The study addresses biases in evaluating molecular optimization methods and proposes methods to reduce these biases.
problem Biases in in silico evaluation of molecular optimization methods.
method Discussion and empirical investigation of bias reduction methods for predictor misspecification and sample reuse.
result Empirical investigation of bias reduction methods for predictor misspecification and sample reuse.
Paper proposes a method to use in silico experiments with foundation models to reduce sample size.
problem Costly and uncertain randomized experiments.
method Integrates predictions from multiple foundation models with experimental data.
result Estimator offers substantial precision gains, equivalent to a 20% reduction in sample size.
The study improves compound selection in in silico screening by focusing on model's ability to predict desirable outcomes.
problem Improving compound selection in in silico screening to reduce errors and enhance generalization.
method Extending learning theory, the study analyzes the impact of selection policies on generalization and proposes a method to mitigate challenges.
result Generalization can be enhanced by considering a model's ability to predict the fraction of desired outcomes in a batch.
This abstract reviews recent methods for predicting protein-ligand binding affinity.
problem Predicting protein-ligand binding affinity for various applications in life sciences.
method Traditional and deep learning models for binding affinity prediction.
result Improved predictive performance of AI-driven models.
SBI improves uncertainty analysis of cardiovascular biomarkers.
problem Mapping waveforms back to plausible physiological parameters.
method Simulation-based inference (SBI) for statistical inference.
result Posterior distributions provide a multi-dimensional representation of uncertainty.
BOAT optimizes multiple antibody properties efficiently.
problem Balancing multiple drug-like properties in antibody design.
method Bayesian optimization framework coupling surrogate modeling and genetic algorithm.
result Competitive performance with state-of-the-art multi-objective protein optimization methods.
UDA improves ABI robustness but fails under certain prior misspecifications.
problem Robustness of ABI in noisy real-world data.
method Systematic evaluation of UDA across various misspecification scenarios.
result UDA aligns summary spaces but can fail under prior misspecifications.
DeepVir uses deep matrix factorization to predict antivirals for COVID-19.
problem Predicting effective antivirals for COVID-19 using known drug-virus associations.
method Graphical deep matrix factorization with HyPALM optimization.
result DeepVir outperforms state-of-the-art techniques in predicting antivirals for COVID-19.
Simulation-based inference aids in predicting disease dynamics for health policy.
problem Predicting disease dynamics to inform public health interventions.
method Simulation-based inference using machine learning.
result Potential for efficient interpretable Bayesian inference in epidemiological models.
LaMBO optimizes biological sequences using autoencoders and Bayesian optimization.
problem Bayesian optimization for drug design is limited by discrete, high-dimensional decision variables.
method Jointly trains denoising autoencoder with a Gaussian process head for gradient-based optimization in latent space.
result LaMBO outperforms genetic optimizers and requires no large pretraining corpus.
Modern treatments for Type 1 diabetes (T1D) use devices known as artificial pancreata (APs), which combine an insulin pump with a continuous glucose monitor (CGM) operating in a closed-loop manner to control blood glucose levels. In practice, poor performance of APs (frequent hyper- or hypoglycemic events) is common en…
Smoothed fitness landscape improves protein optimization.
problem Infeasibility of combinatorially large protein sequence space.
method Formulate protein fitness as a graph signal, smooth using Tikunov regularization, and optimize with Gibbs sampling.
result 2.5 fold fitness improvement over training set.
With the advent of deep generative models in computational chemistry, in silico anticancer drug design has undergone an unprecedented transformation. While state-of-the-art deep learning approaches have shown potential in generating compounds with desired chemical properties, they disregard the genetic profile and prop…
An important task for many if not all the scientific domains is efficient knowledge integration, testing and codification. It is often solved with model construction in a controllable computational environment. In spite of that, the throughput of in-silico simulation-based observations become similarly intractable for …
New metrics improve scRNA-seq perturbation modeling by reducing mode collapse.
problem Outperformed by simple mean prediction in scRNA-seq perturbation modeling.
method Introduce DEG-aware metrics (WMSE, Rw2(Δ)) and negative/positive baselines. result WMSE loss function reduces mode collapse and improves model performance.
Accurate prediction of drug-target interaction (DTI) is essential for in silico drug design. For the purpose, we propose a novel approach for predicting DTI using a GNN that directly incorporates the 3D structure of a protein-ligand complex. We also apply a distance-aware graph attention algorithm with gate augmentatio…
The paper characterizes brain states and transitions using functional MRI data.
problem Characterizing the dynamic reconfiguration of neural systems in brain states.
method Bayesian model-based characterization of latent brain states and posterior predictive discrepancy using the latent block model.
result The model detects transitions between latent brain states and identifies distinctive community patterns in task-fMRI data.
AntBO optimizes antibody design using Bayesian optimization for efficient and effective CDRH3 sequence generation.
problem Designing optimal antigen-specific CDRH3 regions in antibody design due to combinatorial sequence space.
method Combinatorial Bayesian optimization framework with trust region for developability.
result AntBO designs CDRH3 regions with diverse biophysical properties and outperforms existing methods.
In silico drug-target interaction (DTI) prediction is an important and challenging problem in biomedical research with a huge potential benefit to the pharmaceutical industry and patients. Most existing methods for DTI prediction including deep learning models generally have binary endpoints, which could be an oversimp…
New Bayesian optimization models for efficient material screening.
problem Efficiently screening materials with expensive and cheap tests.
method Flexible multi-test Bayesian optimization models with complex relationships.
result Demonstrated power on synthetic and real data.
In line with recent advances in neural drug design and sensitivity prediction, we propose a novel architecture for interpretable prediction of anticancer compound sensitivity using a multimodal attention-based convolutional encoder. Our model is based on the three key pillars of drug sensitivity: compounds' structure i…
How spiking networks are able to perform probabilistic inference is an intriguing question, not only for understanding information processing in the brain, but also for transferring these computational principles to neuromorphic silicon circuits. A number of computationally powerful spiking network models have been pro…
Stem uses diffusion models to infer gene expression from H&E images.
problem Inference of gene expression from H&E stained images is time-consuming and expensive.
method Conditional diffusion generative model to infer gene expression.
result Stem achieves state-of-the-art performance in spatial gene expression prediction.
AbDiffuser generates full-atom antibodies with sequence and structure fidelity.
problem Generating high-fidelity antibodies with both structure and sequence information.
method Equivariant and physics-informed diffusion model with novel protein structure representation.
result AbDiffuser generates antibodies with sequence and structural properties matching a reference set.
Expands experimental design for causal discovery from limited data.
problem Challenges in causal discovery from observational and interventional data.
method Bayesian optimal experimental design incorporating recent advances in causal discovery.
result Active causal discovery of large, nonlinear SCMs with both intervention target and value selection.
A novel multi-fidelity HMC algorithm improves efficiency and accuracy.
problem High computational cost and gradient inaccessibility in HMC.
method Two-stage HMC with surrogate model for gradient approximation.
result Significantly improved computational and statistical efficiency.
Hybrid Amortized Inference improves PPG model interpretability.
problem Tension between PPG biomarker accuracy and clinical interpretability.
method Introduces PPGen for biophysical PPG signal-physiological parameter relation, and HAI for fast, robust estimation.
result Hybrid Amortized Inference accurately infers physiological parameters from PPG signals.
Computer-assisted synthesis planning aims to help chemists find better reaction pathways faster. Finding viable and short pathways from sugar molecules to value-added chemicals can be modeled as a retrosynthesis planning problem with a catalyst allowed. This is a crucial step in efficient biomass conversion. The tradit…
Multispectral optical imaging is becoming a key tool in the operating room. Recent research has shown that machine learning algorithms can be used to convert pixel-wise reflectance measurements to tissue parameters, such as oxygenation. However, the accuracy of these algorithms can only be guaranteed if the spectra acq…
ChemCPA predicts cellular responses to novel drugs using transfer learning.
problem Scaling high-throughput screens to measure cellular responses for many drugs is costly and challenging.
method ChemCPA, a new encoder-decoder architecture combined with transfer learning.
result Training on existing bulk RNA HTS datasets improves generalization performance, reducing the need for extensive single-cell screens.
Deep neural networks (DNNs) transform stimuli across multiple processing stages to produce representations that can be used to solve complex tasks, such as object recognition in images. However, a full understanding of how they achieve this remains elusive. The complexity of biological neural networks substantially exc…
The World Trade Web (WTW) is a weighted network whose nodes correspond to countries with edge weights reflecting the value of imports and/or exports between countries. In this paper we introduce to this macroeconomic system the notion of extinction analysis, a technique often used in the analysis of ecosystems, for the…
Study uses simulation-based inference to decode brain activity from synthetic stimuli.
problem Reversing the process of brain activity emulation to recover stimuli or their properties.
method Pairing brain emulator with LLMs to learn a probabilistic mapping from brain maps to stimulus parameters.
result LLMs can serve as controllable stimulus generators and parameters can be recovered from brain maps.
Cellina uses supervised disentanglement to predict cell behavior in tissues.
problem Querying counterfactuals on tissue graphs
method Cellina framework using supervised disentanglement
result Outperforms spatially-informed and non-spatial competitors
Bayesian optimization identifies optimal alloy formulations.
problem Accelerated discovery in materials science with autonomous systems.
method Bayesian optimization over problem formulation space.
result Framework converges on optimal alloy formulations.
Paper introduces a method to predict molecule properties from diverse data sources.
problem Limited ability to accommodate scarce or fragmented training data.
method Adaptive Invariance using invariant risk minimization to generalize beyond heterogeneous data.
result Predictor outperforms state-of-the-art transfer learning methods by significant margin.
New method refines model predictions as design evolves.
problem Designing objects with desired properties using data-driven methods.
method Formalized as a game, developed autofocusing strategy for model retraining.
result Autofocusing improves model predictions in design space.
Proteins are commonly used by biochemical industry for numerous processes. Refining these proteins' properties via mutations causes stability effects as well. Accurate computational method to predict how mutations affect protein stability are necessary to facilitate efficient protein design. However, accuracy of predic…
DeepSIBA predicts biological effects of chemical structures using graph neural networks.
problem Predicting biological effects of chemical structures for drug discovery.
method Siamese Graph Convolutional Neural Networks for structure-biological effect mapping.
result Highly accurate predictions of biological effects for structurally dissimilar compounds.
A vast majority of computation in the brain is performed by spiking neural networks. Despite the ubiquity of such spiking, we currently lack an understanding of how biological spiking neural circuits learn and compute in-vivo, as well as how we can instantiate such capabilities in artificial spiking circuits in-silico.…
Meta-learning improves GNN initializations for low-resource drug discovery.
problem Limited labeled data hinders deep learning in drug discovery.
method Model-Agnostic Meta-Learning (MAML) and its variants for graph neural networks initializations.
result Meta-initializations outperform multi-task pre-training baselines on 16 out of 20 tasks and all out-of-distribution tasks.
Machine learning identifies potential drugs for COVID-19.
problem Finding effective treatments for COVID-19.
method Trained neural network models on virus protein sequences and antiviral drugs.
result Identified potential drug candidates for treating COVID-19.
Multi-StyleGAN simulates live cell microscopy imagery.
problem Costly and complex live cell experiments.
method Generative adversarial network (GAN) synthesizing multi-domain time-lapse images.
result Captures biophysical factors and time dependencies in cell imagery.
Recent work suggests goal-driven training of neural networks can be used to model neural activity in the brain. While response properties of neurons in artificial neural networks bear similarities to those in the brain, the network architectures are often constrained to be different. Here we ask if a neural network can…
Bayesian optimization of antibodies learns from immune system evolution.
problem Efficiently optimizing antibody sequences in a large space of possibilities.
method Bayesian optimization guided by a generative model of evolving antibody sequences.
result CloneBO optimizes antibodies more efficiently than previous methods.
P3BO optimizes biological sequence design by combining multiple methods.
problem Variability in performance of black-box optimization methods for biological sequence design.
method Population-Based Black-Box Optimization (P3BO) that samples sequences from an ensemble of methods, weighting by past performance.
result P3BO outperforms individual methods, proposing higher quality and more diverse sequences.
Machine learning algorithms can be fooled by small well-designed adversarial perturbations. This is reminiscent of cellular decision-making where ligands (called antagonists) prevent correct signalling, like in early immune recognition. We draw a formal analogy between neural networks used in machine learning and model…
Deep learning uses ROC cost functions to improve virtual screening accuracy.
problem Challenges in training deep learning models for virtual screening, especially class imbalance and lack of ground truth labels.
method Proposes using ROC cost functions to optimize deep learning models for virtual screening, introduces new training schemes and cost functions.
result Demonstrates improved performance of ROC-based approaches on PubChem datasets.