arXiv subjects

Senthilnath Jayavelu

Publications and source records attributed to Senthilnath Jayavelu.

21 records · Page 2Linked to original sources

arXiv2021

An invertible crystallographic representation for general inverse design of inorganic crystals with targeted properties

Realizing general inverse design could greatly accelerate the discovery of new materials with user-defined properties. However, state-of-the-art generative models tend to be limited to a specific composition or crystal structure. Herein, we present a framework capable of general inverse design (not limited to a given set of elements or crystal structures), featuring a generalized invertible representation that encodes crystals in both real and reciprocal space, and a property-structured latent space from a variational autoencoder (VAE). In three design cases, the framework generates 142 new crystals with user-defined formation energies, bandgap, thermoelectric (TE) power factor, and combinations thereof. These generated crystals, absent in the training database, are validated by first-principles calculations. The success rates (number of first-principles-validated target-satisfying crystals/number of designed crystals) ranges between 7.1% and 38.9%. These results represent a significant step toward property-driven general inverse design using generative models, although practical challenges remain when coupled with experimental synthesis.

physics.comp-ph↗

arXiv2021

Predicting antimicrobial activity of conjugated oligoelectrolyte molecules via machine learning

New antibiotics are needed to battle growing antibiotic resistance, but the development process from hit, to lead, and ultimately to a useful drug, takes decades. Although progress in molecular property prediction using machine-learning methods has opened up new pathways for aiding the antibiotics development process, many existing solutions rely on large datasets and finding structural similarities to existing antibiotics. Challenges remain in modelling of unconventional antibiotics classes that are drawing increasing research attention. In response, we developed an antimicrobial activity prediction model for conjugated oligoelectrolyte molecules, a new class of antibiotics that lacks extensive prior structure-activity relationship studies. Our approach enables us to predict minimum inhibitory concentration for E. coli K12, with 21 molecular descriptors selected by recursive elimination from a set of 5,305 descriptors. This predictive model achieves an R2 of 0.65 with no prior knowledge of the underlying mechanism. We find the molecular representation optimum for the domain is the key to good predictions of antimicrobial activity. In the case of conjugated oligoelectrolytes, a representation reflecting the 3-dimensional shape of the molecules is most critical. Although it is demonstrated with a specific example of conjugated oligoelectrolytes, our proposed approach for creating the predictive model can be readily adapted to other novel antibiotic candidate domains.

physics.app-ph↗

arXiv2021

Does Adversarial Oversampling Help us?

Traditional oversampling methods are generally employed to handle class imbalance in datasets. This oversampling approach is independent of the classifier; thus, it does not offer an end-to-end solution. To overcome this, we propose a three-player adversarial game-based end-to-end method, where a domain-constraints mixture of generators, a discriminator, and a multi-class classifier are used. Rather than adversarial minority oversampling, we propose an adversarial oversampling (AO) and a data-space oversampling (DO) approach. In AO, the generator updates by fooling both the classifier and discriminator, however, in DO, it updates by favoring the classifier and fooling the discriminator. While updating the classifier, it considers both the real and synthetically generated samples in AO. But, in DO, it favors the real samples and fools the subset class-specific generated samples. To mitigate the biases of a classifier towards the majority class, minority samples are over-sampled at a fractional rate. Such implementation is shown to provide more robust classification boundaries. The effectiveness of our proposed method has been validated with high-dimensional, highly imbalanced and large-scale multi-class tabular datasets. The results as measured by average class specific accuracy (ACSA) clearly indicate that the proposed method provides better classification accuracy (improvement in the range of 0.7% to 49.27%) as compared to the baseline classifier.

cs.LG↗