Work done during an internship at NVIDIA.

However, most existing machine learning methods for small molecule generation suffer from poor synthesizability of candidate compounds, making experimental validation difficult.

Generative models hold great promise for small molecule discovery, significantly increasing the size of search space compared to traditional in silico screening libraries. However, most existing machine learning methods for small molecule generation suffer from poor synthesizability of candidate compounds, making experimental validation difficult. In this paper we propose Reaction-GFlowNet (RGFN), an extension of the GFlowNet framework that operates directly in the space of chemical reactions, thereby allowing out-of-the-box synthesizability while maintaining comparable quality of generated candidates. We demonstrate that with the proposed set of reactions and building blocks, it is possible to obtain a search space of molecules orders of magnitude larger than existing screening libraries coupled with low cost of synthesis. We also show that the approach scales to very large fragment libraries, further increasing the number of potential molecules. We demonstrate the effectiveness of the proposed approach across a range of oracle models, including pretrained proxy models and GPU-accelerated docking.

The constrained nature of synthesizable chemical space poses a significant challenge for sampling molecules that are both synthetically accessible and possess desired properties. In this work, we present PrexSyn, an efficient and programmable model for molecular discovery within synthesizable chemical space. PrexSyn is based on a decoder-only transformer trained on a billion-scale datastream of synthesizable pathways paired with molecular properties, enabled by a real-time, high-throughput C++-based data generation engine. The large-scale training data allows PrexSyn to reconstruct the synthesizable chemical space nearly perfectly at a high inference speed and learn the association between properties and synthesizable molecules. Based on its learned property-pathway mappings, PrexSyn can generate synthesizable molecules that satisfy not only single-property conditions but also composite property queries joined by logical operators, thereby allowing users to ``program'' generation objectives. Moreover, by exploiting this property-based querying capability, PrexSyn can efficiently optimize molecules against black-box oracle functions via iterative query refinement, achieving higher sampling efficiency than even synthesis-agnostic baselines, making PrexSyn a powerful general-purpose molecular optimization tool. Overall, PrexSyn pushes the frontier of synthesizable molecular design by setting a new state of the art in synthesizable chemical space coverage, molecular sampling efficiency, and inference speed.

Work done during an internship at NVIDIA.

However, most existing machine learning methods for small molecule generation suffer from poor synthesizability of candidate compounds, making experimental validation difficult.

Generative models hold great promise for small molecule discovery, significantly increasing the size of search space compared to traditional in silico screening libraries. However, most existing machine learning methods for small molecule generation suffer from poor synthesizability of candidate compounds, making experimental validation difficult. In this paper we propose Reaction-GFlowNet (RGFN), an extension of the GFlowNet framework that operates directly in the space of chemical reactions, thereby allowing out-of-the-box synthesizability while maintaining comparable quality of generated candidates. We demonstrate that with the proposed set of reactions and building blocks, it is possible to obtain a search space of molecules orders of magnitude larger than existing screening libraries coupled with low cost of synthesis. We also show that the approach scales to very large fragment libraries, further increasing the number of potential molecules. We demonstrate the effectiveness of the proposed approach across a range of oracle models, including pretrained proxy models and GPU-accelerated docking.

Even though thermodynamic energy-based crystal structure prediction (CSP) has revolutionized materials discovery, the energy-driven CSP approaches often struggle to identify experimentally realizable metastable materials synthesized through kinetically controlled pathways, creating a critical gap between theoretical predictions and experimental synthesis. Here, we propose a synthesizability-driven CSP framework that integrates symmetry-guided structure derivation with a Wyckoff encode-based machine-learning model, allowing for the efficient localization of subspaces likely to yield highly synthesizable structures. Within the identified promising subspaces, a structure-based synthesizability evaluation model, fine-tuned using recently synthesized structures to enhance predictive accuracy, is employed in conjunction with ab initio calculations to systematically identify synthesizable candidates. The framework successfully reproduces 13 experimentally known XSe (X = Sc, Ti, Mn, Fe, Ni, Cu, Zn) structures, demonstrating its effectiveness in predicting synthesizable structures. Notably, 92,310 structures are filtered from the 554,054 candidates predicted by GNoME, exhibiting great potential for promising synthesizability. Additionally, eight thermodynamically favorable Hf-X-O (X = Ti, V, and Mn) structures have been identified, among which three HfV$_2$O$_7$ candidates exhibit high synthesizability, presenting viable candidates for experimental realization and potentially associated with experimentally observed temperature-induced phase transitions. This work establishes a data-driven paradigm for machine-learning-assisted inorganic materials synthesis, highlighting its potential to bridge the gap between computational predictions and experimental realization while unlocking new opportunities for the targeted discovery of novel functional materials.

Fragment-based drug discovery, in which molecular fragments are assembled into new molecules with desirable biochemical properties, has achieved great success. However, many fragment-based molecule generation methods show limited exploration beyond the existing fragments in the database as they only reassemble or slightly modify the given ones. To tackle this problem, we propose a new fragment-based molecule generation framework with retrieval augmentation, namely Fragment Retrieval-Augmented Generation (f-RAG). f-RAG is based on a pre-trained molecular generative model that proposes additional fragments from input fragments to complete and generate a new molecule. Given a fragment vocabulary, f-RAG retrieves two types of fragments: (1) hard fragments, which serve as building blocks that will be explicitly included in the newly generated molecule, and (2) soft fragments, which serve as reference to guide the generation of new fragments through a trainable fragment injection module. To extrapolate beyond the existing fragments, f-RAG updates the fragment vocabulary with generated fragments via an iterative refinement process which is further enhanced with post-hoc genetic fragment modification. f-RAG can achieve an improved exploration-exploitation trade-off by maintaining a pool of fragments and expanding it with novel and high-quality fragments through a strong generative prior.

A significant challenge in wet lab experiments with current drug design generative models is the trade-off between pharmacological properties and synthesizability. Molecules predicted to have highly desirable properties are often difficult to synthesize, while those that are easily synthesizable tend to exhibit less favorable properties. As a result, evaluating the synthesizability of molecules in general drug design scenarios remains a significant challenge in the field of drug discovery. The commonly used synthetic accessibility (SA) score aims to evaluate the ease of synthesizing generated molecules, but it falls short of guaranteeing that synthetic routes can actually be found. Inspired by recent advances in top-down synthetic route generation, we propose a new, data-driven metric to evaluate molecule synthesizability. Our approach directly assesses the feasibility of synthetic routes for a given molecule through our proposed round-trip score. This novel metric leverages the synergistic duality between retrosynthetic planners and reaction predictors, both of which are trained on extensive reaction datasets. To demonstrate the efficacy of our method, we conduct a comprehensive evaluation of round-trip scores alongside search success rate across a range of representative molecule generative models.