ET-Flow: Equivariant Flow-Matching for Molecular Conformer Generation

Authors: majdi  hassan
nikhil  shenoy
jungyoon  lee
hannes  stärk
stephan  thaler
dominique  beaini
Venue: NeurIPS_cc_2024_Conference
Published: 2024-05-15 19:13:31

Abstract: Predicting low-energy molecular conformations given a molecular graph is an 
important but challenging task in computational drug discovery. Existing state-
of-the-art approaches either resort to large scale transformer-based models that
diffuse over conformer fields, or use computationally expensive methods to gen-
erate initial structures and diffuse over torsion angles. In this work, we introduce
Equivariant Transformer Flow (ET-Flow). We showcase that a well-designed
flow matching approach with equivariance and harmonic prior alleviates the need
for complex internal geometry calculations and large architectures, contrary to
the prevailing methods in the field. Our approach results in a straightforward
and scalable method that directly operates on all-atom coordinates with minimal
assumptions. With the advantages of equivariance and flow matching, ET-Flow
significantly increases the precision and physical validity of the generated con-
formers, while being a lighter model and faster at inference. Code is available
https://github.com/shenoynikhil/ETFlow.

Main paper: 
 introduction: 
 Generating low-energy 3D representations of molecules, called conformers, from the molecular graph is a fundamental task in computational chemistry as the 3D structure of a molecule is responsible for several biological, chemical and physical properties (Guimarães et al., 2012; Schütt et al., 2018 Schütt et al., , 2021;; Gasteiger et al., 2020; Axelrod and Gomez-Bombarelli, 2023) . Conventional approaches to molecular conformer generation consist of stochastic and systematic methods. While stochastic methods such as Molecular Dynamics (MD) accurately generate conformations, they can be slow, cost-intensive, and have low sample diversity (Shim and MacKerell Jr, 2011; Ballard et al., 2015; De Vivo et al., 2016; Hawkins, 2017; Pracht et al., 2020) . Systematic (rule-based) methods (Hawkins et al., 2010; Bolton et al., 2011; Li et al., 2007; Miteva et al., 2010; Cole et al., 2018; Lagorce et al., 2009) that rely on torsional profiles and knowledge base of fragments are much faster but become less accurate Figure 1 : (a) Overview of ET-Flow. The model predicts a conditional vector field ⃗ v θ using interpolated positions (x t ), molecular structure (G), and time-step (t). Samples are drawn from the harmonic prior (x 0 ∼ p 0 ) and then rotationally aligned with the samples from data (x 1 ∼ p 1 ). A conditional probability path is constructed between pairs of x 0 and x 1 , and x t is then sampled from this path at a random time t. (b) The ET-Flow architecture consists of a representation module based on the TorchMD-NET architecture (Thölke and De Fabritiis, 2022) and an equivariant vector output module. For detailed architecture and input preprocessing information, see Section A.1. with larger molecules. Therefore, there has been an increasing interest in developing scalable and accurate generative modeling methods in molecular conformer generation.Existing machine learning based approaches use diffusion models (Ho et al., 2020; Song and Ermon, 2019) to sample diverse and high quality samples given access to low-energy conformations. Prior methods typically fall into two categories: diffusing the atomic coordinates in the Cartesian space (Xu et al., 2022; Wang et al., 2024) or diffusing along the internal geometry such as pairwise distances, bond angles, and torsion angles (Ganea et al., 2021; Jing et al., 2022) .Early approaches based on diffusion (Shi et al., 2021; Luo et al., 2021; Xu et al., 2022) faced challenges such as lengthy inference and training times as well as having lower accuracy compared to cheminformatics methods. Torsional Diffusion (Jing et al., 2022) was the first to outperform cheminformatics methods by diffusing only on torsion angles after producing an initial conformer with the chemoinformatics tool RDKiT. This reliance on RDKiT structures instead of employing an end-to-end approach comes with several limitations, such as restricting the tool to applications where the local structures produced by RDKiT are of sufficient accuracy. Unlike prior approaches, the current state-of-the-art MCF (Wang et al., 2024) proposes a domain-agnostic approach by learning to diffuse over functions by scaling transformers and learning soft inductive bias from the data (Zhuang et al., 2022) . Consequently, it comes with drawbacks such as high computational demands due to large number of parameters, limited sample efficiency from a lack of inductive biases like euclidean symmetries, and potential difficulties in scenarios with sparse data -a common challenge in this field.In this paper, we propose Equivariant Transformer Flow (ET-Flow), a simple yet powerful flowmatching model designed to generate low-energy 3D structures of small molecules with minimal assumptions. We utilize flow matching (Lipman et al., 2022; Albergo et al., 2023; Liu et al., 2022) , which enables the learning of arbitrary probability paths beyond diffusion paths, enhancing both training and inference efficiency compared to conventional diffusion generative models. Departing from traditional equivariant architectures like EGNN (Satorras et al., 2021) , we adopt an Equivariant Transformer (Thölke and De Fabritiis, 2022) to better capture geometric features. Additionally, our method integrates a Harmonic Prior (Jing et al., 2023; Stark et al., 2023) , leveraging the inductive bias that atoms connected by a bond should be in close proximity. We further optimize our flow matching objective by initially conducting rotational alignment on the harmonic prior, thereby constructing shorter probability paths between source and target distributions at minimal computational cost.Our contributions can be summarized as follows:1. We obtain state-of-the-art precision for molecule conformer prediction, resulting in more physically realistic and reliable molecules for practitioners. We improve upon the previous methods by a large margin on ensemble property prediction. 2. We highlight the effectiveness of incorporating equivariance and more informed priors in generating physically-grounded molecules in our simple yet well-engineered method. 3. Our parameter-efficient model requires orders of magnitude fewer sampling steps than GeoDiff (Xu et al., 2022) and has significantly fewer parameters than MCF (Wang et al., 2024) . 
background: 
 Diffusion Generative Models. Diffusion models (Song and Ermon, 2019; Song et al., 2020; Ho et al., 2020) enables a high-quality and diverse sampling from an unknown data distribution by approximating the Stochastic Differential Equation(SDE) that maps a simple density i.e. Gaussian to the unknown data density. Concretely, it involves training a neural network to learn the score, represented as ∇ x log p t (x) of the diffused data. During inference, the model generates sample by iteratively solving the reverse SDE. However, diffusion models have inherent drawbacks, as they (i) require on longer training times (ii) are restricted to specific probability paths and (iii) depend on the use of complicated tricks to speed up sampling (Song et al., 2020; Zhang and Chen, 2022) .Flow Matching. Flow Matching (Albergo et al., 2023; Lipman et al., 2022; Liu et al., 2022) provides a general framework to learn Continuous normalizing flows (CNFs) while improving upon diffusion models in simplicity, generality, and inference speed in several applications. Through simple regression against the vector field reminiscent of the score-matching objective in diffusion models, Flow matching has enabled a fast, simulation-free training of CNFs. Several subsequent studies have then expanded the scope of flow matching objective to manifolds (Chen and Lipman, 2024), arbitrary sources (Pooladian et al., 2023) , and conditional flow matching with arbitrary transport maps and optimal couplings between source and target samples (Tong et al., 2023) .Molecular Conformer Generation. Various machine learning (ML) based approaches (Kingma and Welling, 2013; Liberti et al., 2014; Dinh et al., 2016; Simm and Hernández-Lobato, 2019; Shi et al., 2021; Luo et al., 2021; Xu et al., 2021; Ganea et al., 2021; Xu et al., 2022; Jing et al., 2022; Wang et al., 2024) have been developed to improve upon the limitations of conventional methods, among which the most advanced are TorsionDiff (Jing et al., 2022) and Molecular Conformer Fields (MCF) (Wang et al., 2024) . TorsionDiff designs a diffusion model on the torsion angles while incorporating the local structure from RDKiT ETKDG (Riniker and Landrum, 2015) . MCF trains a diffusion model over functions that map elements from the molecular graph to points in 3D space.Equivariant Architectures for Atomistic Systems. Inductive biases play an important role in generalization and sample efficiency. In the case of 3D atomistic modelling, one example of a useful inductive bias is the euclidean group SO(3) which represents rotation equivariance in 3D space.Recently, various equivariant architectures (Duval et al., 2023) have been developed that act on both Cartesian (Satorras et al., 2021; Thölke and De Fabritiis, 2022; Simeon and De Fabritiis, 2024; Du et al., 2022; Frank et al., 2022) and spherical basis (Musaelian et al., 2023; Batatia et al., 2022; Fuchs et al., 2020; Liao et al., 2023; Passaro and Zitnick, 2023; Anderson et al., 2019; Thomas et al., 2018) . For molecular conformer generation, initial methods like ConfGF, DGSM utilize invariant networks as they act upon inter-atomic distances, whereas the use of equivariant GNNs have been used in GeoDiff (Xu et al., 2022) and Torsional Diffusion (Jing et al., 2022) . GeoDiff utilizes EGNN (Satorras et al., 2021) , a Cartesian basis equivariant architecture while Torsional Diffusion uses Tensor Field Networks (Thomas et al., 2018) to output pseudoscalars.Question: Does the paper discuss the limitations of the work performed by the authors?Answer: [Yes] Justification: Yes, the paper discussed the limitations in the Section 6.Guidelines:• The answer NA means that the paper has no limitation while the answer No means that the paper has limitations, but those are not discussed in the paper. • The authors are encouraged to create a separate "Limitations" section in their paper.• The paper should point out any strong assumptions and how robust the results are to violations of these assumptions (e.g., independence assumptions, noiseless settings, model well-specification, asymptotic approximations only holding locally). The authors should reflect on how these assumptions might be violated in practice and what the implications would be. • The authors should reflect on the scope of the claims made, e.g., if the approach was only tested on a few datasets or with a few runs. In general, empirical results often depend on implicit assumptions, which should be articulated. • The authors should reflect on the factors that influence the performance of the approach. For example, a facial recognition algorithm may perform poorly when image resolution is low or images are taken in low lighting. Or a speech-to-text system might not be used reliably to provide closed captions for online lectures because it fails to handle technical jargon. • The authors should discuss the computational efficiency of the proposed algorithms and how they scale with dataset size. • If applicable, the authors should discuss possible limitations of their approach to address problems of privacy and fairness. • While the authors might fear that complete honesty about limitations might be used by reviewers as grounds for rejection, a worse outcome might be that reviewers discover limitations that aren't acknowledged in the paper. The authors should use their best judgment and recognize that individual actions in favor of transparency play an important role in developing norms that preserve the integrity of the community. Reviewers will be specifically instructed to not penalize honesty concerning limitations. 
method: 
 We design ET-Flow, a scalable equivariant model that generates energy-minimized conformers given a molecular graph. In this section, we layout the framework to achieve this objective by detailing the generative process in flow matching, the rotation alignment between distributions, stochastic sampling, and finally the architecture details.Preliminaries We define notation that we use throughout this paper. Inputs are continuous atom positions x ∈ R N ×3 where N is the number of atoms. We use the notation v t (x) interchangeably with v(t, x) for vector field.The aim is to learn a time-dependent vector field v t (x) : R N ×3 × [0, 1] → R N ×3 associated with the transport map X t : R N ×3 × [0, 1] → R N ×3 that pushes forward samples from a base distribution ρ 0 , often an easy-to-sample distribution, to samples from a more complex target distribution ρ 1 , the low-energy conformations of a molecule. This can be defined as an ordinary differential equation (ODE),EQUATIONwhere x 0 ∼ ρ 0 . We can construct the v t via a time-differentiable interpolation between samples from ρ 0 and ρ 1 that gives rise to a probability path ρ t that we can easily sample (Lipman et al., 2022; Liu et al., 2022; Albergo and Vanden-Eijnden, 2023; Tong et al., 2023) . The general interpolation between samples x 0 ∼ ρ 0 and x 1 ∼ ρ 1 can be defined as:I t (x 0 , x 1 ) = α t x 1 + β t x 0 .(2)Given this interpolant that couples x 0 and x 1 , we can define the conditional probability path as ρ t (x|x 0 , x 1 ) = N (x|I t (x 0 , x 1 ), σ 2 t I), and the vector field can be computed as v t (x) = ∂ t ρ t (x|x 0 , x 1 ) which has the following formEQUATIONHere we use αt as a shorthand notation for ∂ t α t , and similarly we apply the same notation to β and σ.In our work, we use linear interpolation where α t = t, β t = 1 -t, and σ t = σ t(1 -t), resulting in the vector fieldEQUATIONNow, we can define the objective function for learning a vector field v θ (x) that generates a probability path ρ t between a base density ρ 0 and the target density ρ 1 as,EQUATION)For training, we sample (i) x 0 ∼ ρ 0 , x 1 ∼ ρ 1 , and t ∼ U(0, 1), (ii) interpolate according to Equation 2, (iii) add noise from a standard Gaussian, and (iv) minimize the loss defined in Equation 5.For sampling, we sample x 0 ∼ ρ 0 and integrate from t = 0 to t = 1 using the Euler's method. At each time-step, the Euler solver iteratively predicts the vector field for x t and updates its position x t+∆t = x t + v θ (t, x)∆t. More details on the training and sampling algorithms are provided in Appendix B.Several previous works (Tong et al., 2023; Klein et al., 2024; Jing et al., 2024; Song et al., 2024) demonstrate that constructing a straighter path between base distribution ρ 0 and target distribution ρ 1 minimizes the transport costs and improves performance. In our work, we reduce the transport costs between samples from the harmonic prior ρ 0 and samples from the data distribution ρ 1 by rotationally aligning them using the Kabsch algorithm (Kabsch, 1976) similar to (Klein et al., 2024; Jing et al., 2024) . This approach leads to faster convergence and reduces the path length between atoms by leveraging the similarity in "shape" of the samples as seen in Figure 1a without incurring high computational cost.We employ a variant of the stochastic sampling technique inspired by (Karras et al., 2022) . Specifically, we inject noise at each time step to construct an intermediate state, evaluate the vector field from the intermediate state, and then perform the deterministic ODE step from the noisy state. The original method utilizes a second-order integration, which averages the denoiser output at the noisy intermediate state and the state at the next time step after integration. In our experiment, we use the stochastic sampler without this second-order correction term, which empirically provided a performance boost comparable to the second-order method. We apply stochastic sampling only during the final part of the integration steps, specifically within the range t ∈ [0.8, 1.0]. This helps prevent drifting towards overpopulated density regions and improves the quality of the samples (Karras et al., 2022) . Stochastic sampling has improved both diversity and accuracy of the generated conformers, measured by Coverage and Average Minimum RMSD (AMR) respectively as shown in Table 1 . Detailed information on the stochastic sampling algorithm is provided in algorithm B.While generating conformations, it is necessary to take account of the stereochemistry of atoms bonded to four distinct groups also referred to as tetrahedral chiral centers. To generate conformations with the correct chirality, we propose a simple post hoc trick as done in GeoMol (Ganea et al., 2021) . We compare the oriented volume (OV) (Equation 6) of the generated conformation and the required orientation with the RDKit tags. In the case of a mismatch, we simply flip the conformation against the z-axis. This correction step can be efficiently performed as a batched operation since it involves a simple comparison with the required RDKit tags and an inversion of position if necessary.EQUATIONWe also consider an alternative approach for chirality correction. Instead of using the post hoc correction with our O(3) equivariant architecture, we slightly tweak our architecture to make it SO(3) equivariant by introducing a cross product term in the update layers. We compare these methods on both the GEOM-DRUGS and GEOM-QM9 dataset in Table 1 and Table 2 . Our base method (ET-Flow) corresponds to using the post hoc correction whereas the SO(3) variant is referred by ET-Flow-SO(3). We empirically observe that using an additional chirality correction step is not only computationally efficient, but also performs better. We provide details on the architectural modification and proof of SO(3) equivariance in Section A.1 and Section C.1 respectively.ET-Flow (Figure 1b ) consists of two main components: (1) a representation module based on the equivariant transformer architecture from TorchMD-NET (Thölke and De Fabritiis, 2022) and (2) the equivariant vector output module. In the representation module, an embedding layer encodes the inputs (atomic positions, atomic numbers, atom features, bond features and the time-step) into a set of invariant features. Initial equivariant features are constructed using normalized edge vectors where the edges are constructed using a radius graph of 10 angstrom and the bonds from the 2D molecular graph. Then, a series of equivariant attention-based layers update both the invariant and equivariant features using a multi-head attention mechanism. Finally, the vector field is produced by the output layer, which updates the equivariant features using gated equivariant blocks (Schütt et al., 2018) . Given that TorchMD-NET was originally designed for modeling neural network potentials, we implement several modifications to its architecture to better suit generative modeling, as detailed in Section A.1.Question: For each theoretical result, does the paper provide the full set of assumptions and a complete (and correct) proof?Answer: [Yes] Justification: All assumptions and proofs are stated as needed in the manuscript.Guidelines:• The answer NA means that the paper does not include theoretical results.• All the theorems, formulas, and proofs in the paper should be numbered and cross-referenced.• All assumptions should be clearly stated or referenced in the statement of any theorems.• The proofs can either appear in the main paper or the supplemental material, but if they appear in the supplemental material, the authors are encouraged to provide a short proof sketch to provide intuition. • Inversely, any informal proof provided in the core of the paper should be complemented by formal proofs provided in appendix or supplemental material. • Theorems and Lemmas that the proof relies upon should be properly referenced. 
experiments: 
 We empirically evaluate ET-Flow by comparing the generated and ground-truth conformers in terms of distance-based RMSD (Section 4.2) and chemical property based metrics (Section 4.4). We Dataset: We conduct our experiments on the GEOM dataset (Axelrod and Gomez-Bombarelli, 2022) , which offers curated conformer ensembles produced through meta-dynamics in CREST (Pracht et al., 2024) . Our primary focus is on GEOM-DRUGS, the most extensive and pharmacologically relevant subset comprising 304k drug-like molecules, each with an average of 44 atoms. We use a train/validation/test (243473/30433/1000) split as provided in (Ganea et al., 2021 ) Additionally, we train and test model on GEOM-QM9, a subset of smaller molecules with an average of 11 atoms. Finally, in order to assess the model's ability to generalize to larger molecules, we evaluate the model trained on GEOM-DRUGS on a GEOM-XL dataset, a subset of large molecules with more than 100 atoms. The results for GEOM-QM9 and GEOM-XL can be found in the Appendix D.Evaluation: Our evaluation methodology is similar to that of (Jing et al., 2022) . First, we look at RMSD based metrics like Coverage and Average Minimum RMSD (AMR) between generated and ground truth conformer ensembles. For this, we generate 2K conformers for a molecule with K ground truth conformers. Second, we look at chemical similarity using properties like Energy (E), dipole moment (µ), HOMO-LUMO gap (∆ϵ) and the minimum energy (E min ) calculated using xTB (Bannwarth et al., 2019) .Baselines: We benchmark ET-Flow against leading approaches outlined in Section 2. Specifically, we assess the performance of GeoMol (Ganea et al., 2021) , GeoDiff (Xu et al., 2022) , Torsional Diffusion (Jing et al., 2022) , and MCF (Wang et al., 2024) . Notably, the most recent among these, MCF, has demonstrated superior performance across evaluation metrics compared to its predecessors. It's worth mentioning that GeoDiff initially utilized a limited subset of the GEOM-DRUGS dataset; thus, for a fair comparison, we consider its re-evaluated performance as presented in (Jing et al., 2022) .As shown in Table 1 and Table 2 , ET-Flow outperforms all preceding methodologies and demonstrates competitive performance with the previous state-of-the-art, MCF (Wang et al., 2024) . Despite being significantly smaller with only 8.3M parameters, ET-Flow shows a substantial improvement in the quality of generated conformers, as evidenced by superior Precision metrics across all MCF models, including the largest MCF-L. When compared to MCF-S, which is closer in size, ET-Flow achieves markedly better Precision while the impact on Recall is less significant and limited to Recall Coverage. Notably, our Recall AMR remains competitive with much bigger MCF-B, underscoring the inherent advantage of our method in accurately predicting overall structures. We compare the coverage metrics of ET-Flow against Torsional diffusion (Jing et al., 2022) and MCF (Wang et al., 2024) against a wide range of thresholds on the GEOM DRUGS dataset in Figure 3 . ET-Flow consistently outperforms previous methods in precision-based metrics. In terms of recall, our approach demonstrates better performance than Torsional Diffusion across all thresholds. Despite MCF performing better at higher thresholds, ET-Flow outperforms in the lower thresholds, underscoring its proficiency in generating accurate conformer predictions. We emphasize the better performance of ET-Flow at lower thresholds in both Recall and Precision metrics.RMSD provides a geometric measure for assessing ensemble quality, but it is also essential to consider the chemical similarity between generated and ground truth ensembles. For a random 100-molecule subset of the test set of GEOM-DRUGS, if a molecule has K ground truth conformers, we generate a minimum of 2K and a maximum of 32 conformers per molecule. These conformers are then relaxed using GFN2-xTB (Bannwarth et al., 2019) , and the Boltzmann-weighted properties of the generated and ground truth ensembles are compared. Specifically, using xTB (Bannwarth et al., 2019) , we compute properties such as energy (E), dipole moment (µ), HOMO-LUMO gap (∆ϵ), and the minimum energy (E min ). Table 3 illustrates the median errors for ET-Flow and the baselines, highlighting our method's capability to produce chemically accurate ensembles. Notably, we achieve significant improvements over both TorsionDiff and MCF across all evaluated properties. In Table 1 , our sampling process with ET-Flow utilizes 50 inference steps. To evaluate the method's performance under constrained computational resources, we conducted an ablation study by progressively reducing the number of inference steps. Specifically, we sample for 5, 10 and 20 time-steps.The results on GEOM-DRUGS are presented in Table 4 . We observed minimal performance degradation with a decrease in the number of steps. Notably, ET-Flow demonstrates high efficiency, maintaining performance across all precision and recall metrics even with as few as 5 inference steps. Interestingly, ET-Flow with 5 steps still achieves superior precision metrics compared to all existing methods. This underscores ET-Flow's ability to generate high-quality conformations while operating within limited computational budgets. We demonstrate the ability of ET-Flow to generate samples efficiently. We evaluate the inference time per molecule over varying number of time steps and report the average time across 1000 random samples from the test set of GEOM-DRUGS. Figure 4 shows that ET-Flow outperforms Torsional diffusion (Jing et al., 2022) in inference across all time steps. While ET-Flow may not achieve the fastest raw inference times (potentially due to MCF variants benefiting from optimized CUDA kernels for attention), it maintains competitive speeds while ensuring higher precision. We suspect that concurrent work on improving equivariant operations with optimized CUDA kernels (Lee et al., 2024) should lead to similar efficiency gains as seen in transformer-based architectures. 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conclusion: 
 In this paper, we present our simple and scalable method ET-Flow, which utilizes an equivariant transformer with flow matching to achieve state-of-the-art performance on multiple molecular conformer generation benchmarks. By incorporating inductive biases, such as equivariance, and enhancing probability paths with a harmonic prior and RMSD alignment, we significantly improve the precision of the generated molecules, and consequently generate more physically plausible molecules. Importantly, our approach maintains parameter and speed efficiency, making it not only effective but also accessible for practical high-throughput applications.Question: Does the paper provide open access to the data and code, with sufficient instructions to faithfully reproduce the main experimental results, as described in supplemental material? Answer: [Yes] Justification: We provide links to our our code and data.Guidelines:• The answer NA means that paper does not include experiments requiring code. • Providing as much information as possible in supplemental material (appended to the paper) is recommended, but including URLs to data and code is permitted. 
limitations and future works: 
 While ET-Flow demonstrates competitive performance in molecular conformer generation, there are areas where it can be enhanced. One such area is the recall metrics, which capture the diversity of generated conformations. Another area is the use of an additional chirality correction step that is used to predict conformations with the desired chirality. Moreover, although our performance on the GEOM-XL dataset is comparable to MCF-S and TorsionDiff, there is still room for improvement.We propose three future directions here. First, we observe during experiments that a well-designed sampling process incorporating stochasticity can enhance the quality and diversity of generated samples. An extension of our current approach could involve using Stochastic Differential Equations (SDEs), which utilize both vector field and score in the integration process, potentially improving the diversity of samples. Second, we propose to scale the number of parameters of ET-Flow, which has not only been shown to be useful across different domains of deep learning, but has also shown to be useful in molecular conformer generation for MCF (Wang et al., 2024) . Third, to better handle the chirality problem, we aim to explore alternatives for incorporating SO(3)-equivariance into the model in the future. Question: Does the paper specify all the training and test details (e.g., data splits, hyperparameters, how they were chosen, type of optimizer, etc.) necessary to understand the results?Answer: [Yes] Justification: Data splits is detailed in Section 4, and the hyperparameters are detailed in Section A.4.Guidelines:• The answer NA means that the paper does not include experiments.• The experimental setting should be presented in the core of the paper to a level of detail that is necessary to appreciate the results and make sense of them. • The full details can be provided either with the code, in appendix, or as supplemental material. 
experiment statistical significance: 
 Question: Does the paper report error bars suitably and correctly defined or other appropriate information about the statistical significance of the experiments?Answer: [No] Justification: We follow the same data splits as previous works (Ganea et al., 2021; Jing et al., 2022; Wang et al., 2024) .Guidelines:• The answer NA means that the paper does not include experiments. • The authors should answer "Yes" if the results are accompanied by error bars, confidence intervals, or statistical significance tests, at least for the experiments that support the main claims of the paper. • The factors of variability that the error bars are capturing should be clearly stated (for example, train/test split, initialization, random drawing of some parameter, or overall run with given experimental conditions). • The method for calculating the error bars should be explained (closed form formula, call to a library function, bootstrap, etc.) • The assumptions made should be given (e.g., Normally distributed errors). • It should be clear whether the error bar is the standard deviation or the standard error of the mean. • It is OK to report 1-sigma error bars, but one should state it. The authors should preferably report a 2-sigma error bar than state that they have a 96% CI, if the hypothesis of Normality of errors is not verified. • For asymmetric distributions, the authors should be careful not to show in tables or figures symmetric error bars that would yield results that are out of range (e.g. negative error rates). • If error bars are reported in tables or plots, The authors should explain in the text how they were calculated and reference the corresponding figures or tables in the text. 
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 Question: For each experiment, does the paper provide sufficient information on the computer resources (type of compute workers, memory, time of execution) needed to reproduce the experiments?Answer: [Yes] Justification: We provide these details in Section A.4.Guidelines:• The answer NA means that the paper does not include experiments.• The paper should indicate the type of compute workers CPU or GPU, internal cluster, or cloud provider, including relevant memory and storage.• Datasets that have been scraped from the Internet could pose safety risks. The authors should describe how they avoided releasing unsafe images. • We recognize that providing effective safeguards is challenging, and many papers do not require this, but we encourage authors to take this into account and make a best faith effort.12. Licenses for existing assets Question: Are the creators or original owners of assets (e.g., code, data, models), used in the paper, properly credited and are the license and terms of use explicitly mentioned and properly respected?Answer: [Yes] Justification: Yes, we cite all creators and original owners of work referenced in this manuscript.Guidelines:• The answer NA means that the paper does not use existing assets.• The authors should cite the original paper that produced the code package or dataset.• The authors should state which version of the asset is used and, if possible, include a URL.• The name of the license (e.g., CC-BY 4.0) should be included for each asset.• For scraped data from a particular source (e.g., website), the copyright and terms of service of that source should be provided. • If assets are released, the license, copyright information, and terms of use in the package should be provided. For popular datasets, paperswithcode.com/datasets has curated licenses for some datasets. Their licensing guide can help determine the license of a dataset. • For existing datasets that are re-packaged, both the original license and the license of the derived asset (if it has changed) should be provided. • If this information is not available online, the authors are encouraged to reach out to the asset's creators. 
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 Appendix: The ET-Flow architecture (Figure 5 ) consists of 2 major components, a representation layer and an output layer.For the representation layer, we use a modified version of the embedding and equivariant attention-based update layers from the equivariant transformer architecture of TorchMD-NET (Thölke and De Fabritiis, 2022) . The output layer utilizes the gated equivariant blocks from (Schütt et al., 2018) . We highlight our modifications over the original TorchMD-NET architecture with this color. These modifications enable stabilized training since we use a larger network than the one proposed in the TorchMD-NET (Thölke and De Fabritiis, 2022) paper. Additionally, since our input structures are interpolations between structures sampled from a prior and actual conformations, it is important to ensure our network is numerically stable when the interpolations contain two atoms very close to each other.Embedding Layer: The embedding layer maps each atom's physical and chemical properties into a learned representation space, capturing both local atomic features and geometric neighborhood information. For the i-th atom in a molecule with N atoms, we compute an invariant embedding xi through the following process:EQUATION)where zi is the atomic number and hi represents atomic attributes (detailed in Appendix A). The MLP projects atomic attributes into a feature vector of dimension d h .Next, we compute a neighborhood embedding ni that captures local atomic environment:EQUATIONHere, embed nbh (zj) provides a separate embedding for neighboring atomic numbers, dij is the distance between atoms i and j, and lij encodes edge features (either from a radius-based graph or molecular bonds). The interaction function g(dij, lij) combines distance and edge information:EQUATIONwhere e RBF k are K exponential radial basis functions following (Unke and Meuwly, 2019), and ϕ(dij) is a smooth cutoff function:EQUATIONFinally, we combine all features into the atom's embedding through a linear projection:EQUATIONwhere t represents the time-step, and [•, •] denotes concatenation. The resulting embedding xi ∈ R d serves as input to subsequent layers of the network.Attention Mechanism: The multi-head dot-product attention operation uses atom features xi, atom attributes hi, time-step t and inter-atomic distances dij to compute attention weights. The input atom-level features xi are mixed with the atom attributes hi and the time-step t using an MLP and then normalized using a LayerNorm (Ba et al., 2016) . To compute the attention matrix, the inter-atomic distances dij are projected into two dimensional filters D K and D V as:D K = σ W D K e RBF (dij) + b D K D V = σ W D V e RBF (dij) + b D V (13)The atom level features are then linearly projected along with a LayerNorm operation to derive the query Q and key K vectors. The value vector V is computed with only the linear projection of atom-level features. Applying LayerNorm on Q, K vectors (also referred to as QK-Norm) has proven to stabilize un-normalized values in the attention matrix (Dehghani et al., 2023; Esser et al., 2024) when scaling networks to large number of parameters. The Q and K vectors are then used along with the distance filter D K for a dot-product operation over the feature dimension:EQUATION)The attention matrix is derived by passing the above dot-product operation matrix through a non-linearity and weighting it using a cosine cutoff ϕ(dij) (similar to the embedding layer) which ensures the attention weights are non-zero only when two atoms are within a specified cutoff:EQUATIONUsing the value vector V and the distance filter DV , we derive 3 equally sized filters by splitting along the feature dimension,EQUATIONA linear projection is then applied to combine the attention matrix and the vectors s 3 ij to derive an atom level feature yi = W O N j Aij • s 3 ij . The output of the attention operation are yi (an atom level feature) and two scalar filters s 1 ij and s 2 ij (edge-level features). Update Layer: The update layer computes interactions between atoms in the attention block and uses the outputs to update the scalar feature xi and the vector feature ⃗ vi. First, the scalar feature output yi from the attention mechanism is split into three features (q 1 i , q 2 i , q 3 i ), out of which q 1 i and q 2 i are used for the scalar feature update as, ∆xi = qEQUATIONwhere ⟨U1⃗ vi • U2⃗ vi⟩ is the inner product between linear projections of vector features ⃗ vi with matrices U1, U2.The edge vector update consists of two components. First, we compute a vector ⃗ wi, which for each atom is computed as a weighted sum of vector features and a clamped-norm of the edge vectors over all neighbors:EQUATION∆⃗ vi = ⃗ wi + q 3 i • U3⃗ vi (20) where U1 and U3 are projection matrices over the feature dimension of the vector feature ⃗ vi. In this layer, we clamp the minimum value of the norm (to ϵ = 0.01) to prevent numerically large values in cases where positions of two atoms are sampled too close from the prior.We also design an SO(3) equivariant architecture by adding an additional cross product term in Equation 19 as follows,EQUATIONwhere sij 4 is derived by modifying the split operation Equation 17in the attention layer where the value vector V and distance filter DV is projected into 4 equally sized filters instead of 3.Output Layer: The output layer consists of Gated Equivariant Blocks from (Schütt et al., 2018) . Given atom scalar xi and vector features ⃗ vi, the updates in each block is defined as,xi,updated, ⃗ wi = split(MLP([xi, U1⃗ vi)])) (22) ⃗ vi,updated = (U2⃗ vi) • ⃗ wi (23)Here, U1 and U2 are linear projection matrices that act along feature dimension. Our modification is to use LayerNorm in the MLP to improve training stability.Atomic features (or Node Features) are computed using RDKit (Landrum et al., 2013) features as described in Table 5 . For computing edge features and edge index, we use a combination of global (radius based edges) and local (molecular graph edges) similar to (Jing et al., 2022) . Following the approaches of (Ganea et al., 2021; Xu et al., 2022; Jing et al., 2022) , we utilize Average Minimum RMSD (AMR) and Coverage (COV) to assess the performance of molecular conformer generation. Here, Cg denotes the set of generated conformations, and Cr denotes the set of reference conformations. For both AMR and COV, we calculate and report Recall (R) and Precision (P). Recall measures the extent to which the generated conformers capture the ground-truth conformers, while Precision indicates the proportion of generated conformers that are accurate. The specific formulations for these metrics are detailed in the following equations:AMR-R(Cg, Cr) = 1 |Cr| R∈Cr min R∈Cg RMSD(R, R) COV-R(Cg, Cr) = 1 |Cr| |{R ∈ Cr|RMSD(R, R) < δ, R ∈ Cg}| AMR-P(Cr, Cg) = 1 |Cg| R∈Cg min R∈Cr RMSD( R, R) COV-P(Cr, Cg) = 1 |Cg| |{ R ∈ Cg|RMSD( R, R) < δ, R ∈ Cr}|A lower AMR score signifies improved accuracy, while a higher COV score reflects greater diversity in the generative model. Following (Jing et al., 2022) , the threshold δ is set to 0.5Å for GEOM-QM9 and 0.75Å for GEOM-DRUGS.For GEOM-DRUGS, we train ET-Flow for a fixed 250 epochs with a batch size of 64 and 5000 training batches per epoch per GPU on 8 A100 GPUs. For the learning rate, we use the Adam Optimizer with a cosine annealing learning rate which goes from a maximum of 10 -3 to a minimum 10 -7 over 250 epochs with a weight decay of 10 -10 . For GEOM-QM9, we train ET-Flow for 200 epochs with a batch size of 128, and use all of the training dataset per epoch on 4 A100 GPUs. We use the cosine annealing learning rate schedule with maximum of 8 • 10 -4 to minimum of 10 -7 over 100 epochs, post which the maximum is reduced by a factor of 0.05. We select checkpoints based on the lowest validation error. The following algorithms go over the pseudo-code for the training and sampling procedure. For each molecule, we use up to 30 conformations with the highest boltzmann weights as provided by CREST (Pracht et al., 2024) similar to that of (Jing et al., 2022) Algorithm 1: Training procedureInput: molecules [G 0 , ..., G N ] each with true conformers [C G,1 , ...C G,K G ],the harmonic prior ρ 0 , learning rate α, number of epochs N e , initialized vector field v θ Output: trained flow matching modelv θ for i ← 1 to N e do for G in [G 0 , ..., G N ] do Sample t ∼ U[0, 1] and C 1 ∈ [C G,1 , ...C G,K G ]; Sample prior C 0 ∼ ρ 0 (G); Align C 0 ← RMSDAlign(C 0 , C 1 ); Sample C t = tC 1 + (1 -t)C 0 + σ 2 t(1 -t)z, z ∼ N (0, I); Construct vector field u t ← x 1 -x 0 + 1-2t 2 √ t(1-t) z;Compute loss ← ∥v θ (t, C t ) -u t ∥ 2 ; Take gradient step θ ← θ -α∇ θ ;Algorithm 2: Inference procedure Input: molecular graph G, number conformers K, number of sampling steps N Output: provided by Torsional Diffusion, we encountered 27 failed cases for generation likely due to RDKit failures, similar to the observations in MCF albeit with slightly different exact numbers. In both experiments involving all 102 molecules and a subset of 75 molecules, ET-Flow achieves performance comparable to Torsional Diffusion and MCF-S, but falls short of matching the performance of MCF-B and MCF-L. It's worth noting that MCF-B and MCF-L are significantly larger models, potentially affording them an advantage in generalization tasks. As part of our future work, we plan to scale up our model and conduct further tests to explore its performance in this regard. To further evaluate the generalization performance of ET-Flow, we conduct two more out-of-distribution experiments in addition to GEOM-XL. First, we test the model on scaffold-based splits of the GEOM-QM9 and GEOM-DRUGS dataset, which offers a more challenging alternative to the standard random split. We split the datasets based on Murcko scaffolds of the molecules into an 80:10:10 ratio for train, validation, and test sets. We evaluate our method on 1000 randomly sampled molecules from the resulting test set. The second experiment involves training the model on GEOM-DRUGS and assessing its performance on GEOM-QM9, a dataset with significantly smaller molecules. This experiment complements the generalization task to larger molecules in GEOM-XL by assessing ability for ET-Flow to generalize to smaller molecules. The results, presented in Table 9 , indicate that the model's performance degrades only marginally on the scaffold-based split. Furthermore, the model demonstrates robust performance on GEOM-QM9 even when trained on GEOM-DRUGS.predicted conformers [C 1 , ...C K ] for C in [C 1 , ...C K ] do sample prior Ĉ ∼ ρ 0 (G); for n ← 0 to N -1 do Set t ← n N ; Set ∆t ← 1 N ; Predict v = v θ (t, Ĉ); Update Ĉ = Ĉ + v∆tFigure 6 shows randomly selected examples of sampled conformers from ET-Flow for GEOM-DRUGS. The left column is the reference molecule from the ground truth, and the remaining columns are samples generated with 50 sampling steps. Figure 7 showcases the ability for ET-Flow to generate quality samples with fewer sampling steps. Guidelines:• The answer NA means that the abstract and introduction do not include the claims made in the paper. • The abstract and/or introduction should clearly state the claims made, including the contributions made in the paper and important assumptions and limitations. A No or NA answer to this question will not be perceived well by the reviewers. • The claims made should match theoretical and experimental results, and reflect how much the results can be expected to generalize to other settings. • It is fine to include aspirational goals as motivation as long as it is clear that these goals are not attained by the paper. 


Decision: The paper presents a conformer generation approach using flow matching. In this task, given a graph a generative model generates 3D configurations of molecules which  coincide with energy minima (conformers). The approach is of limited technical novelty, but a nice display of how a simple, well-engineered model can achieve state of the art results. During discussion the authors engage well with the concerns raise by the reviewers, in particular, they add a number of important ablations.

Reviews: review: paper_summary: paper_summary: The paper describes an equivariant flow matching model for conformer generation.  The stated contributions are accurate - the model performance is state-of-the-art and largely due to good engineering.
strength_weakness: strength_weakness: Very little evaluation of out-of-distribution performance is considered (a small evaluation is in the appendix).  The ensemble property averages evaluation seems to be done on molecules drawn from the training data (if this is not the case, it needs to be more clear).  The paper would be stronger if generalization performance was more comprehensively evaluated.

Although efficiency is one of the main claims, there's no evaluation of inference time.

I think "DRUGS" is used as a short-hand for GEOM-DRUGS - this is confusing, use consistent nomenclature throughout.
questions: questions: What is the out-of-distribution performance?  How well does the model generalize to different chemotypes (not just larger) and how does this compare to conventional and other generative models?

It would be interesting to see MCF trained using the same frame work as ETflow - e.g. how much of the performance is due to the choices in Table 6 versus the model architecture.

Can you perform evaluations that demonstrate these conformers are better for downstream tasks than those generated through conventional approaches?
limitations: limitations: Some recent work has pointed to the fact that improved recall/precision on these GEOM benchmarks does not necessarily result in better performance on downstream tasks that use conformers.  At least some discussion of this limitation would be appreciated.
paper_summary: paper_summary: The paper proposes the Equivariant Transformer Flow (ET-Flow) which predicts low-energy molecular conformations given the molecular graphs. Unlike existing methods that rely on large transformer-based models for conformed fields or complex internal geometry calculations, ET-Flow leverages flow matching with equivariance and harmonic prior which directly operates on all-atom coordinates with minimal assumptions. The extensive experimental results illustrate that ET-Flow achieves state-of-the-art performance in molecular conformer generation benchmarks with fewer parameters and faster inference times, outperforming or matching previous methods while maintaining high accuracy and efficiency.
strength_weakness: strength_weakness: 1. ET-Flow achieves SOTA or near-SOTA performance on the benchmarks. However, my concern is that TorchMD-Net is already a strong model with a well-established architecture that leverages equivariant transformers for molecular modeling. Given this, it can be challenging to attribute the performance improvements of ET-Flow to the flow matching approach. Ablation studies focusing on the flow matching component or results from simpler architectures might be useful. 

1. The need for a post hoc chirality correction step suggests that the model does not inherently handle stereochemistry (baseline models like MCF do not require such an explicit correction). Such a weakness may result in issues in practical applications. 

1. ET-Flow primarily combines TorchMD-Net with the flow matching technique. While both components are robust and effective, the novelty of the approach is limited as it largely builds on existing methodologies. This integration, although leading to performance improvements, does not significantly advance the state-of-the-art in terms of methodological innovation.
questions: questions: 1. The proposed model utilizes an equivariant model architecture. Meanwhile, it is widely argued that equivariance is not a requirement for molecular machine learning (as suggested in the MCF paper). Without equivariance, the model is more easily generalized and scaled, and the symmetry could be implicitly learned from the data. I would like to ask the authors about the thoughts on this. In particular, I'm interested in the scaling performance (with respect to data or model size) of ET-Flow compared to MCF. 

1. Have the authors considered conducting data augmentation to improve the diversity of generated conformations and enhance recall metrics?
limitations: limitations: The authors have discussed the limitations of recall performance and additional chirality correction steps. No potential negative societal impact is involved.
paper_summary: paper_summary: The paper proposes the Equivariant Transformer Flow (ET-Flow) to generate high-quality molecule conformations. The authors use rotational alignment, stochastic sampling, and chirality correction to improve the flow matching framework for this task. Additionally, the paper modifies the TorchMD-NET equivariant transformer architecture to parameterize the target vector field. Experiments on the GEOM dataset show that  ET-Flow can perform well on the conformation prediction task. Furthermore, conformations generated by ET-Flow can also be used to predict ensemble properties with great performance.
strength_weakness: strength_weakness: 1. Lack of experiments. The experiments on the GEOM dataset are not enough to show the empirical performance of the framework. Some further experiments on large-scale datasets with more data and larger system size are necessary. I suggest the authors do experiments on OC20/OC22(Open Catalyst 2020/2022) datasets to test the performance of the ET-Flow framework.
2. The novelty of this work is not enough. I think the idea and method of this paper is very similar to [1], but in this work, the authors use a transformer-based model. Additionally, this paper proposes several tricks such as rotational alignment, stochastic sampling, and chirality correction. So the authors should clarify the novelty of this work.

[1]. Klein, Leon, Andreas Krämer, and Frank Noé. "Equivariant flow matching." Advances in Neural Information Processing Systems 36 (2024).
questions: questions: See the sections above.
limitations: limitations: N/A

Comments: comment: For the scaffold split experiment, we divide the GEOM-QM9 smiles based on molecular scaffolds into an 80:10:10 ratio for train, validation, and test sets.  Our results based on 1000 randomly sampled molecules from the test set are as follows,

| Method | Recall Coverage (mean) | Recall Coverage (median) | Recall AMR (mean) | Recall AMR (median) | Precision Coverage (mean) | Precision Coverage (median) | Precision AMR (mean) | Precision AMR (median) |
|--------|------------------------|--------------------------|-------------------|---------------------|---------------------------|-----------------------------|-----------------------|------------------------|
| ET-Flow (Random Split) | 94.99 | 100.00 | 0.083 | 0.035 | 91.00 | 100.00 | 0.116 | 0.047 |
| ET-Flow (Scaffold Split) | 95.00 | 100.00 | 0.083 | 0.029 | 90.25 | 100.00 | 0.124 | 0.053 |

It seems that generalization across scaffolds is possible. We will include the same experiments on GEOM-DRUGS, which are still running. 

Thanks for the suggestion - this experiment is a nice addition! Please let us know if they sufficiently address your concern.
Thanks for the nice suggestion! In OC20, one aims to find the relaxed structure of a molecule conditioned on a slab, which differs fundamentally from our work. The catalyst periodicity requires specialized approaches, such as AdsorbDiff[1].

To compare the OC20 dataset size and diversity with our datasets:
- The GEOM-DRUGS training dataset contains ~240,000 molecules and up to 30 conformations each, resulting in 5.7 million conformations. OC20 contains 82 molecules.
- GEOM-DRUGS molecules (\~44 atoms) are larger than the average size of the adsorbates (structure to be relaxed) in OC20 (\~5 atoms)
- To evaluate on larger molecules, we also evaluate on GEOM-XL (>100 atoms) with larger molecules than the training distribution. The results are shown in Appendix C.1 table 7. Do the experiments on Geom-XL address your concerns sufficiently under these considerations?

We appreciate your insights and look forward to your feedback on this approach.

[1] Kolluru, A., & Kitchin, J. R., 2024. AdsorbDiff: Adsorbate Placement via Conditional Denoising Diffusion. arXiv preprint arXiv:2405.03962.
We sincerely thank the reviewer for their thoughtful feedback and insightful discussion. This has greatly contributed to enhancing the quality of our work.
We would like to thank the reviewer for the valuable feedback. We will indeed incorporate the additional evaluations into the manuscript. Currently, we are conducting an experiment on GEOM-QM9 using a scaffold split, and we expect to upload the results within a day. We also plan to run a scaffold split experiment on GEOM-DRUGS, but given time and compute constraints, we will not be able to provide those results immediately. We will include both scaffold-split experiments in the manuscript.

Are there any additional experiments or discussions the reviewer would recommend to further enhance the quality of the paper?
Thank the authors for the response. The additional experimental results and thorough analysis provided in the rebuttal effectively address most of my concerns and strongly support the paper's ideas. With that, I'd like to raise my score.
Thanks for your reply. 

As you have mentioned in the paper, your goal is to construct a "scalable equivariant model that generates energy-minimized conformers given a molecular graph". I think you can test your framework in the OC20/22 datasets because the 
IS2RS task (predict the relaxation structure based on the initial structure) is equivalent to "generate an energy-minimized conformer".  Indeed, it is a nontrivial task but it's necessary to test your method on large-scale datasets with more data and larger system size.

I thank you again for clarifying the novelty of your work.
The additional evaluations (out of distribution, inference time, and ablation studies) definitely strengthen the paper (assuming they get included).

A way to evaluate generalization to novel chemotypes is to perform a scaffold split of the training data. 

Downstream tasks from conformer generation include molecular docking, shape similarity, and pharmacophore search.  While I would not expect a comprehensive evaluation of ET-Flow's performance in these tasks in this paper, if the goal of the authors is to develop methods that advance drug discovery and not just to get a bold number in an ML conference paper, they should be evaluated and compared to standard approaches (e.g. RDKit ensembles - see https://pubs.acs.org/doi/full/10.1021/acs.jcim.3c01245).