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.
New method infers centromere locations in yeast using Hi-C data.
Bayesian method discovers local causal relationships among genes from gene expression data.
High throughput sequencing techniques have highly impactedon modern biology, widening the gap between sequenced andannotated data. Automatic annotation tools are thereforeof the foremost importance to guide biologists' experiments. However, most of the state-of-the-art methods rely on annotation transfer, offering reli…
We use a semisupervised learning algorithm based on a topological data analysis approach to assign functional categories to yeast proteins using similarity graphs. This new approach to analyzing biological networks yields results that are as good as or better than state of the art existing approaches.
Cost-effective feature selection improves network model choice.
Liquid chromatography coupled with tandem mass spectrometry, also known as shotgun proteomics, is a widely-used high-throughput technology for identifying proteins in complex biological samples. Analysis of the tens of thousands of fragmentation spectra produced by a typical shotgun proteomics experiment begins by assi…
Paper proposes learning causal graphs with only relevant variables.
Multi-StyleGAN simulates live cell microscopy imagery.
Protein function prediction is the important problem in modern biology. In this paper, the un-normalized, symmetric normalized, and random walk graph Laplacian based semi-supervised learning methods will be applied to the integrated network combined from multiple networks to predict the functions of all yeast proteins …
Most network-based protein (or gene) function prediction methods are based on the assumption that the labels of two adjacent proteins in the network are likely to be the same. However, assuming the pairwise relationship between proteins or genes is not complete, the information a group of genes that show very similar p…
We consider the problem of learning a high-dimensional multi-task regression model, under sparsity constraints induced by presence of grouping structures on the input covariates and on the output predictors. This problem is primarily motivated by expression quantitative trait locus (eQTL) mapping, of which the goal is …
Gene regulatory networks play a crucial role in controlling an organism's biological processes, which is why there is significant interest in developing computational methods that are able to extract their structure from high-throughput genetic data. A typical approach consists of a series of conditional independence t…
A method clusters genes in large gene regulatory networks using semi-supervised hierarchical clustering.
Convolutional neural networks (CNN) have achieved state of the art performance on both classification and segmentation tasks. Applying CNNs to microscopy images is challenging due to the lack of datasets labeled at the single cell level. We extend the application of CNNs to microscopy image classification and segmentat…
We propose a network structure discovery model for continuous observations that generalizes linear causal models by incorporating a Gaussian process (GP) prior on a network-independent component, and random sparsity and weight matrices as the network-dependent parameters. This approach provides flexible modeling of net…
A novel regularizer of the PARAFAC decomposition factors capturing the tensor's rank is proposed in this paper, as the key enabler for completion of three-way data arrays with missing entries. Set in a Bayesian framework, the tensor completion method incorporates prior information to enhance its smoothing and predictio…
We consider constraint-based methods for causal structure learning, such as the PC-, FCI-, RFCI- and CCD- algorithms (Spirtes et al. (2000, 1993), Richardson (1996), Colombo et al. (2012), Claassen et al. (2013)). The first step of all these algorithms consists of the PC-algorithm. This algorithm is known to be order-d…
Cellular regulatory dynamics is driven by large and intricate networks of interactions at the molecular scale, whose sheer size obfuscates understanding. In light of limited experimental data, many parameters of such dynamics are unknown, and thus models built on the detailed, mechanistic viewpoint overfit and are not …
Many tasks require finding groups of elements in a matrix of numbers, symbols or class likelihoods. One approach is to use efficient bi- or tri-linear factorization techniques including PCA, ICA, sparse matrix factorization and plaid analysis. These techniques are not appropriate when addition and multiplication of mat…
The detection of rare variants is important for understanding the genetic heterogeneity in mixed samples. Recently, next-generation sequencing (NGS) technologies have enabled the identification of single nucleotide variants (SNVs) in mixed samples with high resolution. Yet, the noise inherent in the biological processe…
To survive environmental conditions, cells transcribe their response activities into encoded mRNA sequences in order to produce certain amounts of protein concentrations. The external conditions are mapped into the cell through the activation of special proteins called transcription factors (TFs). Due to the difficult …
Develops probabilistic models for gene regulatory network inference.
The paper develops methods to identify stable associations across multiple studies.
Generative Distribution Embeddings learn multiscale representations of distributions.
We consider the problem of estimating a sparse multi-response regression function, with an application to expression quantitative trait locus (eQTL) mapping, where the goal is to discover genetic variations that influence gene-expression levels. In particular, we investigate a shrinkage technique capable of capturing a…
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 …
Researchers infer gene activity in dividing cells, accounting for protein inheritance and division history.
Graph edges, along with their labels, can represent information of fundamental importance, such as links between web pages, friendship between users, the rating given by users to other users or items, and much more. We introduce LEAP, a trainable, general framework for predicting the presence and properties of edges on…
ART adapts class-wise resampling to improve imbalanced classification performance.
A new method prioritizes and recycles experiences for better reinforcement learning.
Reverse Experience Replay improves Deep Q-learning for sparse rewards.
This project combines recent advances in experience replay techniques, namely, Combined Experience Replay (CER), Prioritized Experience Replay (PER), and Hindsight Experience Replay (HER). We show the results of combinations of these techniques with DDPG and DQN methods. CER always adds the most recent experience to th…
ReaPER improves learning efficiency by prioritizing reliable experiences.
Algorithm creates synthetic experiences to enhance Deep Reinforcement Learning.
Unified model optimizes experiment performance and reduces duration.
New method designs experiments robustly for nonlinear estimation, improving parameter knowledge.
Experience reuse is key to sample-efficient reinforcement learning. One of the critical issues is how the experience is represented and stored. Previously, the experience can be stored in the forms of features, individual models, and the average model, each lying at a different granularity. However, new tasks may requi…
Optimal tests developed for sequential experiments with asymptotic properties.
Bayesian optimization for long-term outcomes using fast and slow experiments.
Two methods estimate effect size for online experiments, improving accuracy and efficiency.
Experience replay enables reinforcement learning agents to memorize and reuse past experiences, just as humans replay memories for the situation at hand. Contemporary off-policy algorithms either replay past experiences uniformly or utilize a rule-based replay strategy, which may be sub-optimal. In this work, we consid…
Study finds real-world datasets contain natural experiments that can improve model performance.
We reduce variance in monetization metrics for ranking experiments.
AES improves policy gradient performance by adaptively selecting experience.
New framework for choosing optimal proxy metrics from past experiments.
Experience replay is widely used in deep reinforcement learning algorithms and allows agents to remember and learn from experiences from the past. In an effort to learn more efficiently, researchers proposed prioritized experience replay (PER) which samples important transitions more frequently. In this paper, we propo…
LiDER refreshes past experiences in RL by dreaming about them.
Efficient actor-critic learning with shared experience replay improves data efficiency.