The advent of single-cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq) offers an innovative perspective for deciphering regulatory mechanisms by assembling a vast repository of single-cell chromatin accessibility data. While foundation models have achieved significant success in single-cell transcriptomics, there is currently no foundation model for scATAC-seq that supports zero-shot high-quality cell identification and comprehensive multi-omics analysis simultaneously. Key challenges lie in the high dimensionality and sparsity of scATAC-seq data, as well as the lack of a standardized schema for representing open chromatin regions (OCRs). Here, we present ChromFound, a foundation model tailored for scATAC-seq. ChromFound utilizes a hybrid architecture and genome-aware tokenization to effectively capture genome-wide long contexts and regulatory signals from dynamic chromatin landscapes. Pretrained on 1.97 million cells from 30 tissues and 6 disease conditions, ChromFound demonstrates broad applicability across 6 diverse tasks. Notably, it achieves robust zero-shot performance in generating universal cell representations and exhibits excellent transferability in cell type annotation and cross-omics prediction. By uncovering enhancer-gene links undetected by existing computational methods, ChromFound offers a promising framework for understanding disease risk variants in the noncoding genome.

Occlusion is one of the fundamental challenges in crowd counting. In the community, various data-driven approaches have been developed to address this issue, yet their effectiveness is limited. This is mainly because most existing crowd counting datasets on which the methods are trained are based on passive cameras, restricting their ability to fully sense the environment. Recently, embodied navigation methods have shown significant potential in precise object detection in interactive scenes. These methods incorporate active camera settings, holding promise in addressing the fundamental issues in crowd counting.

Despite impressive recent advances in reinforcement learning (RL), its deployment in real-world physical systems is often complicated by unexpected events, limited data, and the potential for expensive failures. In this paper, we describe an application of RL "in the wild" to the task of regulating temperatures and airflow inside a large-scale data center (DC). Adopting a data-driven, model-based approach, we demonstrate that an RL agent with little prior knowledge is able to effectively and safely regulate conditions on a server floor after just a few hours of exploration, while improving operational efficiency relative to existing PID controllers.

We propose a new approach, called cooperative neural networks (CoNN), which use a set of cooperatively trained neural networks to capture latent representations that exploit prior given independence structure. The model is more flexible than traditional graphical models based on exponential family distributions, but incorporates more domain specific prior structure than traditional deep networks or variational autoencoders. The framework is very general and can be used to exploit the independence structure of any graphical model. We illustrate the technique by showing that we can transfer the independence structure of the popular Latent Dirichlet Allocation (LDA) model to a cooperative neural network, CoNN-sLDA. Empirical evaluation of CoNN-sLDA on supervised text classification tasks demonstrate that the theoretical advantages of prior independence structure can be realized in practice - we demonstrate a 23 percent reduction in error on the challenging MultiSent data set compared to state-of-the-art.

The ever-increasing number of parameters in deep neural networks poses challenges for memory-limited applications. Regularize-and-prune methods aim at meeting these challenges by sparsifying the network weights. In this context we quantify the output sensitivity to the parameters (i.e.

Stochastic regularisation is an important weapon in the arsenal of a deep learning practitioner. However, despite recent theoretical advances, our understanding of how noise influences signal propagation in deep neural networks remains limited. By extending recent work based on mean field theory, we develop a new framework for signal propagation in stochastic regularised neural networks. Our \textit{noisy signal propagation} theory can incorporate several common noise distributions, including additive and multiplicative Gaussian noise as well as dropout. We use this framework to investigate initialisation strategies for noisy ReLU networks. We show that no critical initialisation strategy exists using additive noise, with signal propagation exploding regardless of the selected noise distribution. For multiplicative noise (e.g.\ dropout), we identify alternative critical initialisation strategies that depend on the second moment of the noise distribution. Simulations and experiments on real-world data confirm that our proposed initialisation is able to stably propagate signals in deep networks, while using an initialisation disregarding noise fails to do so.

Data representations that contain all the information about target variables but are invariant to nuisance factors benefit supervised learning algorithms by preventing them from learning associations between these factors and the targets, thus reducing overfitting. We present a novel unsupervised invariance induction framework for neural networks that learns a split representation of data through competitive training between the prediction task and a reconstruction task coupled with disentanglement, without needing any labeled information about nuisance factors or domain knowledge. We describe an adversarial instantiation of this framework and provide analysis of its working. Our unsupervised model outperforms state-of-the-art methods, which are supervised, at inducing invariance to inherent nuisance factors, effectively using synthetic data augmentation to learn invariance, and domain adaptation. Our method can be applied to any prediction task, eg., binary/multi-class classification or regression, without loss of generality.

Inferring directional couplings from the spike data of networks is desired in various scientific fields such as neuroscience. Here, we apply a recently proposed objective procedure to the spike data obtained from the Hodgkin-Huxley type models and in vitro neuronal networks cultured in a circular structure. As a result, we succeed in reconstructing synaptic connections accurately from the evoked activity as well as the spontaneous one. To obtain the results, we invent an analytic formula approximately implementing a method of screening relevant couplings. This significantly reduces the computational cost of the screening method employed in the proposed objective procedure, making it possible to treat large-size systems as in this study.

A widespread folklore for explaining the success of Convolutional Neural Networks (CNNs) is that CNNs use a more compact representation than the Fully-connected Neural Network (FNN) and thus require fewer training samples to accurately estimate their parameters. We initiate the study of rigorously characterizing the sample complexity of estimating CNNs. We show that for an $m$-dimensional convolutional filter with linear activation acting on a $d$-dimensional input, the sample complexity of achieving population prediction error of $\epsilon$ is $\widetilde{O(m/\epsilon^2)$, whereas the sample-complexity for its FNN counterpart is lower bounded by $\Omega(d/\epsilon^2)$ samples. Since, in typical settings $m \ll d$, this result demonstrates the advantage of using a CNN. We further consider the sample complexity of estimating a one-hidden-layer CNN with linear activation where both the $m$-dimensional convolutional filter and the $r$-dimensional output weights are unknown. For this model, we show that the sample complexity is $\widetilde{O}\left((m+r)/\epsilon^2\right)$ when the ratio between the stride size and the filter size is a constant. For both models, we also present lower bounds showing our sample complexities are tight up to logarithmic factors. Our main tools for deriving these results are a localized empirical process analysis and a new lemma characterizing the convolutional structure. We believe that these tools may inspire further developments in understanding CNNs.

We demonstrate that a very deep ResNet with stacked modules that have one neuron per hidden layer and ReLU activation functions can uniformly approximate any Lebesgue integrable function in d dimensions, i.e. \ell_1(R^d). Due to the identity mapping inherent to ResNets, our network has alternating layers of dimension one and d. This stands in sharp contrast to fully connected networks, which are not universal approximators if their width is the input dimension d [21,11]. Hence, our result implies an increase in representational power for narrow deep networks by the ResNet architecture.