Related papers: Molecule Design by Latent Prompt Transformer

Rich data and powerful machine learning models allow us to design drugs for a specific protein target \textit{in silico}. Recently, the inclusion of 3D structures during targeted drug design shows superior performance to other target-free…

Many applications of machine learning methods involve an iterative protocol in which data are collected, a model is trained, and then outputs of that model are used to choose what data to consider next. For example, one data-driven approach…

Probing Pre-trained Language Models (PLMs) using prompts has indirectly implied that language models (LMs) can be treated as knowledge bases. To this end, this phenomena has been effective especially when these LMs are fine-tuned towards…

Prompt tuning is a parameter-efficient tuning (PETuning) method for utilizing pre-trained models (PTMs) that simply prepends a soft prompt to the input and only optimizes the prompt to adapt PTMs to downstream tasks. Although it is…

Significant interests have recently risen in leveraging sequence-based large language models (LLMs) for drug design. However, most current applications of LLMs in drug discovery lack the ability to comprehend three-dimensional (3D)…

Transformer-based autoregressive models offer an efficient alternative to diffusion- and flow-matching-based approaches for generating 3D molecules. One challenge remains: standard transformer architectures require a sequential ordering of…

Automatic Chemical Design is a framework for generating novel molecules with optimized properties. The original scheme, featuring Bayesian optimization over the latent space of a variational autoencoder, suffers from the pathology that it…

This paper presents a novel approach for guiding a Generative Adversarial Network trained on the FashionGen dataset to generate designs corresponding to target fashion styles. Finding the latent vectors in the generator's latent space that…

Structure-based drug design aims at generating high affinity ligands with prior knowledge of 3D target structures. Existing methods either use conditional generative model to learn the distribution of 3D ligands given target binding sites,…

Current supervised learning can learn spurious correlation during the data-fitting process, imposing issues regarding interpretability, out-of-distribution (OOD) generalization, and robustness. To avoid spurious correlation, we propose a…

Continual learning requires to overcome catastrophic forgetting when training a single model on a sequence of tasks. Recent top-performing approaches are prompt-based methods that utilize a set of learnable parameters (i.e., prompts) to…

Molecular design requires systematic and broadly applicable methods to extract structure-property relationships. The focus of this study is on learning thermodynamic properties from molecular-liquid simulations. The methodology relies on an…

Deep generative models have been applied with increasing success to the generation of two dimensional molecules as SMILES strings and molecular graphs. In this work we describe for the first time a deep generative model that can generate 3D…

Large Transformer-based language models are pre-trained on corpora of varying sizes, for a different number of steps and with different batch sizes. At the same time, more fundamental components, such as the pre-training objective or…

We introduce the Latent Fourier Transform (LatentFT), a framework that provides novel frequency-domain controls for generative music models. LatentFT combines a diffusion autoencoder with a latent-space Fourier transform to separate musical…

Many machine learning tasks such as multiple instance learning, 3D shape recognition, and few-shot image classification are defined on sets of instances. Since solutions to such problems do not depend on the order of elements of the set,…

The main target of retrosynthesis is to recursively decompose desired molecules into available building blocks. Existing template-based retrosynthesis methods follow a template selection stereotype and suffer from limited training…

Knowing a biomolecule's structure is inherently linked to and a prerequisite for any detailed understanding of its function. Significant effort has gone into developing technologies for structural characterization. These technologies do not…

Translation into morphologically-rich languages challenges neural machine translation (NMT) models with extremely sparse vocabularies where atomic treatment of surface forms is unrealistic. This problem is typically addressed by either…

Antibody therapeutics are among the most successful modern medicines, yet computationally designing antibodies with desirable binding and developability properties remains challenging. While protein language models (pLMs) have emerged as…