9 accepted papers
Computational antibody design seeks to automatically create an antibody that binds to an antigen. The binding affinity is governed by the 3D binding interface where antibody residues (paratope) closely interact with antigen residues (epitope). Thus, the key question of antibody design is how to pred…
We develop a new approach to multi-label conformal prediction in which we aim to output a precise set of promising prediction candidates with a bounded number of incorrect answers. Standard conformal prediction provides the ability to adapt to model uncertainty by constructing a calibrated candidate…
Predicting how a drug-like molecule binds to a specific protein target is a core problem in drug discovery. An extremely fast computational binding method would enable key applications such as fast virtual screening or drug engineering. Existing methods are computationally expensive as they rely on…
While unbiased machine learning models are essential for many applications, bias is a human-defined concept that can vary across tasks. Given only input-label pairs, algorithms may lack sufficient information to distinguish stable (causal) features from unstable (spurious) features. However, related…
We develop a novel approach to conformal prediction when the target task has limited data available for training. Conformal prediction identifies a small set of promising output candidates in place of a single prediction, with guarantees that the set contains the correct answer with high probability…
Generative autoencoders offer a promising approach for controllable text generation by leveraging their learned sentence representations. However, current models struggle to maintain coherent latent spaces required to perform meaningful text manipulations via latent vector operations. Specifically,…
Graph generation techniques are increasingly being adopted for drug discovery. Previous graph generation approaches have utilized relatively small molecular building blocks such as atoms or simple cycles, limiting their effectiveness to smaller molecules. Indeed, as we demonstrate, their performance…
Generative models in molecular design tend to be richly parameterized, data-hungry neural models, as they must create complex structured objects as outputs. Estimating such models from data may be challenging due to the lack of sufficient training data. In this paper, we propose a surprisingly effec…
Drug discovery aims to find novel compounds with specified chemical property profiles. In terms of generative modeling, the goal is to learn to sample molecules in the intersection of multiple property constraints. This task becomes increasingly challenging when there are many property constraints.…