抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

The modern science of networks has brought significant advances to our understanding of complex systems. One of the most relevant features of graphs representing real systems is community structure, or clustering, i. e. the organization of vertices in clusters, with many edges joining vertices of the same cluster and comparatively few edges joining vertices of different clusters. Such clusters, or communities, can be considered as fairly independent compartments of a graph, playing a similar role like, e. g., the tissues or the organs in the human body. Detecting communities is of great importance in sociology, biology and computer science, disciplines where systems are often represented as graphs. This problem is very hard and not yet satisfactorily solved, despite the huge effort of a large interdisciplinary community of scientists working on it over the past few years. We will attempt a thorough exposition of the topic, from the definition of the main elements of the problem, to the presentation of most methods developed, with a special focus on techniques designed by statistical physicists, from the discussion of crucial issues like the significance of clustering and how methods should be tested and compared against each other, to the description of applications to real networks.

/pdf/community-detection-in-graphs-34rogm3r6p.pdf

Community detection in graphs

With the capability of modeling bidirectional contexts, denoising autoencoding based pretraining like BERT achieves better performance than pretraining approaches based on autoregressive language modeling. However, relying on corrupting the input with masks, BERT neglects dependency between the masked positions and suffers from a pretrain-finetune discrepancy. In light of these pros and cons, we propose XLNet, a generalized autoregressive pretraining method that (1) enables learning bidirectional contexts by maximizing the expected likelihood over all permutations of the factorization order and (2) overcomes the limitations of BERT thanks to its autoregressive formulation. Furthermore, XLNet integrates ideas from Transformer-XL, the state-of-the-art autoregressive model, into pretraining. Empirically, under comparable experiment setting, XLNet outperforms BERT on 20 tasks, often by a large margin, including question answering, natural language inference, sentiment analysis, and document ranking.

/pdf/xlnet-generalized-autoregressive-pretraining-for-language-1n7eqy2uw6.pdf

XLNet: Generalized Autoregressive Pretraining for Language Understanding

With the capability of modeling bidirectional contexts, denoising autoencoding based pretraining like BERT achieves better performance than pretraining approaches based on autoregressive language modeling. However, relying on corrupting the input with masks, BERT neglects dependency between the masked positions and suffers from a pretrain-finetune discrepancy. In light of these pros and cons, we propose XLNet, a generalized autoregressive pretraining method that (1) enables learning bidirectional contexts by maximizing the expected likelihood over all permutations of the factorization order and (2) overcomes the limitations of BERT thanks to its autoregressive formulation. Furthermore, XLNet integrates ideas from Transformer-XL, the state-of-the-art autoregressive model, into pretraining. Empirically, under comparable experiment settings, XLNet outperforms BERT on 20 tasks, often by a large margin, including question answering, natural language inference, sentiment analysis, and document ranking.

Uncovering the topics within short texts, such as tweets and instant messages, has become an important task for many content analysis applications. However, directly applying conventional topic models (e.g. LDA and PLSA) on such short texts may not work well. The fundamental reason lies in that conventional topic models implicitly capture the document-level word co-occurrence patterns to reveal topics, and thus suffer from the severe data sparsity in short documents. In this paper, we propose a novel way for modeling topics in short texts, referred as biterm topic model (BTM). Specifically, in BTM we learn the topics by directly modeling the generation of word co-occurrence patterns (i.e. biterms) in the whole corpus. The major advantages of BTM are that 1) BTM explicitly models the word co-occurrence patterns to enhance the topic learning; and 2) BTM uses the aggregated patterns in the whole corpus for learning topics to solve the problem of sparse word co-occurrence patterns at document-level. We carry out extensive experiments on real-world short text collections. The results demonstrate that our approach can discover more prominent and coherent topics, and significantly outperform baseline methods on several evaluation metrics. Furthermore, we find that BTM can outperform LDA even on normal texts, showing the potential generality and wider usage of the new topic model.

http://www.bigdatalab.ac.cn/~lanyanyan/papers/2013/WWW2013-yan.pdf

A biterm topic model for short texts

In recent years, deep neural networks have led to exciting breakthroughs in speech recognition, computer vision, and natural language processing (NLP) tasks. However, there have been few positive results of deep models on ad-hoc retrieval tasks. This is partially due to the fact that many important characteristics of the ad-hoc retrieval task have not been well addressed in deep models yet. Typically, the ad-hoc retrieval task is formalized as a matching problem between two pieces of text in existing work using deep models, and treated equivalent to many NLP tasks such as paraphrase identification, question answering and automatic conversation. However, we argue that the ad-hoc retrieval task is mainly about relevance matching while most NLP matching tasks concern semantic matching, and there are some fundamental differences between these two matching tasks. Successful relevance matching requires proper handling of the exact matching signals, query term importance, and diverse matching requirements. In this paper, we propose a novel deep relevance matching model (DRMM) for ad-hoc retrieval. Specifically, our model employs a joint deep architecture at the query term level for relevance matching. By using matching histogram mapping, a feed forward matching network, and a term gating network, we can effectively deal with the three relevance matching factors mentioned above. Experimental results on two representative benchmark collections show that our model can significantly outperform some well-known retrieval models as well as state-of-the-art deep matching models.

A Deep Relevance Matching Model for Ad-hoc Retrieval

Short texts are popular on today’s web, especially with the emergence of social media. Inferring topics from large scale short texts becomes a critical but challenging task for many content analysis tasks. Conventional topic models such as latent Dirichlet allocation (LDA) and probabilistic latent semantic analysis (PLSA) learn topics from document-level word co-occurrences by modeling each document as a mixture of topics, whose inference suffers from the sparsity of word co-occurrence patterns in short texts. In this paper, we propose a novel way for short text topic modeling, referred as biterm topic model (BTM) . BTM learns topics by directly modeling the generation of word co-occurrence patterns (i.e., biterms) in the corpus, making the inference effective with the rich corpus-level information. To cope with large scale short text data, we further introduce two online algorithms for BTM for efficient topic learning. Experiments on real-word short text collections show that BTM can discover more prominent and coherent topics, and significantly outperform the state-of-the-art baselines. We also demonstrate the appealing performance of the two online BTM algorithms on both time efficiency and topic learning.

BTM: Topic Modeling over Short Texts

This paper addresses the problem of Named Entity Recognition in Query (NERQ), which involves detection of the named entity in a given query and classification of the named entity into predefined classes. NERQ is potentially useful in many applications in web search. The paper proposes taking a probabilistic approach to the task using query log data and Latent Dirichlet Allocation. We consider contexts of a named entity (i.e., the remainders of the named entity in queries) as words of a document, and classes of the named entity as topics. The topic model is constructed by a novel and general learning method referred to as WS-LDA (Weakly Supervised Latent Dirichlet Allocation), which employs weakly supervised learning (rather than unsupervised learning) using partially labeled seed entities. Experimental results show that the proposed method based on WS-LDA can accurately perform NERQ, and outperform the baseline methods.

/pdf/named-entity-recognition-in-query-4k228ovuxk.pdf

Jiafeng Guo

Papers

A biterm topic model for short texts

A Deep Relevance Matching Model for Ad-hoc Retrieval

A Deep Relevance Matching Model for Ad-hoc Retrieval

BTM: Topic Modeling over Short Texts

Named entity recognition in query