Selective Metal Cation Capture by Soft Anionic Metal-Organic Frameworks via Drastic Single-Crystal-to-Single-Crystal Transformations

In this paper we describe a novel framework for the discovery of the topical content of a data corpus, and the tracking of its complex structural changes across the temporal dimension. In contrast to previous work our model does not impose a prior on the rate at which documents are added to the corpus nor does it adopt the Markovian assumption which overly restricts the type of changes that the model can capture. Our key technical contribution is a framework based on (i) discretization of time into epochs, (ii) epoch-wise topic discovery using a hierarchical Dirichlet process-based model, and (iii) a temporal similarity graph which allows for the modelling of complex topic changes: emergence and disappearance, evolution, and splitting and merging. The power of the proposed framework is demonstrated on the medical literature corpus concerned with the autism spectrum disorder (ASD) - an increasingly important research subject of significant social and healthcare importance. In addition to the collected ASD literature corpus which we will make freely available, our contributions also include two free online tools we built as aids to ASD researchers. These can be used for semantically meaningful navigation and searching, as well as knowledge discovery from this large and rapidly growing corpus of literature.Comment: In Proc. Pacific-Asia Conference on Knowledge Discovery and Data Mining (PAKDD), 201

Cutoff Scanning Matrix (CSM): structural classification and function prediction by protein inter-residue distance patterns

BACKGROUND: The unforgiving pace of growth of available biological data has increased the demand for efficient and scalable paradigms, models and methodologies for automatic annotation. In this paper, we present a novel structure-based protein function prediction and structural classification method: Cutoff Scanning Matrix (CSM). CSM generates feature vectors that represent distance patterns between protein residues. These feature vectors are then used as evidence for classification. Singular value decomposition is used as a preprocessing step to reduce dimensionality and noise. The aspect of protein function considered in the present work is enzyme activity. A series of experiments was performed on datasets based on Enzyme Commission (EC) numbers and mechanistically different enzyme superfamilies as well as other datasets derived from SCOP release 1.75. RESULTS: CSM was able to achieve a precision of up to 99% after SVD preprocessing for a database derived from manually curated protein superfamilies and up to 95% for a dataset of the 950 most-populated EC numbers. Moreover, we conducted experiments to verify our ability to assign SCOP class, superfamily, family and fold to protein domains. An experiment using the whole set of domains found in last SCOP version yielded high levels of precision and recall (up to 95%). Finally, we compared our structural classification results with those in the literature to place this work into context. Our method was capable of significantly improving the recall of a previous study while preserving a compatible precision level. CONCLUSIONS: We showed that the patterns derived from CSMs could effectively be used to predict protein function and thus help with automatic function annotation. We also demonstrated that our method is effective in structural classification tasks. These facts reinforce the idea that the pattern of inter-residue distances is an important component of family structural signatures. Furthermore, singular value decomposition provided a consistent increase in precision and recall, which makes it an important preprocessing step when dealing with noisy data

Concepts in topics. using word embeddings to leverage the outcomes of topic modeling for the exploration of digitized archival collections

Within the field of Digital Humanities, unsupervised machine learning techniques such as topic modeling have gained a lot of attention over the last years to explore vast volumes of non-structured textual data. Even if this technique is useful to capture recurring themes across document sets which have no metadata, the interpretation of topics has been consistently highlighted in the literature as problematic. This paper proposes a novel method based on Word Embeddings to facilitate the interpretation of terms which constituted a topic, allowing to discern different concepts automatically within a topic. In order to demonstrate this method, the paper uses the “Cabinet Papers” held and digitised by the The National Archives (TNA) of the United Kingdom (UK). After a discussion of our results, based on coherence measures, we provide details of how we can linguistically interpret these results.SCOPUS: cp.kinfo:eu-repo/semantics/publishe

Joint Word and Entity Embeddings for Entity Retrieval from a Knowledge Graph

© 2020, Springer Nature Switzerland AG. Recent years have witnessed the emergence of novel models for ad-hoc entity search in knowledge graphs of varying complexity. Since these models are based on direct term matching, their accuracy can suffer from a mismatch between vocabularies used in queries and entity descriptions. Although successful applications of word embeddings and knowledge graph entity embeddings to address the issues of vocabulary mismatch in ad-hoc document retrieval and knowledge graph noisiness and incompleteness, respectively, have been reported in recent literature, the utility of joint word and entity embeddings for entity search in knowledge graphs has been relatively unexplored. In this paper, we propose Knowledge graph Entity and Word Embedding for Retrieval (KEWER), a novel method to embed entities and words into the same low-dimensional vector space, which takes into account a knowledge graph’s local structure and structural components, such as entities, attributes, and categories, and is designed specifically for entity search. KEWER is based on random walks over the knowledge graph and can be considered as a hybrid of word and network embedding methods. Similar to word embedding methods, KEWER utilizes contextual co-occurrences as training data, however, it treats words and entities as different objects. Similar to network embedding methods, KEWER takes into account knowledge graph’s local structure, however, it also differentiates between structural components. Experiments on publicly available entity search benchmarks and state-of-the-art word and joint word and entity embedding methods indicate that a combination of KEWER and BM25F results in a consistent improvement in retrieval accuracy over BM25F alone

Toward Optimized Multimodal Concept Indexing

Information retrieval on the (social) web moves from a pure term-frequency-based approach to an enhanced method that includes conceptual multimodal features on a semantic level. In this paper, we present an approach for semantic-based keyword search and focus especially on its optimization to scale it to real-world sized collections in the social media domain. Furthermore, we present a faceted indexing framework and architecture that relates content to semantic concepts to be indexed and searched semantically. We study the use of textual concepts in a social media domain and observe a significant improvement from using a concept-based solution for keyword searching. We address the problem of time-complexity that is a critical issue for concept-based methods by focusing on optimization to enable larger and more real world style application