Lingxiang Jia

Zipeng Zhong, Jie Song, Zunlei Feng et al.

Chemical reaction prediction, involving forward synthesis and retrosynthesis prediction, is a fundamental problem in organic synthesis. A popular computational paradigm formulates synthesis prediction as a sequence-to-sequence translation problem, where the typical SMILES is adopted for molecule representations. However, the general-purpose SMILES neglects the characteristics of chemical reactions, where the molecular graph topology is largely unaltered from reactants to products, resulting in the suboptimal performance of SMILES if straightforwardly applied. In this article, we propose the root-aligned SMILES (R-SMILES), which specifies a tightly aligned one-to-one mapping between the product and the reactant SMILES for more efficient synthesis prediction. Due to the strict one-to-one mapping and reduced edit distance, the computational model is largely relieved from learning the complex syntax and dedicated to learning the chemical knowledge for reactions. We compare the proposed R-SMILES with various state-of-the-art baselines and show that it significantly outperforms them all, demonstrating the superiority of the proposed method.

Zipeng Zhong, Jie Song, Zunlei Feng et al.

Retrosynthesis is the cornerstone of organic chemistry, providing chemists in material and drug manufacturing access to poorly available and brand-new molecules. Conventional rule-based or expert-based computer-aided synthesis has obvious limitations, such as high labor costs and limited search space. In recent years, dramatic breakthroughs driven by artificial intelligence have revolutionized retrosynthesis. Here we aim to present a comprehensive review of recent advances in AI-based retrosynthesis. For single-step and multi-step retrosynthesis both, we first list their goal and provide a thorough taxonomy of existing methods. Afterwards, we analyze these methods in terms of their mechanism and performance, and introduce popular evaluation metrics for them, in which we also provide a detailed comparison among representative methods on several public datasets. In the next part we introduce popular databases and established platforms for retrosynthesis. Finally, this review concludes with a discussion about promising research directions in this field.

Jiacong Hu, Jingwen Ye, Zunlei Feng et al.

Convolutional Neural Networks (CNNs) are well-known for their vulnerability to adversarial attacks, posing significant security concerns. In response to these threats, various defense methods have emerged to bolster the model's robustness. However, most existing methods either focus on learning from adversarial perturbations, leading to overfitting to the adversarial examples, or aim to eliminate such perturbations during inference, inevitably increasing computational burdens. Conversely, clean training, which strengthens the model's robustness by relying solely on clean examples, can address the aforementioned issues. In this paper, we align with this methodological stream and enhance its generalizability to unknown adversarial examples. This enhancement is achieved by scrutinizing the behavior of latent features within the network. Recognizing that a correct prediction relies on the correctness of the latent feature's pattern, we introduce a novel and effective Feature Pattern Consistency Constraint (FPCC) method to reinforce the latent feature's capacity to maintain the correct feature pattern. Specifically, we propose Spatial-wise Feature Modification and Channel-wise Feature Selection to enhance latent features. Subsequently, we employ the Pattern Consistency Loss to constrain the similarity between the feature pattern of the latent features and the correct feature pattern. Our experiments demonstrate that the FPCC method empowers latent features to uphold correct feature patterns even in the face of adversarial examples, resulting in inherent adversarial robustness surpassing state-of-the-art models.