seqme: a Python library for evaluating biological sequence design

Recent advances in computational methods for designing biological sequences have sparked the development of metrics to evaluate these methods performance in terms of the fidelity of the designed sequences to a target distribution and their attainment of desired properties. However, a single software library implementing these metrics was lacking. In this work we introduce seqme, a modular and highly extendable open-source Python library, containing model-agnostic metrics for evaluating computational methods for biological sequence design. seqme considers three groups of metrics: sequence-based, embedding-based, and property-based, and is applicable to a wide range of biological sequences: small molecules, DNA, ncRNA, mRNA, peptides and proteins. The library offers a number of embedding and property models for biological sequences, as well as diagnostics and visualization functions to inspect the results. seqme can be used to evaluate both one-shot and iterative computational design methods.

Unified Molecule Generation and Property Prediction

Modeling the joint distribution of the data samples and their properties allows to construct a single model for both data generation and property prediction, with synergistic capabilities reaching beyond purely generative or predictive models. However, training joint models presents daunting architectural and optimization challenges. Here, we propose Hyformer, a transformer-based joint model that successfully blends the generative and predictive functionalities, using an alternating attention mask together with a unified pre-training scheme. We show that Hyformer rivals other joint models, as well as state-of-the-art molecule generation and property prediction models. Additionally, we show the benefits of joint modeling in downstream tasks of molecular representation learning, hit identification and antimicrobial peptide design.

De Novo Drug Design with Joint Transformers

De novo drug design requires simultaneously generating novel molecules outside of training data and predicting their target properties, making it a hard task for generative models. To address this, we propose Joint Transformer that combines a Transformer decoder, a Transformer encoder, and a predictor in a joint generative model with shared weights. We show that training the model with a penalized log-likelihood objective results in state-of-the-art performance in molecule generation, while decreasing the prediction error on newly sampled molecules, as compared to a fine-tuned decoder-only Transformer, by 42%. Finally, we propose a probabilistic black-box optimization algorithm that employs Joint Transformer to generate novel molecules with improved target properties, as compared to the training data, outperforming other SMILES-based optimization methods in de novo drug design.

A pragmatic approach to estimating average treatment effects from EHR data: the effect of prone positioning on mechanically ventilated COVID-19 patients

Despite the recent progress in the field of causal inference, to date there is no agreed upon methodology to glean treatment effect estimation from observational data. The consequence on clinical practice is that, when lacking results from a randomized trial, medical personnel is left without guidance on what seems to be effective in a real-world scenario. This article showcases a pragmatic methodology to obtain preliminary estimation of treatment effect from observational studies. Our approach was tested on the estimation of treatment effect of the proning maneuver on oxygenation levels, on a cohort of COVID-19 Intensive Care patients. We modeled our study design on a recent RCT for proning (the PROSEVA trial). Linear regression, propensity score models such as blocking and DR-IPW, BART and two versions of Counterfactual Regression were employed to provide estimates on observational data comprising first wave COVID-19 ICU patient data from 25 Dutch hospitals. 6371 data points, from 745 mechanically ventilated patients, were included in the study. Estimates for the early effect of proning -- P/F ratio from 2 to 8 hours after proning -- ranged between 14.54 and 20.11 mm Hg depending on the model. Estimates for the late effect of proning -- oxygenation from 12 to 24 hours after proning -- ranged between 13.53 and 15.26 mm Hg. All confidence interval being strictly above zero indicated that the effect of proning on oxygenation for COVID-19 patient was positive and comparable in magnitude to the effect on non COVID-19 patients. These results provide further evidence on the effectiveness of proning on the treatment of COVID-19 patients. This study, along with the accompanying open-source code, provides a blueprint for treatment effect estimation in scenarios where RCT data is lacking. Funding: SIDN fund, CovidPredict consortium, Pacmed.

Improved Quantum Boosting

Boosting is a general method to convert a weak learner (which generates hypotheses that are just slightly better than random) into a strong learner (which generates hypotheses that are much better than random). Recently, Arunachalam and Maity gave the first quantum improvement for boosting, by combining Freund and Schapire's AdaBoost algorithm with a quantum algorithm for approximate counting. Their booster is faster than classical boosting as a function of the VC-dimension of the weak learner's hypothesis class, but worse as a function of the quality of the weak learner. In this paper we give a substantially faster and simpler quantum boosting algorithm, based on Servedio's SmoothBoost algorithm.