Dissecting Deep Learning Networks—Visualizing Mutual Information

Deep Learning (DL) networks are recent revolutionary developments in artificial intelligence research. Typical networks are stacked by groups of layers that are further composed of many convolutional kernels or neurons. In network design, many hyper-parameters need to be defined heuristically before training in order to achieve high cross-validation accuracies. However, accuracy evaluation from the output layer alone is not sufficient to specify the roles of the hidden units in associated networks. This results in a significant knowledge gap between DL’s wider applications and its limited theoretical understanding. To narrow the knowledge gap, our study explores visualization techniques to illustrate the mutual information (MI) in DL networks. The MI is a theoretical measurement, reflecting the relationship between two sets of random variables even if their relationship is highly non-linear and hidden in high-dimensional data. Our study aims to understand the roles of DL units in classification performance of the networks. Via a series of experiments using several popular DL networks, it shows that the visualization of MI and its change patterns between the input/output with the hidden layers and basic units can facilitate a better understanding of these DL units’ roles. Our investigation on network convergence suggests a more objective manner to potentially evaluate DL networks. Furthermore, the visualization provides a useful tool to gain insights into the network performance, and thus to potentially facilitate the design of better network architectures by identifying redundancy and less-effective network units

SCALE method for single-cell ATAC-seq analysis via latent feature extraction.

Single-cell ATAC-seq (scATAC-seq) profiles the chromatin accessibility landscape at single cell level, thus revealing cell-to-cell variability in gene regulation. However, the high dimensionality and sparsity of scATAC-seq data often complicate the analysis. Here, we introduce a method for analyzing scATAC-seq data, called Single-Cell ATAC-seq analysis via Latent feature Extraction (SCALE). SCALE combines a deep generative framework and a probabilistic Gaussian Mixture Model to learn latent features that accurately characterize scATAC-seq data. We validate SCALE on datasets generated on different platforms with different protocols, and having different overall data qualities. SCALE substantially outperforms the other tools in all aspects of scATAC-seq data analysis, including visualization, clustering, and denoising and imputation. Importantly, SCALE also generates interpretable features that directly link to cell populations, and can potentially reveal batch effects in scATAC-seq experiments

Information Bottleneck: Exact Analysis of (Quantized) Neural Networks

The information bottleneck (IB) principle has been suggested as a way to analyze deep neural networks. The learning dynamics are studied by inspecting the mutual information (MI) between the hidden layers and the input and output. Notably, separate fitting and compression phases during training have been reported. This led to some controversy including claims that the observations are not reproducible and strongly dependent on the type of activation function used as well as on the way the MI is estimated. Our study confirms that different ways of binning when computing the MI lead to qualitatively different results, either supporting or refusing IB conjectures. To resolve the controversy, we study the IB principle in settings where MI is non-trivial and can be computed exactly. We monitor the dynamics of quantized neural networks, that is, we discretize the whole deep learning system so that no approximation is required when computing the MI. This allows us to quantify the information flow without measurement errors. In this setting, we observed a fitting phase for all layers and a compression phase for the output layer in all experiments; the compression in the hidden layers was dependent on the type of activation function. Our study shows that the initial IB results were not artifacts of binning when computing the MI. However, the critical claim that the compression phase may not be observed for some networks also holds true

Single Cell Proteomics in Biomedicine: High-dimensional Data Acquisition, Visualization and Analysis

New insights on cellular heterogeneity in the last decade provoke the development of a variety of single cell omics tools at a lightning pace. The resultant high-dimensional single cell data generated by these tools require new theoretical approaches and analytical algorithms for effective visualization and interpretation. In this review, we briefly survey the state-of-the-art single cell proteomic tools with a particular focus on data acquisition and quantification, followed by an elaboration of a number of statistical and computational approaches developed to date for dissecting the high-dimensional single cell data. The underlying assumptions, unique features, and limitations of the analytical methods with the designated biological questions they seek to answer will be discussed. Particular attention will be given to those information theoretical approaches that are anchored in a set of first principles of physics and can yield detailed (and often surprising) predictions

Empiricism without Magic: Transformational Abstraction in Deep Convolutional Neural Networks

In artificial intelligence, recent research has demonstrated the remarkable potential of Deep Convolutional Neural Networks (DCNNs), which seem to exceed state-of-the-art performance in new domains weekly, especially on the sorts of very difficult perceptual discrimination tasks that skeptics thought would remain beyond the reach of artificial intelligence. However, it has proven difficult to explain why DCNNs perform so well. In philosophy of mind, empiricists have long suggested that complex cognition is based on information derived from sensory experience, often appealing to a faculty of abstraction. Rationalists have frequently complained, however, that empiricists never adequately explained how this faculty of abstraction actually works. In this paper, I tie these two questions together, to the mutual benefit of both disciplines. I argue that the architectural features that distinguish DCNNs from earlier neural networks allow them to implement a form of hierarchical processing that I call “transformational abstraction”. Transformational abstraction iteratively converts sensory-based representations of category exemplars into new formats that are increasingly tolerant to “nuisance variation” in input. Reflecting upon the way that DCNNs leverage a combination of linear and non-linear processing to efficiently accomplish this feat allows us to understand how the brain is capable of bi-directional travel between exemplars and abstractions, addressing longstanding problems in empiricist philosophy of mind. I end by considering the prospects for future research on DCNNs, arguing that rather than simply implementing 80s connectionism with more brute-force computation, transformational abstraction counts as a qualitatively distinct form of processing ripe with philosophical and psychological significance, because it is significantly better suited to depict the generic mechanism responsible for this important kind of psychological processing in the brain

Learning in Feedforward Neural Networks Accelerated by Transfer Entropy

Current neural networks architectures are many times harder to train because of the increasing size and complexity of the used datasets. Our objective is to design more efficient training algorithms utilizing causal relationships inferred from neural networks. The transfer entropy (TE) was initially introduced as an information transfer measure used to quantify the statistical coherence between events (time series). Later, it was related to causality, even if they are not the same. There are only few papers reporting applications of causality or TE in neural networks. Our contribution is an information-theoretical method for analyzing information transfer between the nodes of feedforward neural networks. The information transfer is measured by the TE of feedback neural connections. Intuitively, TE measures the relevance of a connection in the network and the feedback amplifies this connection. We introduce a backpropagation type training algorithm that uses TE feedback connections to improve its performance

SMILE: Scaling Mixture-of-Experts with Efficient Bi-level Routing

The mixture of Expert (MoE) parallelism is a recent advancement that scales up the model size with constant computational cost. MoE selects different sets of parameters (i.e., experts) for each incoming token, resulting in a sparsely-activated model. Despite several successful applications of MoE, its training efficiency degrades significantly as the number of experts increases. The routing stage in MoE relies on the efficiency of the All2All communication collective, which suffers from network congestion and has poor scalability. To mitigate these issues, we introduce SMILE, which exploits heterogeneous network bandwidth and splits a single-step routing into bi-level routing. Our experimental results show that the proposed method obtains a 2.5x speedup over Switch Transformer in terms of pretraining throughput on the Colossal Clean Crawled Corpus without losing any convergence speed