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This article is devoted to the mathematical modeling of migration of neuroblasts, precursor cells of neurons, along the pathway they usually follow before maturing. This pathway is determined mainly by chemotaxis and the heterogeneous mobility of neuroblasts in different regions of the brain. In numerical simulations, the application of novel discontinuous Galerkin methods allows to maintain the properties of the continuous model such as the maximum principle. We present some successful computer tests including parameter adjust to fit real data from rodent brains.

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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: · MoDELS · 模態 · 可理解性 · Integration ·
2024 年 7 月 12 日

Proteins are fundamental components of biological systems and can be represented through various modalities, including sequences, structures, and textual descriptions. Despite the advances in deep learning and scientific large language models (LLMs) for protein research, current methodologies predominantly focus on limited specialized tasks -- often predicting one protein modality from another. These approaches restrict the understanding and generation of multimodal protein data. In contrast, large multimodal models have demonstrated potential capabilities in generating any-to-any content like text, images, and videos, thus enriching user interactions across various domains. Integrating these multimodal model technologies into protein research offers significant promise by potentially transforming how proteins are studied. To this end, we introduce HelixProtX, a system built upon the large multimodal model, aiming to offer a comprehensive solution to protein research by supporting any-to-any protein modality generation. Unlike existing methods, it allows for the transformation of any input protein modality into any desired protein modality. The experimental results affirm the advanced capabilities of HelixProtX, not only in generating functional descriptions from amino acid sequences but also in executing critical tasks such as designing protein sequences and structures from textual descriptions. Preliminary findings indicate that HelixProtX consistently achieves superior accuracy across a range of protein-related tasks, outperforming existing state-of-the-art models. By integrating multimodal large models into protein research, HelixProtX opens new avenues for understanding protein biology, thereby promising to accelerate scientific discovery.

The development of a satisfying and rigorous mathematical understanding of the performance of neural networks is a major challenge in artificial intelligence. Against this background, we study the expressive power of neural networks through the example of the classical NP-hard Knapsack Problem. Our main contribution is a class of recurrent neural networks (RNNs) with rectified linear units that are iteratively applied to each item of a Knapsack instance and thereby compute optimal or provably good solution values. We show that an RNN of depth four and width depending quadratically on the profit of an optimum Knapsack solution is sufficient to find optimum Knapsack solutions. We also prove the following tradeoff between the size of an RNN and the quality of the computed Knapsack solution: for Knapsack instances consisting of $n$ items, an RNN of depth five and width $w$ computes a solution of value at least $1-\mathcal{O}(n^2/\sqrt{w})$ times the optimum solution value. Our results build upon a classical dynamic programming formulation of the Knapsack Problem as well as a careful rounding of profit values that are also at the core of the well-known fully polynomial-time approximation scheme for the Knapsack Problem. A carefully conducted computational study qualitatively supports our theoretical size bounds. Finally, we point out that our results can be generalized to many other combinatorial optimization problems that admit dynamic programming solution methods, such as various Shortest Path Problems, the Longest Common Subsequence Problem, and the Traveling Salesperson Problem.

The majority of theoretical analyses of evolutionary algorithms in the discrete domain focus on binary optimization algorithms, even though black-box optimization on the categorical domain has a lot of practical applications. In this paper, we consider a probabilistic model-based algorithm using the family of categorical distributions as its underlying distribution and set the sample size as two. We term this specific algorithm the categorical compact genetic algorithm (ccGA). The ccGA can be considered as an extension of the compact genetic algorithm (cGA), which is an efficient binary optimization algorithm. We theoretically analyze the dependency of the number of possible categories $K$, the number of dimensions $D$, and the learning rate $\eta$ on the runtime. We investigate the tail bound of the runtime on two typical linear functions on the categorical domain: categorical OneMax (COM) and KVal. We derive that the runtimes on COM and KVal are $O(\sqrt{D} \ln (DK) / \eta)$ and $\Theta(D \ln K/ \eta)$ with high probability, respectively. Our analysis is a generalization for that of the cGA on the binary domain.

In distributed computing by mobile robots, robots are deployed over a region, continuous or discrete, operating through a sequence of \textit{look-compute-move} cycles. An extensive study has been carried out to understand the computational powers of different robot models. The models vary on the ability to 1)~remember constant size information and 2)~communicate constant size message. Depending on the abilities the different models are 1)~$\mathcal{OBLOT}$ (robots are oblivious and silent), 2)~$\mathcal{FSTA}$ (robots have finite states but silent), 3)~$\mathcal{FCOM}$ (robots are oblivious but can communicate constant size information) and, 4)~$\mathcal{LUMI}$ (robots have finite states and can communicate constant size information). Another factor that affects computational ability is the scheduler that decides the activation time of the robots. The main three schedulers are \textit{fully-synchronous}, \textit{semi-synchronous} and \textit{asynchronous}. Combining the models ($M$) with schedulers ($K$), we have twelve combinations $M^K$. In the euclidean domain, the comparisons between these twelve variants have been done in different works for transparent robots, opaque robots, and robots with limited visibility. There is a vacant space for similar works when robots are operating on discrete regions like networks. It demands separate research attention because there have been a series of works where robots operate on different networks, and there is a fundamental difference when robots are operating on a continuous domain versus a discrete domain in terms of robots' movement. This work contributes to filling the space by giving a full comparison table for all models with two synchronous schedulers: fully-synchronous and semi-synchronous.

We present a novel approach to automating the identification of risk factors for diseases from medical literature, leveraging pre-trained models in the bio-medical domain, while tuning them for the specific task. Faced with the challenges of the diverse and unstructured nature of medical articles, our study introduces a multi-step system to first identify relevant articles, then classify them based on the presence of risk factor discussions and, finally, extract specific risk factor information for a disease through a question-answering model. Our contributions include the development of a comprehensive pipeline for the automated extraction of risk factors and the compilation of several datasets, which can serve as valuable resources for further research in this area. These datasets encompass a wide range of diseases, as well as their associated risk factors, meticulously identified and validated through a fine-grained evaluation scheme. We conducted both automatic and thorough manual evaluation, demonstrating encouraging results. We also highlight the importance of improving models and expanding dataset comprehensiveness to keep pace with the rapidly evolving field of medical research.

Recently, graph neural networks have been gaining a lot of attention to simulate dynamical systems due to their inductive nature leading to zero-shot generalizability. Similarly, physics-informed inductive biases in deep-learning frameworks have been shown to give superior performance in learning the dynamics of physical systems. There is a growing volume of literature that attempts to combine these two approaches. Here, we evaluate the performance of thirteen different graph neural networks, namely, Hamiltonian and Lagrangian graph neural networks, graph neural ODE, and their variants with explicit constraints and different architectures. We briefly explain the theoretical formulation highlighting the similarities and differences in the inductive biases and graph architecture of these systems. We evaluate these models on spring, pendulum, gravitational, and 3D deformable solid systems to compare the performance in terms of rollout error, conserved quantities such as energy and momentum, and generalizability to unseen system sizes. Our study demonstrates that GNNs with additional inductive biases, such as explicit constraints and decoupling of kinetic and potential energies, exhibit significantly enhanced performance. Further, all the physics-informed GNNs exhibit zero-shot generalizability to system sizes an order of magnitude larger than the training system, thus providing a promising route to simulate large-scale realistic systems.

Understanding causality helps to structure interventions to achieve specific goals and enables predictions under interventions. With the growing importance of learning causal relationships, causal discovery tasks have transitioned from using traditional methods to infer potential causal structures from observational data to the field of pattern recognition involved in deep learning. The rapid accumulation of massive data promotes the emergence of causal search methods with brilliant scalability. Existing summaries of causal discovery methods mainly focus on traditional methods based on constraints, scores and FCMs, there is a lack of perfect sorting and elaboration for deep learning-based methods, also lacking some considers and exploration of causal discovery methods from the perspective of variable paradigms. Therefore, we divide the possible causal discovery tasks into three types according to the variable paradigm and give the definitions of the three tasks respectively, define and instantiate the relevant datasets for each task and the final causal model constructed at the same time, then reviews the main existing causal discovery methods for different tasks. Finally, we propose some roadmaps from different perspectives for the current research gaps in the field of causal discovery and point out future research directions.

Due to their increasing spread, confidence in neural network predictions became more and more important. However, basic neural networks do not deliver certainty estimates or suffer from over or under confidence. Many researchers have been working on understanding and quantifying uncertainty in a neural network's prediction. As a result, different types and sources of uncertainty have been identified and a variety of approaches to measure and quantify uncertainty in neural networks have been proposed. This work gives a comprehensive overview of uncertainty estimation in neural networks, reviews recent advances in the field, highlights current challenges, and identifies potential research opportunities. It is intended to give anyone interested in uncertainty estimation in neural networks a broad overview and introduction, without presupposing prior knowledge in this field. A comprehensive introduction to the most crucial sources of uncertainty is given and their separation into reducible model uncertainty and not reducible data uncertainty is presented. The modeling of these uncertainties based on deterministic neural networks, Bayesian neural networks, ensemble of neural networks, and test-time data augmentation approaches is introduced and different branches of these fields as well as the latest developments are discussed. For a practical application, we discuss different measures of uncertainty, approaches for the calibration of neural networks and give an overview of existing baselines and implementations. Different examples from the wide spectrum of challenges in different fields give an idea of the needs and challenges regarding uncertainties in practical applications. Additionally, the practical limitations of current methods for mission- and safety-critical real world applications are discussed and an outlook on the next steps towards a broader usage of such methods is given.

As soon as abstract mathematical computations were adapted to computation on digital computers, the problem of efficient representation, manipulation, and communication of the numerical values in those computations arose. Strongly related to the problem of numerical representation is the problem of quantization: in what manner should a set of continuous real-valued numbers be distributed over a fixed discrete set of numbers to minimize the number of bits required and also to maximize the accuracy of the attendant computations? This perennial problem of quantization is particularly relevant whenever memory and/or computational resources are severely restricted, and it has come to the forefront in recent years due to the remarkable performance of Neural Network models in computer vision, natural language processing, and related areas. Moving from floating-point representations to low-precision fixed integer values represented in four bits or less holds the potential to reduce the memory footprint and latency by a factor of 16x; and, in fact, reductions of 4x to 8x are often realized in practice in these applications. Thus, it is not surprising that quantization has emerged recently as an important and very active sub-area of research in the efficient implementation of computations associated with Neural Networks. In this article, we survey approaches to the problem of quantizing the numerical values in deep Neural Network computations, covering the advantages/disadvantages of current methods. With this survey and its organization, we hope to have presented a useful snapshot of the current research in quantization for Neural Networks and to have given an intelligent organization to ease the evaluation of future research in this area.

We consider the problem of explaining the predictions of graph neural networks (GNNs), which otherwise are considered as black boxes. Existing methods invariably focus on explaining the importance of graph nodes or edges but ignore the substructures of graphs, which are more intuitive and human-intelligible. In this work, we propose a novel method, known as SubgraphX, to explain GNNs by identifying important subgraphs. Given a trained GNN model and an input graph, our SubgraphX explains its predictions by efficiently exploring different subgraphs with Monte Carlo tree search. To make the tree search more effective, we propose to use Shapley values as a measure of subgraph importance, which can also capture the interactions among different subgraphs. To expedite computations, we propose efficient approximation schemes to compute Shapley values for graph data. Our work represents the first attempt to explain GNNs via identifying subgraphs explicitly and directly. Experimental results show that our SubgraphX achieves significantly improved explanations, while keeping computations at a reasonable level.

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