restore Mixing (MRM), for protein representation learning. Specifically, inspired by manifold mixup, we mix the hidden representations of original and augmented protein data to generate new samples that restore structural information lost in DA while introducing diverse variations. Furthermore, we develop a sample difficulty scheduler that adjusts the beta distribution in mixup to provide models with progressively challenging mixed samples during training, which improves the final performance. Comprehensive experiments on various PRL backbones and downstream tasks demonstrate the effectiveness and generalization of our method. The complete code and weights will be released upon acceptance. We provide a implementation at https://github.com/KingGugu/MRM.

The Categorical Jacobian of Zhang et al. (2024) reads protein contacts from a language model by perturbing every residue with every alternative amino acid, about $19L$ forward passes. We show the signal it reconstructs is already concentrated in a small subset of attention heads: averaging the top-$K$ contact-relevant heads -- selected on as few as 10 labeled proteins, with no fitted per-pair or per-head weights -- recovers contacts in a single forward pass and matches or beats the Categorical Jacobian for every bidirectional model where it is defined (bar the smallest, 8M). Our primary test is leakage-clean: on a CAMEO split where neither selection nor evaluation touches data the models have plausibly memorized, the head readout beats the Categorical Jacobian on ESM-2-650M by +9pp ($N = 29$, $p < 0.001$), with the within-model margin reproducing across architectures. Ablations localize the gain to labeled head selection, not to averaging: at a matched label budget the unweighted mean ties a supervised $L_1$ logistic regression on the same heads. Both methods fall 30-36pp from their in-distribution Zhang numbers to the leakage-clean split, which we read as an upper bound on how much prior numbers reflect pretraining overlap. We additionally introduce representation-CJ, a hidden-state generalization of the Jacobian to architectures without a masked-LM head (the output-head-independent analogue of logit-CJ), agreeing with the Categorical Jacobian where both are defined (per-protein Pearson $r \approx 0.95$); show that the optimal $K$ tracks how diffusely a model spreads its contact heads; and find both methods lose the signal on the two causal LMs we test, suggesting attention-encoded pair structure may depend on bidirectional pretraining.