Elucidating reaction mechanisms hinges on efficiently generating transition states (TSs), products, and complete reaction networks. Recent generative models, such as diffusion models for TS sampling and sequence-based architectures for product generation, offer faster alternatives to quantum-chemistry searches. But diffusion models remain constrained by their stochastic differential equation (SDE) dynamics, which suffer from inefficiency and limited controllability. We show that flow matching, a deterministic ordinary differential (ODE) formulation, can replace SDE-based diffusion for molecular and reaction generation. We introduce MolGEN, a conditional flow-matching framework that learns an optimal transport path to transport Gaussian priors to target chemical distributions. On benchmarks used by TSDiff and OA-ReactDiff, MolGEN surpasses TS geometry accuracy and barrier-height prediction while reducing sampling to sub-second inference. MolGEN also supports open-ended product generation with competitive top-k accuracy and avoids mass/electron-balance violations common to sequence models. In a realistic test on the $γ$-ketohydroperoxide decomposition network, MolGEN yields higher fractions of valid and intended TSs with markedly fewer quantum-chemistry evaluations than string-based baselines. These results demonstrate that deterministic flow matching provides a unified, accurate, and computationally efficient foundation for molecular generative modeling, signaling that flow matching is the future for molecular generation across chemistry.

Reaction mechanism search tools have demonstrated the ability to provide insights into likely products and rate-limiting steps of reacting systems. However, reactions involving several concerted bond changes - as can be found in many key steps of natural product synthesis - can complicate the search process. To mitigate these complications, we present a mechanism search strategy particularly suited to help expedite exploration of an exemplary family of such complex reactions, cyclizations. We provide a cost-effective strategy for identifying relevant elementary reaction steps by combining graph-based enumeration schemes and machine learning techniques for intermediate filtering. Key to this approach is our use of a neural network potential (NNP), AIMNet2-rxn, for computational evaluation of each candidate reaction pathway. In this article, we evaluate the NNP's ability to estimate activation energies, demonstrate the correct anticipation of stereoselectivity, and recapitulate complex enabling steps in natural product synthesis.

We propose a regularization framework inspired by thermodynamic work for guiding pre-trained probability flow generative models (e.g., continuous normalizing flows or diffusion models) by minimizing excess work, a concept rooted in statistical mechanics and with strong conceptual connections to optimal transport. Our approach enables efficient guidance in sparse-data regimes common to scientific applications, where only limited target samples or partial density constraints are available. We introduce two strategies: Path Guidance for sampling rare transition states by concentrating probability mass on user-defined subsets, and Observable Guidance for aligning generated distributions with experimental observables while preserving entropy. We demonstrate the framework's versatility on a coarse-grained protein model, guiding it to sample transition configurations between folded/unfolded states and correct systematic biases using experimental data. The method bridges thermodynamic principles with modern generative architectures, offering a principled, efficient, and physics-inspired alternative to standard fine-tuning in data-scarce domains. Empirical results highlight improved sample efficiency and bias reduction, underscoring its applicability to molecular simulations and beyond.

Identifying minimum-energy paths (MEPs) is crucial for understanding chemical reaction mechanisms but remains computationally demanding. We introduce MEPIN, a scalable machine-learning method for efficiently predicting MEPs from reactant and product configurations, without relying on transition-state geometries or pre-optimized reaction paths during training. The task is defined as predicting deviations from geometric interpolations along reaction coordinates. We address this task with a continuous reaction path model based on a symmetry-broken equivariant neural network that generates a flexible number of intermediate structures. The model is trained using an energy-based objective, with efficiency enhanced by incorporating geometric priors from geodesic interpolation as initial interpolations or pre-training objectives. Our approach generalizes across diverse chemical reactions and achieves accurate alignment with reference intrinsic reaction coordinates, as demonstrated on various small molecule reactions and [3+2] cycloadditions. Our method enables the exploration of large chemical reaction spaces with efficient, data-driven predictions of reaction pathways.

Pretrained foundation models learn embeddings that can be used for a wide range of downstream tasks. These embeddings optimise general performance, and if insufficiently accurate at a specific task the model can be fine-tuned to improve performance. For all current methodologies this operation necessarily degrades performance on all out-of-distribution tasks. In this work we present 'fill-tuning', a novel methodology to generate datasets for continued pretraining of foundation models that are not suited to a particular downstream task, but instead aim to correct poor regions of the embedding. We present the application of roughness analysis to latent space topologies and illustrate how it can be used to propose data that will be most valuable to improving the embedding. We apply fill-tuning to a set of state-of-the-art materials foundation models trained on $O(10^9)$ data points and show model improvement of almost 1% in all downstream tasks with the addition of only 100 data points. This method provides a route to the general improvement of foundation models at the computational cost of fine-tuning.

Understanding surgical tasks represents an important challenge for autonomy in surgical robotic systems. To achieve this, we propose an online task segmentation framework that uses hierarchical transition state clustering to activate predefined robot assistance. Our approach involves performing a first clustering on visual features and a subsequent clustering on robot kinematic features for each visual cluster. This enables to capture relevant task transition information on each modality independently. The approach is implemented for a pick-and-place task commonly found in surgical training. The validation of the transition segmentation showed high accuracy and fast computation time. We have integrated the transition recognition module with predefined robot-assisted tool positioning. The complete framework has shown benefits in reducing task completion time and cognitive workload.

Understanding transition paths between meta-stable states in molecular systems is fundamental for material design and drug discovery. However, sampling these paths via molecular dynamics simulations is computationally prohibitive due to the high-energy barriers between the meta-stable states. Recent machine learning approaches are often restricted to simple systems or rely on collective variables (CVs) extracted from expensive domain knowledge. In this work, we propose to leverage generative flow networks (GFlowNets) to sample transition paths without relying on CVs. We reformulate the problem as amortized energy-based sampling over molecular trajectories and train a bias potential by minimizing the squared log-ratio between the target distribution and the generator, derived from the flow matching objective of GFlowNets. Our evaluation on three proteins (Alanine Dipeptide, Polyproline, and Chignolin) demonstrates that our approach, called TPS-GFN, generates more realistic and diverse transition paths than the previous CV-free machine learning approach.

Theoretical studies on chemical reaction mechanisms have been crucial in organic chemistry. Traditionally, calculating the manually constructed molecular conformations of transition states for chemical reactions using quantum chemical calculations is the most commonly used method. However, this way is heavily dependent on individual experience and chemical intuition. In our previous study, we proposed a research paradigm that uses enhanced sampling in QM/MM molecular dynamics simulations to study chemical reactions. This approach can directly simulate the entire process of a chemical reaction. However, the computational speed limits the use of high-precision potential energy functions for simulations. To address this issue, we present a scheme for training high-precision force fields for molecular modeling using our developed graph-neural-network-based molecular model, molecular configuration transformer. This potential energy function allows for highly accurate simulations at a low computational cost, leading to more precise calculations of the mechanism of chemical reactions. We have used this approach to study a Cope rearrangement reaction and a Carbonyl insertion reaction catalyzed by Manganese. This "AI+Physics" based simulation approach is expected to become a new trend in the theoretical study of organic chemical reaction mechanisms.

The $K$-means algorithm remains one of the most widely-used clustering methods due to its simplicity and general utility. The performance of $K$-means depends upon location of minima low in cost function, amongst a potentially vast number of solutions. Here, we use the energy landscape approach to map the change in $K$-means solution space as a result of increasing dataset outliers and show that the cost function surface becomes more funnelled. Kinetic analysis reveals that in all cases the overall funnel is composed of shallow locally-funnelled regions, each of which are separated by areas that do not support any clustering solutions. These shallow regions correspond to different types of clustering solution and their increasing number with outliers leads to longer pathways within the funnel and a reduced correlation between accuracy and cost function. Finally, we propose that the rates obtained from kinetic analysis provide a novel measure of clustering similarity that incorporates information about the paths between them. This measure is robust to outliers and we illustrate the application to datasets containing multiple outliers.

The ability to explain decisions made by machine learning models remains one of the most significant hurdles towards widespread adoption of AI in highly sensitive areas such as medicine, cybersecurity or autonomous driving. Great interest exists in understanding which features of the input data prompt model decision making. In this contribution, we propose a novel approach to identify relevant features of the input data, inspired by methods from the energy landscapes field, developed in the physical sciences. By identifying conserved weights within groups of minima of the loss landscapes, we can identify the drivers of model decision making. Analogues to this idea exist in the molecular sciences, where coordinate invariants or order parameters are employed to identify critical features of a molecule. However, no such approach exists for machine learning loss landscapes. We will demonstrate the applicability of energy landscape methods to machine learning models and give examples, both synthetic and from the real world, for how these methods can help to make models more interpretable.