抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Probability Distributions.- Linear Models for Regression.- Linear Models for Classification.- Neural Networks.- Kernel Methods.- Sparse Kernel Machines.- Graphical Models.- Mixture Models and EM.- Approximate Inference.- Sampling Methods.- Continuous Latent Variables.- Sequential Data.- Combining Models.

Pattern Recognition and Machine Learning

/pdf/convex-analysisnoer-san-nojin-zhan-nituite-5dl2rbmoyr.pdf

Convex Analysisの二,三の進展について

The reference human genome sequence set the stage for studies of genetic variation and its association with human disease, but epigenomic studies lack a similar reference. To address this need, the NIH Roadmap Epigenomics Consortium generated the largest collection so far of human epigenomes for primary cells and tissues. Here we describe the integrative analysis of 111 reference human epigenomes generated as part of the programme, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression. We establish global maps of regulatory elements, define regulatory modules of coordinated activity, and their likely activators and repressors. We show that disease- and trait-associated genetic variants are enriched in tissue-specific epigenomic marks, revealing biologically relevant cell types for diverse human traits, and providing a resource for interpreting the molecular basis of human disease. Our results demonstrate the central role of epigenomic information for understanding gene regulation, cellular differentiation and human disease.

Integrative analysis of 111 reference human epigenomes

“Unpaired Image-to-Image Translation using Cycle-Consistent Adversarial Networks”の学習報告

Creating noise from data is easy; creating data from noise is generative modeling. We present a stochastic differential equation (SDE) that smoothly transforms a complex data distribution to a known prior distribution by slowly injecting noise, and a corresponding reverse-time SDE that transforms the prior distribution back into the data distribution by slowly removing the noise. Crucially, the reverse-time SDE depends only on the time-dependent gradient field (\aka, score) of the perturbed data distribution. By leveraging advances in score-based generative modeling, we can accurately estimate these scores with neural networks, and use numerical SDE solvers to generate samples. We show that this framework encapsulates previous approaches in score-based generative modeling and diffusion probabilistic modeling, allowing for new sampling procedures and new modeling capabilities. In particular, we introduce a predictor-corrector framework to correct errors in the evolution of the discretized reverse-time SDE. We also derive an equivalent neural ODE that samples from the same distribution as the SDE, but additionally enables exact likelihood computation, and improved sampling efficiency. In addition, we provide a new way to solve inverse problems with score-based models, as demonstrated with experiments on class-conditional generation, image inpainting, and colorization. Combined with multiple architectural improvements, we achieve record-breaking performance for unconditional image generation on CIFAR-10 with an Inception score of 9.89 and FID of 2.20, a competitive likelihood of 2.99 bits/dim, and demonstrate high fidelity generation of 1024 x 1024 images for the first time from a score-based generative model.

Score-Based Generative Modeling through Stochastic Differential Equations

Reliable data on economic livelihoods remain scarce in the developing world, hampering efforts to study these outcomes and to design policies that improve them. Here we demonstrate an accurate, inexpensive, and scalable method for estimating consumption expenditure and asset wealth from high-resolution satellite imagery. Using survey and satellite data from five African countries—Nigeria, Tanzania, Uganda, Malawi, and Rwanda—we show how a convolutional neural network can be trained to identify image features that can explain up to 75% of the variation in local-level economic outcomes. Our method, which requires only publicly available data, could transform efforts to track and target poverty in developing countries. It also demonstrates how powerful machine learning techniques can be applied in a setting with limited training data, suggesting broad potential application across many scientific domains.

Combining satellite imagery and machine learning to predict poverty

Denoising diffusion probabilistic models (DDPMs) have achieved high quality image generation without adversarial training, yet they require simulating a Markov chain for many steps to produce a sample. To accelerate sampling, we present denoising diffusion implicit models (DDIMs), a more efficient class of iterative implicit probabilistic models with the same training procedure as DDPMs. In DDPMs, the generative process is defined as the reverse of a Markovian diffusion process. We construct a class of non-Markovian diffusion processes that lead to the same training objective, but whose reverse process can be much faster to sample from. We empirically demonstrate that DDIMs can produce high quality samples $10 \times$ to $50 \times$ faster in terms of wall-clock time compared to DDPMs, allow us to trade off computation for sample quality, and can perform semantically meaningful image interpolation directly in the latent space.

Denoising Diffusion Implicit Models

We introduce a new generative model where samples are produced via Langevin dynamics using gradients of the data distribution estimated with score matching Because gradients can be ill-defined and hard to estimate when the data resides on low-dimensional manifolds, we perturb the data with different levels of Gaussian noise, and jointly estimate the corresponding scores, ie, the vector fields of gradients of the perturbed data distribution for all noise levels For sampling, we propose an annealed Langevin dynamics where we use gradients corresponding to gradually decreasing noise levels as the sampling process gets closer to the data manifold Our framework allows flexible model architectures, requires no sampling during training or the use of adversarial methods, and provides a learning objective that can be used for principled model comparisons Our models produce samples comparable to GANs on MNIST, CelebA and CIFAR-10 datasets, achieving a new state-of-the-art inception score of 887 on CIFAR-10 Additionally, we demonstrate that our models learn effective representations via image inpainting experiments

Generative Modeling by Estimating Gradients of the Data Distribution

Consider learning a policy from example expert behavior, without interaction with the expert or access to reinforcement signal. One approach is to recover the expert's cost function with inverse reinforcement learning, then extract a policy from that cost function with reinforcement learning. This approach is indirect and can be slow. We propose a new general framework for directly extracting a policy from data, as if it were obtained by reinforcement learning following inverse reinforcement learning. We show that a certain instantiation of our framework draws an analogy between imitation learning and generative adversarial networks, from which we derive a model-free imitation learning algorithm that obtains significant performance gains over existing model-free methods in imitating complex behaviors in large, high-dimensional environments.

Stefano Ermon

Papers

Score-Based Generative Modeling through Stochastic Differential Equations

Combining satellite imagery and machine learning to predict poverty

Denoising Diffusion Implicit Models

Generative Modeling by Estimating Gradients of the Data Distribution

Generative Adversarial Imitation Learning