60 research outputs found
Supplementary Data for NIPS Publication: Protein Interface Prediction using Graph Convolutional Networks.
No full text<p>These data sets can be used to re-run the experiments from our paper, Protein Interface Prediction using Graph Convolutional Networks. The data are derived from protein complexes in the docking benchmark dataset v. 5.0. Each file is a python tuple that has been saved using cPickle and compressed using gzip.</p>
<p>Links:</p>
<p>Paper: https://papers.nips.cc/paper/7231-protein-interface-prediction-using-graph-convolutional-networks</p>
<p>Poster: https://zenodo.org/record/1134154</p>
<p>Code: https://github.com/fouticus/pipgcn</p>
<p> </p>
<p><strong>File Descriptions:</strong></p>
<p>train.cpkl.gz and test.cpkl.gz have the data formatted for neighborhood based graph convolutions. The diffc_ files are the same data formatted for the diffusion convolutional neural networks that we compare against. </p>
<p>train.cpkl.gz is a tuple of length 2:</p>
<ul>
<li>element 0 is a list of length 175 containing the PDB codes from the docking benchmark dataset</li>
<li>element 1 is a list of length 175 containing features for each protein. Each element is a dictionary containing the following keys:
<ul>
<li>r_vertex: vertex (residue) features for the receptor. numpy array of shape (x, 70) where x is the number of residues in the receptor and 70 is the number of features.</li>
<li>l_vertex: vertex (residue) features for the ligand. analogous to above, with shape (y, 70) where y is the number of residues in the ligand.</li>
<li>complex_code: PDB code of the complex. matches the list of codes described above.</li>
<li>l_edge: edge features for the neighborhood around each residue in the ligand. numpy array of shape (y, 20, 2) where y is defined as above. the second dimension is the edges to the 20 nearest neighboring residues, ordered by decreasing distance. The third dimension allows for two features per edge. </li>
<li>r_edge: edge features for the neighborhood around each residue in the receptor. numpy array of shape (x, 20, 2) where x is as above. </li>
<li>l_hood_indices: the index of the 20 closest residues to each residue, ordered by decreasing distance. numpy array of shape (y, 20, 1). "Index" means which row in l_vertex gives the vertex features for the closest neighbor, second closest neighbor, etc. </li>
<li>r_hood_indices: analogous to above, shape (x, 20, 1).</li>
<li>label: 1 or -1 label for each residue pair. numpy array of shape (x*y, 3). Each row looks like (i, j, k) where i is the index of the ligand residue, j is the index of the receptor residue, and k is either -1 (negative example) or 1 (positive example).</li>
</ul>
</li>
</ul>
<p>test.cpkl.gz matches the structure of train.cpkl.gz except it has the test set of 55 complexes. </p>
<p>Descriptions of the vertex and edge features can be found in Appendix A of <a href="https://mountainscholar.org/handle/10217/185661">this.</a></p>
<p>diffc_g2_p2_train.cpkl.gz is a tuple of length 2:</p>
<ul>
<li>element 0 is a list of the same 175 PDB codes as above. </li>
<li>element 1 is a list of features for the 175 complexes. Each element is a dictionary of features with these keys:
<ul>
<li>r_vertex, l_vertex, complex_code, label: these are the same as described above. </li>
<li>'r_power_series': Stacked diffusion matrices which are powers of the similarity matrix used in the DCNN method. numpy array of shape (x, 2, x) where x is the number of receptor residues. the middle dimension 2 indicates how many "hops" is used for that diffusion (1 vs. 2). In other words, element (i, 0, j) is the similarity after 1 hops between residues i and j. element (i, 1, j) is the similarity after 2 hops. See DCNN paper for details.</li>
<li>'l_power_series': same as above but for the ligand. shape is (y, 2, y).</li>
</ul>
</li>
</ul>
<p>diffc_g2_p2_test.cpkl.gz is the same as diffc_g2_p2_train.cpkl.gz but for the 55 test complexes.</p>
<p>diff_g2_p5_train.cpkl.gz and diff_g2_p5_test.cpkl.gz are the same as the p2 version above, except that the diffusion matrices have shape (x, 5, x) and (y, 5, y) because one of our comparisons against the DCNN model uses 5 hops instead of just 2. </p>
<p> </p>
<p>Note: these files were pickled with Python 2.7. If you're unpickling with Python 3.x you might have to specify encoding as 'latin1'. </p>
<p> </p>
<p>Please direct any questions to:</p>
<ul>
<li>Alex Fout ([email protected])</li>
<li>Jonathon Byrd ([email protected])</li>
<li>Basir Shariat ([email protected]</li>
<li>Asa Ben-Hur ([email protected])</li>
</ul>This work was supported by the National Science Foundation under grant no DBI-156484
105 - Alex M Fout
No full textIncludes bibliographical references.This poster was presented at the 2017 Colorado State University Graduate Student Showcase, 9 November 2017.Determining the interface between two interacting proteins can help illuminate cellular biology, improve our understanding of disease, and aid pharmaceutical research. Such determination is expensive and time consuming using wet-lab experiments, which has motivated the development of computational methods. Inspired by the success of deep learning in image processing and other application areas, we adapt convolutional neural networks to work with irregularly structured data, such as proteins. We construct a novel pairwise classification architecture which is trained and tested with data from the Docking Benchmark Dataset versions 4.0 and 5.0. This outperforms the existing state-of-the-art prediction method, PAIRpred.Graduate Student Council - New Graduate Student - Research Top Scholar
Шариатские суды: современная практика и перспективы в России
No full textThe article touches the fundamental principles of shariat judiciary, modern practice of shariat courts activity in Muslim and Western countries as well as the perspectives of their establishment and functioning in Russia. The place which shariat courts occupied in the judicial system of the Muslim state during Middle Ages is shown. The author analyses in general terms the historical evolution of shariat justice institutions. The differences between modern shariat courts and the same structures which existed in the preceding historical periods are mentioned. The role played by modern shariat courts in the Muslim countries depends on the place which Islamic Shariat occupies in their legal systems. Shariat model of judiciary was known in the Western countries from the Middle Ages. Nowadays shariat courts are still functioning in some of them. There are two main forms of such courts. The first one embraces unofficial so called shariat courts as religious and social organizations while the second one consists of shariat courts acting on legal basis and within official legislation. Arbitration tribunals in the UK which apply some concrete shariat norms resolving civil and family disputes are one of the examples of such form. In Russia, shariat institutions of dispute resolution were created in the 19th century. They existed in one or another form in our country to the end of the 1920s. After that, they existed in fact during decades but their decisions did not have any legal force. From the 1990s, shariat courts began to emerge in Russia as religious or civil structures. Russian legislation provides legal basis for establishing shariat institutions of dispute resolution in the form of arbitration court or mediation structure. Such institutions can be an alternative form opposing illegal shariat courts and they could assist securing legal fundamentals and values within Russian Muslims community.Статья посвящена анализу теоретических основ шариатского правосудия, современной практики действия шариатских судов в мусульманских и западных странах, а также обоснованию перспектив их создания и функционирования в России. Показано место шариатских судов в судебной системе средневекового мусульманского государства. В настоящее время шариатские суды заметно отличаются от аналогичных структур, которые существовали в прежние исторические эпохи. Организация и практика функционирования этих институтов позволяют выделить характерные особенности современного шариатского правосудия. Нынешняя роль шариатских судов в мусульманских странах прямо зависит от места шариата в их правовых системах. Шариатская модель правосудия была известна странам Запада еще в Средние века. В настоящее время шариатские суды продолжают функционировать в некоторых из них. Различаются их две основные разновидности. Первая представлена так называемыми неофициальными шариатскими судами, которые являются религиозными или общественными организациями. Их решения, как правило, не обладают юридической силой. Вторую составляют шариатские суды, действующие на основе и в рамках законодательства. Примером таких органов могут служить арбитражные трибуналы в Великобритании, применяющие отдельные нормы шариата при рассмотрении гражданских и семейных споров. В России шариатские институты разрешения споров возникли еще в конце XVIII в., но получили широкое развитие только во второй половине XIX в. В той или иной форме они действовали в нашей стране до конца 20-х годов прошлого столетия. Затем в течение десятилетий они фактически существовали, но их решения не имели юридической силы. С 1990-х годов в России вновь стали возникать шариатские суды в качестве религиозных или общественных организаций. Нередко их практика носит противоправный характер. Российское законодательство создает юридическую базу для образования шариатских институтов разрешения споров в форме третейского суда и института медиации. Такие структуры могут стать альтернативой нелегальным шариатским судам и способствовать утверждению правовых начал в среде российских мусульман
Совместим ли шариат с современным российским правом?
No full textThe article is devoted to analysis of the forms of interaction between Shariat and legislation in action as well as compatibility of Shariat with contemporary Russian law in general. The author touches several reasons of increasing interest to the role which Shariat plays in legal development of Russia. Among these reasons he pays attention to the up-going process of renaissance of Islam, social and political activity of Muslim communities outside the regions where Islam is traditionally spread, the existing threat of Islamic extremism, increasing influence of Shariat upon political and legal development of the Muslim world. Also there are numerous conflicts linked with Muslim minorities in the West which contribute a lot to the interest paid to Shariat.
Several modes of referring to Shariat can be differentiated as far as its correlations with positive legislation are concerned. One of them manifests itself in the actions of Muslim separatists and extremists who directly oppose Shariat to the Russian law. Another mode provides for including of Shariat norms in the official legislation. There is one more form of the above mentioned correlation which is related with the action of Shariat as alternative regulator without opposing it to the official state law.
There is no one definite justification for the realization of Shariat provisions. For instance Muslim radicals refer only to religious arguments to fulfil their plans aiming at replacing official legislation by Shariat. Some Rissian scientists call for legalizing of Shariat norms but they do not put down any legal grounds or justification for their proposals. Russian jurists have different approaches to this issue. Some authors elaborate general conceptions which key point is legal recognition of local traditions and customs including Shariat norms. As a rule these theories concern Russian regions of Northern Caucasus.
The author examines several patterns of possible correlation between Shariat and state legislation. The first one is represented by the direct inclusion of Shariat norms into the legislation. The Russian law provides for such implementation under some conditions. The leading one is choosing among Shariat provisions those which meet criteria of legal norm and can be considered as Islamic law in proper sense. The other form of the correlation mentioned above manifests itself in legal acts which refer to the historical and local traditions. It means in indirect form the possibility of implementation of some Shariat norms. Besides that Shariat provisions can be used for solving issues which are provided for by dispositive norms of state legislation. Generally the author gives positive answer to the question put in the title of the article.Статья посвящена анализу форм взаимодействия шариата с действующим законодательством, его совместимости с современным российским правом в целом. Автор анализирует несколько причин возрастающего интереса к роли шариата в правовом развитии России. Среди них — продолжающийся процесс возрождения ислама, социально-политическая активность мусульманских общин за пределами регионов традиционного распространения ислама, сохраняющаяся угроза исламского экстремизма, усиление роли шариата в правовом и политическом развитии мусульманского мира, а также связанные с мусульманскими меньшинствами конфликты в странах Запада. Различаются несколько вариантов обращения к шариату в сопоставлении с законодательством. Один из них представлен действиями мусульманских сепаратистов и экстремистов, которые противопоставляют шариат российскому праву. Другой предполагает включение норм шариата в законодательство. Еще один вариант связан с обращением к шариату в качестве альтернативного регулятора без его противопоставления официальному праву. Обоснование реализации предписаний шариата не отличается единством. Мусульманские радикалы ссылаются лишь на религиозные аргументы в целях замены законодательства шариатом. Некоторые ученые призывают легализовать нормы шариата, но не подкрепляют свои предложения правовыми аргументами. Юристы придерживаются различных взглядов по этому вопросу. Некоторые авторы предлагают концепции законодательного признания местных традиций, включая нормы шариата. Как правило, они касаются регионов Северного Кавказа. Автор выделяет несколько форм возможного взаимодействия шариата и законодательства. Первая представлена прямым включением норм шариата в законодательство. Российское право такую возможность допускает при определенных условиях. Главное из них — выбор среди норм шариата таких предписаний, которые отвечают критериям права и являются исламским правом в точном смысле. Другая форма сводится к включению в законодательство ссылки на исторические или местные традиции, что дает возможность применять отдельные нормы шариата. Кроме того, шариатские предписания могут действовать по вопросам, урегулированным в законодательстве диспозитивными правилами. В целом на поставленный в названии статьи вопрос автор дает положительный ответ
The Taliban in 2024
No full textReacting to corruption and oppression in the Kandahar of 1994, the Taliban is seen as working with Sunni clerics to foster a shariat movement for advancing economic justice and (corporal) punishment. Before long, the organization began substantially rewarding joiners, arming for jihad, and resisting international forces in Afghanistan. Now, with less foreign resources to fight the Taliban, the Kabul central government has unfinished business with its still-robust challengers. In the face of recent modernization in sectors such as education and media, the author details three plausible scenarios for the Taliban to maintain its core shariat mission. One scenario is for the Taliban to re-secure (through continued force) its initial goal, viz., overall state power to promote and enforce shariat across urban as well as rural areas. Another possibility projects Afghanistan as operating a dualist system of separate zones, one for the Taliban's ‘liberated territory,’ the other for the rest of Afghanistan as governed by Kabul. Achieving scenario three would be formidable: it posits that Taliban leaders may be persuaded that their armed jihad has run its course and can profitably be disconnected from the Middle East's broader Islamic conflict. Conceivably, then, through accommodations with a shariat-accepting Kabul government, Taliban might be able to win buy-in for peace from its own military and its own fighting priests with their strong ties to Afghan communities in Pakistan
PERSPECTIVES OF ISLAMIC LAW IN CONTEMPORARY RUSSIA
No full textСтатья посвящена анализу возможностей и условий
обращения к исламскому праву в современном правовом развитии
России. Рассматриваются причины актуальности проблемы места
шариата и исламского права в правовой жизни современной России.
Исследуются различные позиции по этому вопросу, а также практи-
ческие попытки применения норм исламского права в конце истек-
шего и начале нынешнего столетия. Сравниваются взгляды мусуль-
манских религиозных лидеров, российских государственных структур
и ученых относительно возможной роли шариата в правовой
действительности России. Обосновываются направления и условия
включения отдельных норм и институтов исламского права в
правовую систему страны. Оцениваются перспективы создания и
функционирования шариатских судов в современной России.The article is devoted to the analysis of possibilities and
conditions of appealing to Islamic law for the modern legal development
of Russia. The reasons of increasing importance of the problems linked
with the place occupied of Shariat as well as the Islamic law in the legal
life of contemporary Russia are also discussed. The author covers
different approaches to this issue as well as practical attempts to implement
Islamic legal norms in the end of previous century and the beginning of
the new millennium. The views of Muslim religious leaders, Russian
government institutions and scientists on possible role of Shariat in Russian legal life are evaluated. The author puts forward the principle
directions and conditions of including some norms and institutions of
Islamic law within the legal system of the country. The perspectives of
creating of Shariat courts in contemporary Russia are evaluated.343-36
PERSPECTIVES OF ISLAMIC LAW IN CONTEMPORARY RUSSIA
No full text343-366Статья посвящена анализу возможностей и условий
обращения к исламскому праву в современном правовом развитии
России. Рассматриваются причины актуальности проблемы места
шариата и исламского права в правовой жизни современной России.
Исследуются различные позиции по этому вопросу, а также практи-
ческие попытки применения норм исламского права в конце истек-
шего и начале нынешнего столетия. Сравниваются взгляды мусуль-
манских религиозных лидеров, российских государственных структур
и ученых относительно возможной роли шариата в правовой
действительности России. Обосновываются направления и условия
включения отдельных норм и институтов исламского права в
правовую систему страны. Оцениваются перспективы создания и
функционирования шариатских судов в современной России.The article is devoted to the analysis of possibilities and
conditions of appealing to Islamic law for the modern legal development
of Russia. The reasons of increasing importance of the problems linked
with the place occupied of Shariat as well as the Islamic law in the legal
life of contemporary Russia are also discussed. The author covers
different approaches to this issue as well as practical attempts to implement
Islamic legal norms in the end of previous century and the beginning of
the new millennium. The views of Muslim religious leaders, Russian
government institutions and scientists on possible role of Shariat in Russian legal life are evaluated. The author puts forward the principle
directions and conditions of including some norms and institutions of
Islamic law within the legal system of the country. The perspectives of
creating of Shariat courts in contemporary Russia are evaluated
Transmission Expansion Planning of Transnational Offshore Grids: A Techno-Economic and Legal Approach Case Study of the North Sea Offshore Grid
No full textThe new energy policy of the European Union (EU) with the core objectives of competitiveness, reliability and sustainability, has driven Europe into a transition towards a low carbon & sustainable electricity supply systems. Under the new policy, the European energy systems are pursing two major objectives. First is to shift the focus from national to regional or (perhaps) a European level with the ultimate goal of introducing regional markets that facilitates cross-border power trades. Second, is to incorporate large renewable energy sources into the power systems to best exploit the energy resources. In this regards, special attention is oriented towards the development of the offshore gird in the North Sea region where offshore wind is abundant and has potential to become major energy source in the area. This thesis looks into transmission expansion planing in the North Sea region. It presents a market based approach to solve a long-term transmission expansion planning for a meshed VSC-HVDC offshore grid that connect regional markets. The main goal here is to determine the grid design that enables harnessing the offshore wind energy most efficiently, at the same time, creating capacity for conducting cross-border power exchange. Development of an offshore grid in the North Sea can encounter various technical, legal and economic barriers. Consequently advanced planning frameworks are required that enables accounting for these issues. The methodology proposed here provides a framework to investigate the impact of each of these factors on the development of offshore infrastructures. More precisely, the contributions of this thesis can be summarized as follows: \u95 Static Transmission Expansion Planning framework (STEP) In Chapter 5, I have proposed a multiple time-period static transmission expansion planning framework that is applicable to VSC-HVDC meshed grids. I have shown that the analytical solution to the problem gives the pricing mechanism that expresses the relationship between the electricity price of different zones and the congestion charges associated with the interconnectors between them. It is an extension of the work of Schweppe et al. that has been proven for and applied to VSC-HVDC grids. The proposed formulation includes investment recovery through congestion revenues as an implicit strict equality constraint. It, therefore, computes the expansion plan, such that the investment capital will be fully paid off through congestion revenues by the end of the chosen lifetime of the infrastructure. The framework determines the topology, transmission capacities and the power flows through the offshore grid, and the resulting distribution of social welfare among the price zones. By combining both flow-constraints and investment recovery-constraints and working with historical market data, the framework can deliver useful results that demonstrate how onshore price zones could benefit from an optimal grid design. \u95 Iterative clustering methods for computation feasibility The optimization framework proposed in Chapter 5 was intended to be driven by historical market-data in the form of hourly regional cost curves. The dimensionality of the search space and the computational intensity of the proposed optimization algorithm make the problem intractable. It was desirable to identify and work with only a subset from the total set of operating states. I developed an iterative algorithm that combines an unsupervised clustering technique with the proposed optimization tool to cope with the computational burden of the large-scale optimization problem. Automatic space transformation and clustering were performed to select a subset of representative hourly operating states. The number of samples in the subset was adjusted in order to match the congestion-induced revenues to that of the full data set. This ensured that essential information was not lost. The framework, thus, balances the need for reasonable computation times against the benefits of a model that allows multiple time-periods (as defined by zonal prices and wind power production combinations) and obtains realistic results. Several clustering algorithms (including K-means) and feature reduction techniques (such as Principal Component Analysis (PCA)) have been used in investment planning analysis. Their combination has also been explored in literature. However, this is the first time that an unsupervised PCA/clustering technique has been combined with an optimization tool to refine the clustering results. \u95 StaticWind and Transmission Expansion Planning framework (SWTEP) Chapter 6 describes a novel co-optimization wind and transmission expansion framework applicable to VSC-HVDC meshed grids. This is an extension of the static framework presented in Chapter 5 that adds wind to the TEP formulation, while implementing support schemes, which inherently induce a deviation from perfect competition. This results in a fundamental contradiction between the structure of the competitive market and the nature of support policies. The novelty of the work presented in Chapter 6 is that it has limited the market distortion by excluding the support payments from the market clearing process. To do so, I have proposed a formulation that divides the initial investment of the offshore wind infrastructure into subsidized and unsubsidized parts. Thus, the objective of the optimization problem was to maximize sum of incremental social welfare of all regions at all times, minus the aggregated investment cost of offshore transmission infrastructure and the investment cost of building the offshore wind farms that has not been covered through the support payments. The proposed framework enables the impact of implementing two types of feed-in premium support schemes (i.e., generation-based and capacity-based) to be accounted for in the final development of the grid. The goal of this chapter was to investigate the performance of the two feed-in support policies to verify if investment recovery would be fulfilled under a certain support scheme design. In addition, an ‘optimal’ support level and offshore wind support tariff rate were determined. The analytical solution to the optimization problems confirms the complete recovery of the investment cost of transmission infrastructure. In addition, under the assumption that no offshore wind was curtailed, the revenues collected from market sales of offshore wind farms can pay off the unsubsidized part of the wind farm investment, regardless of the payment basis (generation-based or capacity-based). \u95 Dynamic Transmission Expansion Planning framework (DTEP) In Chapter 7, I have proposed a market-based, multiple stage, multi-time period dynamic transmission expansion planning framework for a meshed offshore grid to connect upcoming offshore wind farms to multiple onshore markets. The main contribution of this framework is that it enables accounting for delays in the construction and implementation of offshore infrastructures, including wind farms and transmission systems. Delays can occur mainly due to legal barriers associated with differing permitting criteria in an international context, but also due to market maturity and supply chain issues. The timing of delays in grid, market and wind farm developments are set exogenously in the model. This is an extension of the work presented in Chapter 5 in which the whole offshore grid was assumed to be built in one instant. The final results include the optimal grid topology, transmission capacities, construction timing and the resulting remuneration and distribution of the social welfare increase and financial benefit among the various onshore price zones. The analytical solution to the optimization problem gives the pricing mechanism that is consistent with the AC onshore counterpart. The proposed market mechanism facilitates the integration of a multi-terminal VSC-HVDC offshore grid into the existing AC grid. In addition, the analytical solution confirms the investment recovery through congestion revenues, regardless of the number of investors that are involved. In the case of multiple investors, an independent financial entity is required that collects the transmission revenues from the grid operators and distributes them appropriately amongst the investors. Under this regulatory assumption, the investment recovery of every cable of every interconnector will be completely fulfilled within the desired economic lifetime.Electrical Sustainable EnergyElectrical Engineering, Mathematics and Computer Scienc
Robust time-series retrieval using adaptive segmental alignment
No full textThe problem of time-series retrieval arises in many fields of science and constitutes many important sub-problems including indexing, storage, representation, similarity measurement, etc. The center piece of time-series retrieval is, however, measurement of similarity between the query and the stored sequences in the data-base. Since different time-series sampled from similar phenomena can have variable lengths and/or warping, simple distance metrics such as Euclidean distance are either undefined or do not provide an accurate similarity measure. Therefore, alignment methods such as dynamic time warping have been proposed. They essentially rely on the distance between every sample point of contrasting sequences and recover their alignment using dynamic programming. These algorithms are effective when the sequences are noise-free and causal. In this work we introduce the concept of segmental sequence alignment. We claim that dynamically dividing the contrasting sequences into subsequences and recovering the optimal and monotonic matching between them instead of individual time-points can result in constructing a similarity measure more robust to noise and non-causality. We propose two different approaches and variants of them to accomplish segmental sequence alignment. The first proposed approach is an isotonic extension of Canonical Correlation Analysis (CCA) properly constrained to satisfy the time monotonicity constraint necessary for an alignment algorithm. The second approach is an extension of pair-HMM, which is a probabilistic model for aligning sequences. We have defined a proper observation model and efficient learning and inference algorithms to jointly recover the segmentation and alignment from segmental pair-HMM. We also propose a relaxation to the probabilistic model to increase the computational efficiency. We have shown the utility of our proposed techniques through extensive experiments on both synthetic and real-world data. We have applied our methods to various data sets from EEG signals to human activity. Our methods showed generally significant improvement over traditional models especially in instances when the sequences are corrupted by high levels of noise or are locally non-causal.Ph. D.Includes bibliographical referencesIncludes vitaby Shahriar Shariat Talkhoonch
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