Question: Are this models usually semi/supervised or unsupervised?
Evidence: Machine translation finds use in cheminformatics in “translation" from one language (e.g. reactants) to another (e.g. products). Machine translation is a challenging task because the syntactic and semantic dependencies of each language differ from one another and this may give rise to ambiguities. Neural Machine Translation (NMT) models benefit from the potential of deep learning architectures to build a statistical model that aims to find the most probable target sequence for an input sequence by learning from a corpus of examples BIBREF110, BIBREF111. The main advantage of NMT models is that they provide an end-to-end system that utilizes a single neural network to convert the source sequence into the target sequence. BIBREF110 refer to their model as a sequence-to-sequence (seq2seq) system that addresses a major limitation of DNNs that can only work with fixed-dimensionality information as input and output. However, in the machine translation task, the length of the input sequences is not fixed, and the length of the output sequences is not known in advance.
The variational Auto-encoder (VAE) is another widely adopted text generation architecture BIBREF101. BIBREF34 adopted this architecture for molecule generation. A traditional auto-encoder encodes the input into the latent space, which is then decoded to reconstruct the input. VAE differs from AE by explicitly defining a probability distribution on the latent space to generate new samples. BIBREF34 hypothesized that the variational part of the system integrates noise to the encoder, so that the decoder can be more robust to the large diversity of molecules. However, the authors also reported that the non-context free property of SMILES caused by matching ring numbers and parentheses might often lead the decoder to generate invalid SMILES strings. A grammar variational auto-encoder (GVAE), where the grammar for SMILES is explicitly defined instead of the auto-encoder learning the grammar itself, was proposed to address this issue BIBREF102. This way, the generation is based on the pre-defined grammar rules and the decoding process generates grammar production rules that should also be grammatically valid. Although syntactic validity would be ensured, the molecules may not have semantic validity (chemical validity). BIBREF103 built upon the VAE BIBREF34 and GVAE BIBREF102 architectures and introduced a syntax-directed variational autoencoder (SD-VAE) model for the molecular generation task. The syntax-direct generative mechanism in the decoder contributed to creating both syntactically and semantically valid SMILES sequences. BIBREF103 compared the latent representations of molecules generated by VAE, GVAE, and SD-VAE, and showed that SD-VAE provided better discriminative features for druglikeness. BIBREF104 proposed an adversarial AE for the same task. Conditional VAEs BIBREF105, BIBREF106 were trained to generate molecules conditioned on a desired property. The challenges that SMILES syntax presents inspired the introduction of new syntax such as DeepSMILES BIBREF29 and SELFIES BIBREF32 (details in Section SECREF3).
Generative Adversarial Network (GAN) models generate novel molecules by using two components: the generator network generates novel molecules, and the discriminator network aims to distinguish between the generated molecules and real molecules BIBREF107. In text generation models, the novel molecules are drawn from a distribution, which are then fine-tuned to obtain specific features, whereas adversarial learning utilizes generator and discriminator networks to produce novel molecules BIBREF107, BIBREF108. ORGAN BIBREF108, a molecular generation methodology, was built upon a sequence generative adversarial network (SeqGAN) from NLP BIBREF109. ORGAN integrated RL in order to generate molecules with desirable properties such as solubility, druglikeness, and synthetizability through using domain-specific rewards BIBREF108.
Machine translation finds use in cheminformatics in “translation" from one language (e.g. reactants) to another (e.g. products).
The variational Auto-encoder (VAE) is another widely adopted text generation architecture BIBREF101.
Generative Adversarial Network (GAN) models generate novel molecules by using two components: the generator network generates novel molecules, and the discriminator network aims to distinguish between the generated molecules and real molecules BIBREF107.
Answer: Both supervised and unsupervised, depending on the task that needs to be solved.