A locally-built, LLM-digested index of recent arXiv papers in quant finance, geometry/topology, and statistical ML — keyword search served straight from SQLite on this machine.
We propose a molecular generative model based on the conditional variational autoencoder for de novo molecular design. It is specialized to control multiple molecular properties simultaneously by imposing them on a latent space. As a proof of concept, we demonstrate that it can be used to generate drug-like molecules w…
A major challenge in computational chemistry is the generation of novel molecular structures with desirable pharmacological and physiochemical properties. In this work, we investigate the potential use of autoencoder, a deep learning methodology, for de novo molecular design. Various generative autoencoders were used t…
We propose a novel computational strategy for de novo design of molecules with desired properties termed ReLeaSE (Reinforcement Learning for Structural Evolution). Based on deep and reinforcement learning approaches, ReLeaSE integrates two deep neural networks - generative and predictive - that are trained separately b…
This work improves molecular design by efficiently selecting diverse candidate molecules.
GEGL uses genetic experts to improve deep learning for molecular design.
In de novo drug design, computational strategies are used to generate novel molecules with good affinity to the desired biological target. In this work, we show that recurrent neural networks can be trained as generative models for molecular structures, similar to statistical language models in natural language process…
Benchmark proposes to assess molecule docking efficiency.
Few-step protein backbone generators reduce sampling time by over 20x.
Non-autoregressive method speeds up protein folding prediction 23 times.
Advanced GNNs improve molecular generation models.
Personalized cancer vaccines are envisioned as the next generation rational cancer immunotherapy. The key step in developing personalized therapeutic cancer vaccines is to identify tumor-specific neoantigens that are on the surface of tumor cells. A promising method for this is through de novo peptide sequencing from m…
Novel RL approach for molecular design using quantum mechanics.
EHVI outperforms scalarized EI in MOBO for molecule design.
Learning policies on data synthesized by models can in principle quench the thirst of reinforcement learning algorithms for large amounts of real experience, which is often costly to acquire. However, simulating plausible experience de novo is a hard problem for many complex environments, often resulting in biases for …
Designing new molecules with a set of predefined properties is a core problem in modern drug discovery and development. There is a growing need for de-novo design methods that would address this problem. We present MolecularRNN, the graph recurrent generative model for molecular structures. Our model generates diverse …
New method designs antimicrobial peptides with high potency and low toxicity.
Chemical autoencoders are attractive models as they combine chemical space navigation with possibilities for de-novo molecule generation in areas of interest. This enables them to produce focused chemical libraries around a single lead compound for employment early in a drug discovery project. Here it is shown that the…
"Deep Archetypal Analysis" generates latent representations of high-dimensional datasets in terms of fractions of intuitively understandable basic entities called archetypes. The proposed method is an extension of linear "Archetypal Analysis" (AA), an unsupervised method to represent multivariate data points as sparse …
Promising results have driven a recent surge of interest in continuous optimization methods for Bayesian network structure learning from observational data. However, there are theoretical limitations on the identifiability of underlying structures obtained from observational data alone. Interventional data provides muc…
Framework designs antiviral drugs using deep learning and RL.
DOCKSTRING simplifies docking simulations for better drug design benchmarks.
As the complexity of neural network models has grown, it has become increasingly important to optimize their design automatically through metalearning. Methods for discovering hyperparameters, topologies, and learning rate schedules have lead to significant increases in performance. This paper shows that loss functions…
MolHF generates complex molecules with hierarchical flow-based model.
Recently exciting progress has been made on protein contact prediction, but the predicted contacts for proteins without many sequence homologs is still of low quality and not very useful for de novo structure prediction. This paper presents a new deep learning method that predicts contacts by integrating both evolution…
CogMol designs novel drug-like molecules for SARS-CoV-2 targets.
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…
Recent advances in high-throughput cDNA sequencing (RNA-Seq) technology have revolutionized transcriptome studies. A major motivation for RNA-Seq is to map the structure of expressed transcripts at nucleotide resolution. With accurate computational tools for transcript reconstruction, this technology may also become us…
In this paper, we propose a semi-supervised deep learning method for detecting the specific types of reads that impede the de novo genome assembly process. Instead of dealing directly with sequenced reads, we analyze their coverage graphs converted to 1D-signals. We noticed that specific signal patterns occur in each r…
CoDrug uses KDE to create valid prediction sets for drug molecules under covariate shift.
Recent methods for generating novel molecules use graph representations of molecules and employ various forms of graph convolutional neural networks for inference. However, training requires solving an expensive graph isomorphism problem, which previous approaches do not address or solve only approximately. In this wor…
New method infers centromere locations in yeast using Hi-C data.
Computational approaches to transcription factor binding site identification have been actively researched for the past decade. Negative examples have long been utilized in de novo motif discovery and have been shown useful in transcription factor binding site search as well. However, understanding of the roles of nega…
Recurrent neural networks have been widely used to generate millions of de novo molecules in a known chemical space. These deep generative models are typically setup with LSTM or GRU units and trained with canonical SMILEs. In this study, we introduce a new robust architecture, Generative Examination Networks GEN, base…
When searching for gene pathways leading to specific disease outcomes, additional information on gene characteristics is often available that may facilitate to differentiate genes related to the disease from irrelevant background when connections involving both types of genes are observed and their relationships to the…
The new wave of successful generative models in machine learning has increased the interest in deep learning driven de novo drug design. However, assessing the performance of such generative models is notoriously difficult. Metrics that are typically used to assess the performance of such generative models are the perc…
New method improves experimental design under model misspecification.
New models suggest molecules that are often unfeasible to synthesize.
fiBAG integrates multiplatform genomic data to identify disease markers.
DE improves GNNs by distinguishing graph substructures, enhancing accuracy.
These lecture notes in the De Rham-Hodge theory are designed for a 1-semester undergraduate course (in mathematics, physics, engineering, chemistry or biology). This landmark theory of the 20th Century mathematics gives a rigorous foundation to modern field and gauge theories in physics, engineering and physiology. The…
Next-generation sequencing technologies provide a revolutionary tool for generating gene expression data. Starting with a fixed RNA sample, they construct a library of millions of differentially abundant short sequence tags or "reads", which constitute a fundamentally discrete measure of the level of gene expression. A…
This paper uses bandit theory and Thompson Sampling to optimize protein sequences.
Survey of de Casteljau's algorithm's applications in geometric data analysis.
Paper proposes a new model and methods for robustly de-interleaving HMP mixtures.
De-identification of electronic health records (EHR) is a vital step towards advancing health informatics research and maximising the use of available data. It is a two-step process where step one is the identification of protected health information (PHI), and step two is replacing such PHI with surrogates. Despite th…
DE-QT detects optimal Q-learning stopping points.
Network medicine predicts repurposable drugs for COVID-19.
dSMC improves parallel processing of state-space models.