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In embryogenesis, epithelial cells, acting as individual entities or as coordinated aggregates in a tissue, exhibit strong coupling between chemical signalling and mechanical responses to internally or externally applied stresses. Intercellular communication in combination with such coordination of morphogenetic movements can lead to drastic modifications in the calcium distribution in the cells. In this paper we extend the recent mechanochemical model in [K. Kaouri, P.K. Maini, P.A. Skourides, N. Christodoulou, S.J. Chapman. J. Math. Biol., 78 (2019) 2059--2092], for an epithelial continuum in one dimension, to a more realistic multi-dimensional case. The resulting parametrised governing equations consist of an advection-diffusion-reaction system for calcium signalling coupled with active-stress linear viscoelasticity and equipped with pure Neumann boundary conditions. We implement a mixed finite element method for the simulation of this complex multiphysics problem. Special care is taken in the treatment of the stress-free boundary conditions for the viscoelasticity in order to eliminate rigid motions from the space of admissible displacements. The stability and solvability of the continuous weak formulation is shown using fixed-point theory. We investigate numerically the solutions of this system and show that solitary waves and periodic wavetrains of calcium propagate through the embryonic epithelial sheet. We analyse the bifurcations of the system guided by the bifurcation analysis of the one-dimensional model. We also demonstrate the nucleation of calcium sparks into synchronous calcium waves coupled with contraction. This coupled model can be employed to gain insights into recent experimental observations in the context of embryogenesis, but also in other biological systems such as cancer cells, wound healing, keratinocytes, or white blood cells.

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ACM/IEEE第23屆模型驅動工程語言和系統國際會議,是模型驅動軟件和系統工程的首要會議系列,由ACM-SIGSOFT和IEEE-TCSE支持組織。自1998年以來,模型涵蓋了建模的各個方面,從語言和方法到工具和應用程序。模特的參加者來自不同的背景,包括研究人員、學者、工程師和工業專業人士。MODELS 2019是一個論壇,參與者可以圍繞建模和模型驅動的軟件和系統交流前沿研究成果和創新實踐經驗。今年的版本將為建模社區提供進一步推進建模基礎的機會,并在網絡物理系統、嵌入式系統、社會技術系統、云計算、大數據、機器學習、安全、開源等新興領域提出建模的創新應用以及可持續性。 官網鏈接: · Performer · Processing(編程語言) · 學成 · 穩健性 ·
2021 年 9 月 3 日

The dominating NLP paradigm of training a strong neural predictor to perform one task on a specific dataset has led to state-of-the-art performance in a variety of applications (eg. sentiment classification, span-prediction based question answering or machine translation). However, it builds upon the assumption that the data distribution is stationary, ie. that the data is sampled from a fixed distribution both at training and test time. This way of training is inconsistent with how we as humans are able to learn from and operate within a constantly changing stream of information. Moreover, it is ill-adapted to real-world use cases where the data distribution is expected to shift over the course of a model's lifetime. The first goal of this thesis is to characterize the different forms this shift can take in the context of natural language processing, and propose benchmarks and evaluation metrics to measure its effect on current deep learning architectures. We then proceed to take steps to mitigate the effect of distributional shift on NLP models. To this end, we develop methods based on parametric reformulations of the distributionally robust optimization framework. Empirically, we demonstrate that these approaches yield more robust models as demonstrated on a selection of realistic problems. In the third and final part of this thesis, we explore ways of efficiently adapting existing models to new domains or tasks. Our contribution to this topic takes inspiration from information geometry to derive a new gradient update rule which alleviate catastrophic forgetting issues during adaptation.

Exploring the intrinsic interconnections between the knowledge encoded in PRe-trained Deep Neural Networks (PR-DNNs) of heterogeneous tasks sheds light on their mutual transferability, and consequently enables knowledge transfer from one task to another so as to reduce the training effort of the latter. In this paper, we propose the DEeP Attribution gRAph (DEPARA) to investigate the transferability of knowledge learned from PR-DNNs. In DEPARA, nodes correspond to the inputs and are represented by their vectorized attribution maps with regards to the outputs of the PR-DNN. Edges denote the relatedness between inputs and are measured by the similarity of their features extracted from the PR-DNN. The knowledge transferability of two PR-DNNs is measured by the similarity of their corresponding DEPARAs. We apply DEPARA to two important yet under-studied problems in transfer learning: pre-trained model selection and layer selection. Extensive experiments are conducted to demonstrate the effectiveness and superiority of the proposed method in solving both these problems. Code, data and models reproducing the results in this paper are available at \url{//github.com/zju-vipa/DEPARA}.

In this paper, we propose Latent Relation Language Models (LRLMs), a class of language models that parameterizes the joint distribution over the words in a document and the entities that occur therein via knowledge graph relations. This model has a number of attractive properties: it not only improves language modeling performance, but is also able to annotate the posterior probability of entity spans for a given text through relations. Experiments demonstrate empirical improvements over both a word-based baseline language model and a previous approach that incorporates knowledge graph information. Qualitative analysis further demonstrates the proposed model's ability to learn to predict appropriate relations in context.

Active learning has long been a topic of study in machine learning. However, as increasingly complex and opaque models have become standard practice, the process of active learning, too, has become more opaque. There has been little investigation into interpreting what specific trends and patterns an active learning strategy may be exploring. This work expands on the Local Interpretable Model-agnostic Explanations framework (LIME) to provide explanations for active learning recommendations. We demonstrate how LIME can be used to generate locally faithful explanations for an active learning strategy, and how these explanations can be used to understand how different models and datasets explore a problem space over time. In order to quantify the per-subgroup differences in how an active learning strategy queries spatial regions, we introduce a notion of uncertainty bias (based on disparate impact) to measure the discrepancy in the confidence for a model's predictions between one subgroup and another. Using the uncertainty bias measure, we show that our query explanations accurately reflect the subgroup focus of the active learning queries, allowing for an interpretable explanation of what is being learned as points with similar sources of uncertainty have their uncertainty bias resolved. We demonstrate that this technique can be applied to track uncertainty bias over user-defined clusters or automatically generated clusters based on the source of uncertainty.

Person re-identification is being widely used in the forensic, and security and surveillance system, but person re-identification is a challenging task in real life scenario. Hence, in this work, a new feature descriptor model has been proposed using a multilayer framework of Gaussian distribution model on pixel features, which include color moments, color space values and Schmid filter responses. An image of a person usually consists of distinct body regions, usually with differentiable clothing followed by local colors and texture patterns. Thus, the image is evaluated locally by dividing the image into overlapping regions. Each region is further fragmented into a set of local Gaussians on small patches. A global Gaussian encodes, these local Gaussians for each region creating a multi-level structure. Hence, the global picture of a person is described by local level information present in it, which is often ignored. Also, we have analyzed the efficiency of earlier metric learning methods on this descriptor. The performance of the descriptor is evaluated on four public available challenging datasets and the highest accuracy achieved on these datasets are compared with similar state-of-the-arts, which demonstrate the superior performance.

We present new intuitions and theoretical assessments of the emergence of disentangled representation in variational autoencoders. Taking a rate-distortion theory perspective, we show the circumstances under which representations aligned with the underlying generative factors of variation of data emerge when optimising the modified ELBO bound in $\beta$-VAE, as training progresses. From these insights, we propose a modification to the training regime of $\beta$-VAE, that progressively increases the information capacity of the latent code during training. This modification facilitates the robust learning of disentangled representations in $\beta$-VAE, without the previous trade-off in reconstruction accuracy.

We consider the task of learning the parameters of a {\em single} component of a mixture model, for the case when we are given {\em side information} about that component, we call this the "search problem" in mixture models. We would like to solve this with computational and sample complexity lower than solving the overall original problem, where one learns parameters of all components. Our main contributions are the development of a simple but general model for the notion of side information, and a corresponding simple matrix-based algorithm for solving the search problem in this general setting. We then specialize this model and algorithm to four common scenarios: Gaussian mixture models, LDA topic models, subspace clustering, and mixed linear regression. For each one of these we show that if (and only if) the side information is informative, we obtain parameter estimates with greater accuracy, and also improved computation complexity than existing moment based mixture model algorithms (e.g. tensor methods). We also illustrate several natural ways one can obtain such side information, for specific problem instances. Our experiments on real data sets (NY Times, Yelp, BSDS500) further demonstrate the practicality of our algorithms showing significant improvement in runtime and accuracy.

Recurrent models for sequences have been recently successful at many tasks, especially for language modeling and machine translation. Nevertheless, it remains challenging to extract good representations from these models. For instance, even though language has a clear hierarchical structure going from characters through words to sentences, it is not apparent in current language models. We propose to improve the representation in sequence models by augmenting current approaches with an autoencoder that is forced to compress the sequence through an intermediate discrete latent space. In order to propagate gradients though this discrete representation we introduce an improved semantic hashing technique. We show that this technique performs well on a newly proposed quantitative efficiency measure. We also analyze latent codes produced by the model showing how they correspond to words and phrases. Finally, we present an application of the autoencoder-augmented model to generating diverse translations.

In this paper, we study the optimal convergence rate for distributed convex optimization problems in networks. We model the communication restrictions imposed by the network as a set of affine constraints and provide optimal complexity bounds for four different setups, namely: the function $F(\xb) \triangleq \sum_{i=1}^{m}f_i(\xb)$ is strongly convex and smooth, either strongly convex or smooth or just convex. Our results show that Nesterov's accelerated gradient descent on the dual problem can be executed in a distributed manner and obtains the same optimal rates as in the centralized version of the problem (up to constant or logarithmic factors) with an additional cost related to the spectral gap of the interaction matrix. Finally, we discuss some extensions to the proposed setup such as proximal friendly functions, time-varying graphs, improvement of the condition numbers.

In this paper, we develop the continuous time dynamic topic model (cDTM). The cDTM is a dynamic topic model that uses Brownian motion to model the latent topics through a sequential collection of documents, where a "topic" is a pattern of word use that we expect to evolve over the course of the collection. We derive an efficient variational approximate inference algorithm that takes advantage of the sparsity of observations in text, a property that lets us easily handle many time points. In contrast to the cDTM, the original discrete-time dynamic topic model (dDTM) requires that time be discretized. Moreover, the complexity of variational inference for the dDTM grows quickly as time granularity increases, a drawback which limits fine-grained discretization. We demonstrate the cDTM on two news corpora, reporting both predictive perplexity and the novel task of time stamp prediction.

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