Graph kernels based on tree patterns for molecules

Motivated by chemical applications, we revisit and extend a family of positive definite kernels for graphs based on the detection of common subtrees, initially proposed by Ramon et al. (2003). We propose new kernels with a parameter to control the complexity of the subtrees used as features to represent the graphs. This parameter allows to smoothly interpolate between classical graph kernels based on the count of common walks, on the one hand, and kernels that emphasize the detection of large common subtrees, on the other hand. We also propose two modular extensions to this formulation. The first extension increases the number of subtrees that define the feature space, and the second one removes noisy features from the graph representations. We validate experimentally these new kernels on binary classification tasks consisting in discriminating toxic and non-toxic molecules with support vector machines

Benchmark of structured machine learning methods for microbial identification from mass-spectrometry data

Microbial identification is a central issue in microbiology, in particular in the fields of infectious diseases diagnosis and industrial quality control. The concept of species is tightly linked to the concept of biological and clinical classification where the proximity between species is generally measured in terms of evolutionary distances and/or clinical phenotypes. Surprisingly, the information provided by this well-known hierarchical structure is rarely used by machine learning-based automatic microbial identification systems. Structured machine learning methods were recently proposed for taking into account the structure embedded in a hierarchy and using it as additional a priori information, and could therefore allow to improve microbial identification systems. We test and compare several state-of-the-art machine learning methods for microbial identification on a new Matrix-Assisted Laser Desorption/Ionization Time-of-Flight mass spectrometry (MALDI-TOF MS) dataset. We include in the benchmark standard and structured methods, that leverage the knowledge of the underlying hierarchical structure in the learning process. Our results show that although some methods perform better than others, structured methods do not consistently perform better than their "flat" counterparts. We postulate that this is partly due to the fact that standard methods already reach a high level of accuracy in this context, and that they mainly confuse species close to each other in the tree, a case where using the known hierarchy is not helpful

The pharmacophore kernel for virtual screening with support vector machines

We introduce a family of positive definite kernels specifically optimized for the manipulation of 3D structures of molecules with kernel methods. The kernels are based on the comparison of the three-points pharmacophores present in the 3D structures of molecul es, a set of molecular features known to be particularly relevant for virtual screening applications. We present a computationally demanding exact implementation of these kernels, as well as fast approximations related to the classical fingerprint-based approa ches. Experimental results suggest that this new approach outperforms state-of-the-art algorithms based on the 2D structure of mol ecules for the detection of inhibitors of several drug targets

Philologie et historiographie du Caucase chrétien

Programme de l’année 2008-2009 : I. L’Arménie et les Arabes (639-884). — II. La royauté bagratide (884-1055)

Philologie et historiographie du Caucase chrétien

Programme de l’année 2019-2020 : I. Histoire primitive du Kartli et Listes royales dans la Conversion de la Géorgie. — II. Le roman des Saints Traducteurs et l’enseignement de la philosophie dans l’Arménie des VIe-XIe siècles

Philologie et historiographie du Caucase chrétien

Programme de l’année 2006-2007 : L’historiographie arménienne de la conversion des Albaniens

Philologie et historiographie du Caucase chrétien

Programme de l’année 2009-2010 : I. L’Arménie Majeure et la Cilicie entre les Seldjoukides et les Mongols (1064-1375). — II. Turcomans, Ottomans, Safavides (1375-1639)

Philologie et historiographie du Caucase chrétien

Programme de l’année 2007-2008 : L’Arménie artaxiade (iie s. avant notre ère)

Philologie et historiographie du Caucase chrétien

Programme de l’année 2008-2009 : I. L’Arménie et les Arabes (639-884). — II. La royauté bagratide (884-1055)