Visualization and validation of (Q)SAR models

Analyzing and modeling relationships between the structure of chemical compounds, their physico-chemical properties, and biological or toxic effects in chemical datasets is a challenging task for scientific researchers in the field of cheminformatics. Therefore, (Q)SAR model validation is essential to ensure future model predictivity on unseen compounds. Proper validation is also one of the requirements of regulatory authorities in order to approve its use in real-world scenarios as an alternative testing method. However, at the same time, the question of how to validate a (Q)SAR model is still under discussion. In this work, we empirically compare a k-fold cross-validation with external test set validation. The introduced workflow allows to apply the built and validated models to large amounts of unseen data, and to compare the performance of the different validation approaches. Our experimental results indicate that cross-validation produces (Q)SAR models with higher predictivity than external test set validation and reduces the variance of the results. Statistical validation is important to evaluate the performance of (Q)SAR models, but does not support the user in better understanding the properties of the model or the underlying correlations. We present the 3D molecular viewer CheS-Mapper (Chemical Space Mapper) that arranges compounds in 3D space, such that their spatial proximity reflects their similarity. The user can indirectly determine similarity, by selecting which features to employ in the process. The tool can use and calculate different kinds of features, like structural fragments as well as quantitative chemical descriptors. Comprehensive functionalities including clustering, alignment of compounds according to their 3D structure, and feature highlighting aid the chemist to better understand patterns and regularities and relate the observations to established scientific knowledge. Even though visualization tools for analyzing (Q)SAR information in small molecule datasets exist, integrated visualization methods that allows for the investigation of model validation results are still lacking. We propose visual validation, as an approach for the graphical inspection of (Q)SAR model validation results. New functionalities in CheS-Mapper 2.0 facilitate the analysis of (Q)SAR information and allow the visual validation of (Q)SAR models. The tool enables the comparison of model predictions to the actual activity in feature space. Our approach reveals if the endpoint is modeled too specific or too generic and highlights common properties of misclassified compounds. Moreover, the researcher can use CheS-Mapper to inspect how the (Q)SAR model predicts activity cliffs. The CheS-Mapper software is freely available at http://ches-mapper.org.

The performativity of nonviolent protest in South Asia (1918 - 1948)

This study seeks to address a gap in the study of nonviolent action. The gap relates to the question of how nonviolence is performed, as opposed to the meaning or impact of nonviolent politics. The dissertation approaches the history of nonviolent protest in South Asia through the lens of performance studies. Such a shift allows for concepts such as performativity and theatricality to be tested in terms of their applicability and relevance to contemporary political and philosophical questions. It also allows for a different perspective on the historiography of nonviolent protest. Using concepts, modes of analysis and tropes of thinking from the emerging field of performance studies, the dissertation analyses two different cases of nonviolent protest, asking how politics is performatively constituted. The first two sections of this study set out the parameters of the key terms of the dissertation: nonviolence and performativity, by tracing their genealogies and legacies as terms. These histories are then located as an intersection in the founding of the nonviolent. The case studies at the analytical core of the dissertation are: fasting as a method in Gandhi's political arsenal, and the army of nonviolent soldiers in the North-West Frontier Province, known as the Khudai Khidmatgar. The study begins with an overview of current theorisations of nonviolence. The approach to the subject is through an investigation of commonly held misconceptions about nonviolent action, such as its supposed passivity, the absence of violence, its ineffectiveness and its spiritual basis. This section addresses the lacunae within existing theories of nonviolence and points to possible fertile spaces for further exploration. Section 3 offers an overview of the different shades of the concept of performativity, asking how it is used in various contexts and how these different nuances can be viewed in relation to each other. The dissertation explores how a theory of performativity may be correlated to the theorisation of nonviolence. The correlations are established in four boundary areas: action/inaction, violence/absence of violence, the actor/opponent and the body/spirit. These boundary areas allow for a theorising of nonviolent action as a performative process. The first case study is Gandhi's use of the fast as a method of nonviolent protest. Using a close reading of his own writings, speeches and letters, as well as a reading of responses to his fast in British newspapers and within India, the dissertation asks what made fasting into Gandhi's most favoured mode of protest and political action. The study reconstructs his unique praxis of the fast from a performative perspective, demonstrating how display and ostentation are vital to the political economy of the fast. It also unveils the cultural context and historical reservoir of body practices, which Gandhi drew from and adapted into 'weapons' of political action. The relationship of Gandhian nonviolence to the body forms a crucial part of the analysis. The second case study is the nonviolent army of the Pashtuns, Khudai Khidmatgar (KK), literally Servants of God. This anti-imperialist movement in the North-West Frontier Province of what is today the border between Pakistan and Afghanistan existed between 1929 and 1948. The movement adopted the organisational form of an army. It conducted protest activities against colonial rule, as well as social reform activities for the Pashtuns. This group was connected to the Congress party of Gandhi, but the dissertation argues that their conceptualisation and praxis of nonviolence emerged from a very different tradition and worldview. Following a brief introduction to the socio-political background of this Pashtun movement, the dissertation explores the activities that this nonviolent army engaged in, looking at their unique understanding of the militancy of an unarmed force, and their mode of combat and confrontation. Of particular interest to the analysis is the way the KK re-combined and mixed what appear to be contradictory ideologies and acts. In doing so, they reframed cultural and historical stereotypes of the Pashtuns as a martial race, juxtaposing the institutional form of the army with a nonviolent praxis based on Islamic principles and social reform. The example of the Khudai Khidmatgar is used to explore the idea that nonviolence is not the opposite of violent conflict, but in fact a dialectical engagement and response to violence. Section 5, in conclusion, returns to the boundary areas of nonviolence: action, violence, the opponent and the body, and re-visits these areas on a comparative note, bringing together elements from Gandhi's fasts and the practices of the KK. The similarities and differences in the two examples are assessed and contextualised in relation to the guiding question of this study, namely the question of the performativity of nonviolent action.