Related papers: Split Optimization for Protein/Ligand Binding Mode…

Cross-validation is a common method for estimating the predictive performance of machine learning models. In a data-scarce regime, where one typically wishes to maximize the number of instances used for training the model, an approach…

Variational Auto-encoders (VAEs) have been very successful as methods for forming compressed latent representations of complex, often high-dimensional, data. In this paper, we derive an alternative variational lower bound from the one…

Mixture proportion estimation (MPE) is the problem of estimating the weight of a component distribution in a mixture, given samples from the mixture and component. This problem constitutes a key part in many "weakly supervised learning"…

In recent years, machine learning has been proposed as a promising strategy to build accurate scoring functions for computational docking finalized to numerically empowered drug discovery. However, the latest studies have suggested that…

Algorithmic Bias can be due to bias in the training data or issues with the algorithm itself. These algorithmic issues typically relate to problems with model capacity and regularisation. This underestimation bias may arise because the…

Embedding is a useful technique to project a high-dimensional feature into a low-dimensional space, and it has many successful applications including link prediction, node classification and natural language processing. Current approaches…

This study assesses the efficiency of several popular machine learning approaches in the prediction of molecular binding affinity: CatBoost, Graph Attention Neural Network, and Bidirectional Encoder Representations from Transformers. The…

Model merging, particularly through weight averaging, has shown surprising effectiveness in saving computations and improving model performance without any additional training. However, the interpretability of why and how this technique…

The arc of drug discovery entails a multiparameter optimization problem spanning vast length scales. They key parameters range from solubility (angstroms) to protein-ligand binding (nanometers) to in vivo toxicity (meters). Through feature…

Variational Autoencoders (VAEs) are expressive latent variable models that can be used to learn complex probability distributions from training data. However, the quality of the resulting model crucially relies on the expressiveness of the…

The paper utilizes the graph embeddings generated for entities of a large biomedical database to perform link prediction to capture various new relationships among different entities. A novel node similarity measure is proposed that…

This letter gives results on improving protein-ligand binding affinity predictions based on molecular dynamics simulations using machine learning potentials with a hybrid neural network potential and molecular mechanics methodology…

Bias is known to be an impediment to fair decisions in many domains such as human resources, the public sector, health care etc. Recently, hope has been expressed that the use of machine learning methods for taking such decisions would…

We derive the ideal train/test split for the ridge regression to high accuracy in the limit that the number of training rows m becomes large. The split must depend on the ridge tuning parameter, alpha, but we find that the dependence is…

Metric-based meta-learning has attracted a lot of attention due to its effectiveness and efficiency in few-shot learning. Recent studies show that metric scaling plays a crucial role in the performance of metric-based meta-learning…

In the rapidly evolving domain of machine learning, ensuring model generalizability remains a quintessential challenge. Overfitting, where a model exhibits superior performance on training data but falters on unseen data, is a recurrent…

This paper proposes the asymmetric linear double autoregression, which jointly models the conditional mean and conditional heteroscedasticity characterized by asymmetric effects. A sufficient condition is established for the existence of a…

We propose a framework for the statistical evaluation of variational auto-encoders (VAEs) and test two instances of this framework in the context of modelling images of handwritten digits and a corpus of English text. Our take on evaluation…

Non-contextual word embedding models have been shown to inherit human-like stereotypical biases of gender, race and religion from the training corpora. To counter this issue, a large body of research has emerged which aims to mitigate these…

We present two deep generative models based on Variational Autoencoders to improve the accuracy of drug response prediction. Our models, Perturbation Variational Autoencoder and its semi-supervised extension, Drug Response Variational…