AI helps in drug discovery with understandable explanations.
problem Understanding the complex models behind AI-generated drugs.
method Explainable AI methods to interpret deep learning models.
result Improved interpretability of AI-generated drug properties.
System automates identification of cancer drug repurposing from PubMed.
problem Manual extraction of cancer drug repurposing evidence from scientific publications is infeasible.
method NLP pipeline including querying, filtering, entity extraction, classification, and study type classification.
result Automated system extracts cancer drug repurposing evidence from PubMed abstracts.
Bayesian methods improve drug discovery experiment design.
problem Optimizing drug screening experiments in high-dimensional data.
method Bayesian inference and optimisation with upper confidence bound algorithms, Thompson sampling, and sparse tree search.
result Sparse tree search techniques outperform other methods in drug toxicity screening.
This study improves lung tumor segmentation in mice MRI scans with nnU-Net, reducing annotation needs.
problem Accurate lung tumor segmentation in mice MRI scans for drug discovery.
method Optimized nnU-Net 3D model for lung tumor segmentation with minimal annotations.
result nnU-Net 3D models outperform 2D models in MRI mice scans, requiring fewer annotations.
Optimal algorithm selects biological models without prior info.
problem Determining the correct biological model without prior knowledge.
method Systems biology models and likelihood-free inference.
result Improved model selection performance over conventional methods.
Automated digital twin discovery from biological data improves drug discovery and personalized medicine.
problem Developing reliable digital twins from noisy, incomplete biological data.
method Symbolic and sparse regression, Bayesian frameworks, deep learning, and large language models.
result Sparse regression generally outperforms symbolic regression, especially with Bayesian frameworks.
Review of automation's role in chemical discoveries.
problem Improving autonomous discovery in chemistry.
method Classification of discovery types, assessment of autonomy, case studies.
result Rapid advancements in automation and machine learning are transforming experimentation and modeling.
ChemCrow enhances LLMs for chemistry tasks, automating complex chemical processes.
problem Limited access to computational chemistry tools for large-language models.
method Integrating 18 expert-designed chemistry tools into an LLM (ChemCrow).
result ChemCrow autonomously plans and executes chemical syntheses and discoveries.
The challenge in controlling stochastic systems in which low-probability events can set the system on catastrophic trajectories is to develop a robust ability to respond to such events without significantly compromising the optimality of the baseline control policy. This paper presents CelluDose, a stochastic simulatio…
Monitoring the biomedical literature for cases of Adverse Drug Reactions (ADRs) is a critically important and time consuming task in pharmacovigilance. The development of computer assisted approaches to aid this process in different forms has been the subject of many recent works. One particular area that has shown pro…
ART automates synthetic biology design with machine learning.
problem Long development times in synthetic biology due to ad-hoc engineering.
method Machine learning and probabilistic modeling for systematic design.
result ART provides optimized strain recommendations and production levels.
Malaria is a life-threatening disease affecting millions. Microscopy-based assessment of thin blood films is a standard method to (i) determine malaria species and (ii) quantitate high-parasitemia infections. Full automation of malaria microscopy by machine learning (ML) is a challenging task because field-prepared sli…
Designing a new drug is a lengthy and expensive process. As the space of potential molecules is very large (10^23-10^60), a common technique during drug discovery is to start from a molecule which already has some of the desired properties. An interdisciplinary team of scientists generates hypothesis about the required…
Generative model designs drug combinations for improved efficacy and reduced side effects.
problem Designing effective drug combinations to overcome resistance and reduce side effects.
method Developed a deep generative model using HVGAE and a novel reward system.
result Network-principled drug combinations show reduced toxicity and potential for new strategies.
Visualizes deep generative models for drug design.
problem Limited visualization tools for deep generative models in drug discovery.
method Proposes a visualization framework for deep graph generative models.
result Interactive visualization and molecular optimization tools.
Improves drug properties using a novel LLM and reinforcement learning.
problem Optimizing drug properties while retaining chemical stability.
method Structured Policy Optimization (SPO) for fine-tuning a large language model.
result Enhanced drug properties across multiple target objectives.
Generative models have achieved impressive results in many domains including image and text generation. In the natural sciences, generative models have led to rapid progress in automated drug discovery. Many of the current methods focus on either 1-D or 2-D representations of typically small, drug-like molecules. Howev…
Drug-drug interactions (DDIs) are a major cause of preventable hospitalizations and deaths. Predicting the occurrence of DDIs helps drug safety professionals allocate investigative resources and take appropriate regulatory action promptly. Traditional DDI prediction methods predict DDIs based on the similarity between …
In medicine, visualizing chromosomes is important for medical diagnostics, drug development, and biomedical research. Unfortunately, chromosomes often overlap and it is necessary to identify and distinguish between the overlapping chromosomes. A segmentation solution that is fast and automated will enable scaling of co…
A new drug embedding method using hierarchical drug relations and chemical structures.
problem Learning accurate drug representations from chemical structures and hierarchies.
method Semi-supervised drug embedding using VAE in hyperbolic space.
result The method accurately places drugs in a hierarchy and predicts side-effects.
Paper proposes a new method for predicting drug interactions using adversarial autoencoders.
problem Predicting drug interactions to prevent adverse events.
method Introduces adversarial autoencoders based on Wasserstein distances and Gumbel-Softmax relaxation to generate high-quality negative samples.
result Significant improvements in link prediction and DDI classification tasks.
Background: The problem of predicting whether a drug combination of arbitrary orders is likely to induce adverse drug reactions is considered in this manuscript. Methods: Novel kernels over drug combinations of arbitrary orders are developed within support vector machines for the prediction. Graph matching methods are …
New method predicts drug interactions from drug images.
problem Predicting drug interactions from molecular structures.
method Siamese neural network using drug structure images.
result First work predicting DDIs from drug images.
Graph-augmented CNN predicts drug interactions with high accuracy.
problem Predicting drug-drug interactions (DDIs) with high accuracy.
method Combining graph CNN with an attentive pooling network to extract structural relations between drug pairs.
result Desirable performance with ROC 0.988, F1-score 0.956, and AUPR 0.986.
HAMN combines CF models to improve drug repositioning.
problem Efficient drug repositioning with cold start problem.
method Hybrid Attentional Memory Network (HAMN) integrating memory and attention mechanisms.
result HAMN outperforms other models in drug repositioning tasks.
CASTER predicts drug interactions using chemical substructures.
problem Identifying potential drug-drug interactions during drug design.
method CASTER uses sequential pattern mining, auto-encoding, and dictionary learning to predict DDIs.
result CASTER outperformed state-of-the-art models and provided interpretable predictions.
Selecting the right drugs for the right patients is a primary goal of precision medicine. In this manuscript, we consider the problem of cancer drug selection in a learning-to-rank framework. We have formulated the cancer drug selection problem as to accurately predicting 1). the ranking positions of sensitive drugs an…
Model predicts anti-cancer drug responses using gene and molecular data.
problem Expensive and time-consuming cancer drug discovery and tailoring.
method Uses variational autoencoders and multi-layer perceptrons to encode gene expression and drug data.
result High average R2 of 0.83 and 0.845 in predicting drug responses for breast and pan-cancer cell lines, respectively. Deep Rule Forests identifies drug-drug and drug-disease interactions causing AKI.
problem Identifying drug-drug and drug-disease interactions leading to AKI.
method Deep Rule Forests (DRF) algorithm discovering rules from multilayer tree models.
result DRF model outperforms other algorithms in prediction accuracy and interpretability.
Quantum machine learning boosts drug discovery efficiency.
problem Enhancing drug discovery through quantum computing.
method Quantum neural networks on gate-based quantum computers.
result Significant advancements in molecular property prediction and generation.
Study reveals similarities in knowledge flows between pharmaceutical and AI industries.
problem Understanding the dynamics of drug pipelines in global pharmaceutical industry.
method Multilayer network analysis of drug pipeline, global supply chain, and ownership data.
result Proven similarities in knowledge flows between pharmaceutical and AI industries.
Drug-drug interactions are preventable causes of medical injuries and often result in doctor and emergency room visits. Computational techniques can be used to predict potential drug-drug interactions. We approach the drug-drug interaction prediction problem as a link prediction problem and present two novel methods fo…
Deep learning predicts drug side-effects from molecular graphs.
problem Predicting drug side-effects from molecular structures.
method Recurrent Graph Neural Networks for multi-class multi-label graph-focused classification.
result Improved classification capability compared to previous methods.
CardiGraphormer uses SSL and GNNs to improve drug discovery.
problem Challenges in drug discovery due to combinatorial chemical space and limited approved drugs.
method Combines self-supervised learning, Graph Neural Networks, and Cardinality Preserving Attention.
result Enhanced predictive performance and interpretability in drug discovery.
Method learns drug-disease representations for repositioning opportunities.
problem Identifying new uses for existing drugs.
method Multi-relation unsupervised graph embedding model.
result Superior prediction performance in repositioning opportunities.
Text classification on drug SMILES strings yields competitive drug type classification results.
problem Classifying drug types using conventional text classification methods.
method Treated drug SMILES as sentences and applied basic NLP methods for classification.
result Competitive drug type classification results achieved.
We present the Network-based Biased Tree Ensembles (NetBiTE) method for drug sensitivity prediction and drug sensitivity biomarker identification in cancer using a combination of prior knowledge and gene expression data. Our devised method consists of a biased tree ensemble that is built according to a probabilistic bi…
Bi-GNN models drug interactions using a bi-level graph approach.
problem Predicting drug-drug interactions using machine learning.
method Bi-level graph neural networks that consider both interaction graph and representation graphs of drugs.
result Bi-GNN model improves DDI prediction accuracy compared to existing methods.
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 Autoencoder (Dr.VAE), learn latent representation of the underlying gene states befor…
Develops a scalable model for drug combination prediction in cancer.
problem Accurate prediction of drug combinations for cancer treatment.
method Permutation invariant multi-output Gaussian Processes with variational approximation and deep generative model.
result Model efficiently borrows information across drug combinations and provides uncertainty quantification.
Predicting the response of cancer cells to drugs is an important problem in pharmacogenomics. Recent efforts in generation of large scale datasets profiling gene expression and drug sensitivity in cell lines have provided a unique opportunity to study this problem. However, one major challenge is the small number of sa…
Computational Drug Repositioning (CDR) is the task of discovering potential new indications for existing drugs by mining large-scale heterogeneous drug-related data sources. Leveraging the patient-level temporal ordering information between numeric physiological measurements and various drug prescriptions provided in E…
Co-Diffusion predicts drug-target affinity by learning latent manifolds and diffusion, improving generalization.
problem Cold-start regimes in drug-target affinity prediction due to label scarcity and domain shifts.
method Two-stage framework: latent manifold alignment and latent diffusion regularization.
result Significantly outperforms state-of-the-art baselines, especially in zero-shot generalization.
In this paper we study the adaptive learnability of decision trees of depth at most d from membership queries. This has many applications in automated scientific discovery such as drugs development and software update problem. Feldman solves the problem in a randomized polynomial time algorithm that asks $\tilde O(2^…
Benchmark proposes to assess molecule docking efficiency.
problem Lack of realistic benchmarks for measuring progress in drug design.
method Proposes a docking-based benchmark using SMINA software.
result Graph-based generative models fail to generate high-scoring molecules.
GENN predicts drug interactions by modeling correlations between link labels.
problem Predicting drug-drug interactions with consideration of link type correlations.
method GENN uses graph energy neural networks to model link type correlations in DDI prediction.
result GENN outperforms baseline models by 13.77% and 5.01% in PR-AUC on two real-world datasets.
Dr.S recommends cancer drugs based on genomic data.
problem Personalizing cancer treatments using genomic information.
method Machine learning to identify optimal drug-gene associations.
result Developed a Drug Recommendation System (Dr.S) for cancer cell lines.
A neural network predicts drug interactions using attention mechanisms.
problem Predicting drug-drug interactions from massive combinations of drugs.
method Siamese self-attention multi-modal neural network integrating drug characteristics.
result The model achieves AUPR scores ranging from 0.77 to 0.92 on various benchmark datasets.