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Formal grammars for intermolecular structure 分子间结构的形式语法
D. Searls
Formal grammars can be used to model general forms of intramolecular structure, such as secondary structure of nucleic acids. A new formalism, called cut grammar, is shown to model intermolecular assemblages such as hybridization products, as well. Formal grammars themselves can be modelled by sets of oligonucleotides, and derivations from any context-free grammar can in theory be simulated by hybridization experiments.<>
形式语法可以用来模拟一般形式的分子内结构,如核酸的二级结构。一种新的形式,称为切割语法,被证明是模拟分子间组装,如杂交产物,以及。形式语法本身可以用一组寡核苷酸来建模,从任何上下文无关的语法衍生出来的语法在理论上都可以通过杂交实验来模拟
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引用次数: 19
A modified cellular automata model of nucleotide interactions and non-enzymatic transcription of DNA 核苷酸相互作用和DNA非酶转录的改进细胞自动机模型
J. Hilke, J. Reggia, R. Navarro‐González, J. Lohn
An important stage in the development of living systems on Earth was the formation of RNA-like molecules capable of self-transcripting and self-replicating. In this paper, the authors attempt to develop a simple, flexible and accurate computer model of nucleotide interactions that lead to the non-enzymatic transcription of an oligonucleotide that acts as a template to catalyze the formation of a suite of oligonucleotides. The authors' computer model is cellular automata based and allows nucleotides to experience random movement and interact locally to associate with a template and/or oligomerize with other nucleotides according to a set of rules. To test the simulation method, results were compared to specific laboratory experimental results. The hypotheses were that the best set of rules developed would be able to produce results which were: 1. More similar to the laboratory experiment's results than random rules; 2. More similar to the laboratory experiment's results than a set of rules which is chemically realistic but has random probabilities; and 3. Statistically similar to the laboratory experiment's results. The test for determining whether the results were statistically similar was done using a regression analysis. At the a=0.05 level: the first two hypothesis were supported, and the third hypothesis has not yet been statistically supported.<>
地球上生命系统发展的一个重要阶段是能够自我转录和自我复制的类rna分子的形成。在本文中,作者试图开发一种简单,灵活和准确的核苷酸相互作用的计算机模型,该模型导致寡核苷酸的非酶转录,寡核苷酸作为模板催化一组寡核苷酸的形成。作者的计算机模型是基于细胞自动机的,允许核苷酸经历随机运动,并根据一套规则与模板和/或与其他核苷酸寡聚在一起进行局部相互作用。为了验证仿真方法的有效性,将仿真结果与实验室具体实验结果进行了对比。假设是,最好的一套规则将能够产生如下结果:1。比随机规则更接近实验室实验结果;2. 更接近于实验室实验的结果,而不是一套化学上真实但具有随机概率的规则;和3。统计上与实验室实验结果相似。使用回归分析来确定结果是否在统计上相似。在a=0.05水平上:前两个假设得到支持,第三个假设尚未得到统计支持。
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引用次数: 2
Splicing systems on graphs 图上的拼接系统
Rudolf Freund
The notion of splicing systems has been introduced by Tom Head (1987) in order to model the recombinational behaviors of double-stranded DNA molecules under the simultaneous influence of specified classes of restriction enzymes. Yet for modelling complex: (bio)chemical processes of three-dimensional (macro)molecules in the three-dimensional space strings turn out to be more or less inadequate objects. Hence in this paper the author suggests graphs as more suitable objects for modelling such processes and introduces graph splicing systems. An illustrating example from the area of DNA splicing is elaborated in order to show the suitability of the new approach. The author exhibits the relation between regular graph splicing systems on graphs and splicing systems on strings and shows that his new model allows him to describe splicing systems on strings as well as on circular strings within a uniform framework.<>
剪接系统的概念是由Tom Head(1987)提出的,目的是模拟在特定类别的限制性内切酶同时影响下双链DNA分子的重组行为。然而,对于三维空间弦中三维(宏观)分子的复杂(生物)化学过程的建模,结果证明或多或少是不充分的对象。因此,在本文中,作者建议图作为更合适的对象来建模这类过程,并介绍了图拼接系统。文中以DNA剪接为例,说明了该方法的适用性。作者展示了图上的正则图拼接系统和弦上的拼接系统之间的关系,并表明他的新模型允许他在统一的框架内描述弦上的拼接系统以及圆弦上的拼接系统。
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引用次数: 29
Some ideas towards a grammatical model of the /spl sigma//sup 54/ bacterial promoters 对/spl sigma//sup 54/细菌启动子语法模型的一些设想
J. Collado-Vides
The integration of large amounts of information on the regulation of gene expression requires conceptual frameworks which should facilitate the discovery of general principles underlying different mechanisms of gene regulation. An exhaustive database of /spl sigma//sup 70/ and /spl sigma//sup 54/ promoters in E. Coli has supported the construction of a grammatical model of the /spl sigma//sup 70/ type of promoters. This grammar generates all and only those regulatory arrangements of the collection, as well as new ones which are consistent with the biological principles of the collection. In this paper, some ideas towards a unified model of the /spl sigma//sup 70/ and the /spl sigma//sup 54/ bacterial promoters are presented. This model should reflect the biological differences on the possible regulatory mechanisms of these collections. The /spl sigma//sup 54/ class represents an intermediate step between the 7/sup 0/ promoters and those present in higher organisms. Based on the biology of these bacterial promoters a hypothesis is proposed which stipulates that in principle it is feasible to activate /spl sigma//sup 70/ promoters at a distance, an exclusive property of the /spl sigma//sup 54/ class shared with promoters from higher organisms. Assuming this hypothesis is correct, some a ideas supporting a unique "universal" grammar for the /spl sigma//sup 70/ and /spl sigma//sup 54/ promoters are presented.<>
整合基因表达调控的大量信息需要概念框架,这应该有助于发现不同基因调控机制背后的一般原则。大肠杆菌中/spl sigma//sup 70/和/spl sigma//sup 54/启动子的详尽数据库支持了/spl sigma//sup 70/类型启动子语法模型的构建。该语法生成所有且仅生成集合的规则安排,以及与集合的生物学原理一致的新安排。本文提出了建立/spl sigma//sup 70/和/spl sigma//sup 54/细菌启动子统一模型的一些设想。该模型应反映出这些集合在可能的调控机制上的生物学差异。/spl sigma//sup 54/类代表了7/sup 0/启动子与高等生物中存在的启动子之间的中间步骤。基于这些细菌启动子的生物学特性,提出了一个假设,即/spl sigma//sup 70/启动子在原则上是可以远距离激活的,这是/spl sigma//sup 54/类启动子与高等生物启动子共有的特性。假设这一假设是正确的,提出了一些支持/spl sigma//sup 70/和/spl sigma//sup 54/启动子的独特“通用”语法的想法。
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引用次数: 0
Synaptically distributed memory vs. synaptically localized memory 突触分布记忆与突触局部记忆
Lipo Wang
We clarify that the only essential difference between the two major "categories" of unsupervised learning rules discussed in theories of artificial neural networks-the competitive learning and the Hebbian learning rules-is that lateral inhibition is present in the former and is absent in the later. We demonstrate analytically that a competitive learning neural network, which has synaptically localized memory, shows better tolerance over noise in training patterns in comparison with the Hopfield neural network, which uses a Hebbian-type learning rule without any lateral inhibition and has synaptically distributed memory.<>
我们澄清,在人工神经网络理论中讨论的两大类无监督学习规则(竞争性学习和Hebbian学习规则)之间的唯一本质区别是,前者存在侧抑制,而后者不存在侧抑制。我们通过分析证明,与Hopfield神经网络相比,具有突触局部记忆的竞争性学习神经网络在训练模式中对噪声表现出更好的耐受性,Hopfield神经网络使用hebbian型学习规则,没有任何侧抑制,具有突触分布记忆
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引用次数: 0
Population dynamics in a radically epistatic genetic system 一个根本上位遗传系统中的种群动态
J. Gattiker, D. Wilson
A genetic system that uses a radically epistatic mapping from genotype to phenotype is defined. This system is proposed in order to study the population dynamics rather than create a new system for function optimization. Two behaviors not found in traditional genetic systems are explored: first, although the genetic system uses only simple generational recombination and fitness scaling, it is capable of distributing a population of solutions on a number of non-adjacent phenotype peaks. This capability is analyzed and empirically explored. Second, the genetic system is shown to have the capability of tracking an environment where the adaptive peaks are changed in a recurrent manner.<>
定义了一个遗传系统,它使用从基因型到表型的根本上位性映射。提出该系统是为了研究种群动态,而不是创建一个新的系统来进行功能优化。探讨了传统遗传系统中没有的两个行为:首先,尽管遗传系统只使用简单的世代重组和适应度缩放,但它能够在许多非相邻的表型峰上分布一个解决方案群体。对这种能力进行了分析和经验探索。其次,遗传系统显示出跟踪环境的能力,其中自适应峰值以周期性的方式变化。
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引用次数: 1
A neocognitron synthesized by production rule for handwritten character recognition 基于生成规则合成的手写体字符识别新认知子
D. Yeung, Hing-Yip Chan, Y. C. Lau
The objective of this paper is to propose a modified neocognitron with production rules embedded for handwritten character recognition. Structured information about the basic features in a character is stored in the production rules constructed by users. A mapping scheme is used to map these rules into the connection weights of the neocognitron. The ability to represent structured information for characters using production rules provides some insights into how this structured information or knowledge can be processed by the network for its character recognition or refinement in the case where a character is misrecognized. The whole process can be controlled by users by analyzing the results of the recognition by refining the production rules to improve the recognition rate. It is much more flexible, and can be used as tools to build a rapid prototype of a pattern recognizer with fault diagnosis capability.<>
本文的目的是提出一种带有生成规则的改进的新认知器,用于手写体字符识别。有关字符基本特征的结构化信息存储在用户构建的生成规则中。使用映射方案将这些规则映射到新认知器的连接权值中。使用生成规则表示字符的结构化信息的能力提供了一些见解,说明网络如何处理这些结构化信息或知识,以便在字符被错误识别的情况下进行字符识别或改进。通过对识别结果的分析,细化生成规则,提高识别率,用户可以控制整个过程。该方法更加灵活,可以作为工具来构建具有故障诊断能力的模式识别器的快速原型。
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引用次数: 2
Discovery of comprehensible symbolic rules in a neural network 神经网络中可理解符号规则的发现
Stéphane Avner
In this paper, we introduce a system that extracts comprehensible symbolic rules from a multilayer perceptron. Once the network has been trained in the usual manner, the training set is presented again, and the actual activations of the units recorded. Logical rules, corresponding to the logical combinations of the incoming signals, are extracted at each activated unit. This procedure is used for all examples belonging to the training set. Thus we obtain a set of rules which account for all logical steps taken by the network to process all known input patterns. Furthermore, we show that if some symbolic meaning were associated to every input unit, then the hidden units, which have formed concepts in order to deal with recurrent features in the input data, possess some symbolic meaning tool. Our algorithm allows the recognition or the understandability of these concepts: they are found to be reducible to conjunctions and negations of the human input concepts. Our rules can also be recombined in different ways, thus constituting some limited but sound generalization of the training set. Neural networks could learn concepts about domains where little theory was known but where many examples were available. Yet, because their knowledge was stored in the synaptic strengths under numerical form, it was difficult to comprehend what they had discovered. This system therefore provides some means of accessing the information contained inside the network.<>
本文介绍了一个从多层感知器中提取可理解符号规则的系统。一旦网络以通常的方式进行了训练,训练集将再次呈现,并记录单元的实际激活。在每个激活单元上提取与输入信号的逻辑组合相对应的逻辑规则。此过程用于属于训练集的所有示例。因此,我们获得了一组规则,这些规则说明了网络处理所有已知输入模式所采取的所有逻辑步骤。此外,我们还证明,如果每个输入单元都有一些符号意义,那么为了处理输入数据中的循环特征而形成概念的隐藏单元就具有一些符号意义工具。我们的算法允许这些概念的识别或可理解性:它们被发现可以简化为人类输入概念的连词和否定。我们的规则也可以以不同的方式重组,从而构成训练集的一些有限但健全的泛化。神经网络可以学习一些领域的概念,这些领域的理论知之甚少,但有很多例子可用。然而,由于他们的知识以数字形式储存在突触强度中,因此很难理解他们的发现。因此,该系统提供了访问网络中包含的信息的一些方法。
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引用次数: 5
Self-organized learning in multi-layer networks 多层网络中的自组织学习
R. Brause
Presents a framework for the self-organized formation of high level learning by a statistical preprocessing of features. The paper focuses first on the formation of the features in the context of layers of feature processing units as a kind of resource-restricted associative learning. The author claims that such an architecture must reach maturity by basic statistical proportions, optimizing the information processing capabilities of each layer. The final symbolic output is learned by pure association of features of different levels and kind of sensorial input. Finally, the author also shows that common error-correction learning can be accomplished by a kind of associative learning.<>
通过特征的统计预处理,提出了一个自组织形成高级学习的框架。本文首先研究了特征处理单元层背景下特征的形成,这是一种资源受限的联想学习。作者认为这样的体系结构必须按照基本的统计比例达到成熟,优化每一层的信息处理能力。最终的符号输出是通过不同层次的特征和各种感官输入的纯粹关联来学习的。最后,作者还证明了常见的纠错学习可以通过一种联想学习来完成
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引用次数: 2
Generating neural networks through the induction of threshold logic unit trees 通过阈值逻辑单元树的归纳生成神经网络
M. Sahami
This paper investigates the generation of neural networks through the induction of binary trees of threshold logic units (TLUs). Initially, we describe the framework for our tree construction algorithm and show how it helps to bridge the gap between pure connectionist (neural network) and symbolic (decision tree) paradigms. We also show how the trees of threshold units that we induce can be transformed into an isomorphic neural network topology. Several methods for learning the linear discriminant functions at each node of the tree structure are examined and shown to produce accuracy results that are comparable to classical information theoretic methods for constructing decision trees (which use single feature tests at each node), but produce trees that are smaller and thus easier to understand. Moreover, our results also show that it is possible to simultaneously learn both the topology and weight settings of a neural network simply using the training data set that we are initially given.<>
本文研究了用阈值逻辑单元二叉树归纳法生成神经网络的方法。首先,我们描述了树构造算法的框架,并展示了它如何帮助弥合纯连接主义(神经网络)和符号(决策树)范式之间的差距。我们还展示了如何将我们诱导的阈值单元树转换为同构神经网络拓扑。在树形结构的每个节点上学习线性判别函数的几种方法进行了检查,并显示出与构建决策树的经典信息理论方法(在每个节点上使用单个特征测试)相当的准确性结果,但产生的树更小,因此更容易理解。此外,我们的结果还表明,简单地使用我们最初给出的训练数据集,可以同时学习神经网络的拓扑和权重设置。
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引用次数: 7
期刊
Proceedings First International Symposium on Intelligence in Neural and Biological Systems. INBS'95
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