Neural-Hidden-CRF: A Robust Weakly-Supervised Sequence Labeler

We propose a neuralized undirected graphical model called Neural-Hidden-CRF to solve the weakly-supervised sequence labeling problem. Under the umbrella of probabilistic undirected graph theory, the proposed Neural-Hidden-CRF embedded with a hidden CRF layer models the variables of word sequence, latent ground truth sequence, and weak label sequence with the global perspective that undirected graphical models particularly enjoy. In Neural-Hidden-CRF, we can capitalize on the powerful language model BERT or other deep models to provide rich contextual semantic knowledge to the latent ground truth sequence, and use the hidden CRF layer to capture the internal label dependencies. Neural-Hidden-CRF is conceptually simple and empirically powerful. It obtains new state-of-the-art results on one crowdsourcing benchmark and three weak-supervision benchmarks, including outperforming the recent advanced model CHMM by 2.80 F1 points and 2.23 F1 points in average generalization and inference performance, respectively.Comment: 13 pages, 4 figures, accepted by SIGKDD-202

Multi-gene phylogenetic evidence indicates that Pleurodesmospora belongs in Cordycipitaceae (Hypocreales, Hypocreomycetidae) and Pleurodesmospora lepidopterorum sp. nov. on pupa from China

A new species, Pleurodesmospora lepidopterorum, isolated from a pupa, is introduced. Morphological comparisons and phylogenetic analyses based on multigene datasets (ITS+RPB1+RPB2+TEF) support the establishment of the new species. Pleurodesmospora lepidopterorum is distinguished from P. coccorum by its longer conidiogenous pegs located in the terminal or lateral conidiophores, and smaller subglobose or ellipsoidal conidia. A combined dataset of RPB1, RPB2, and TEF confirmed the taxonomic placement of Pleurodesmospora in Cordycipitaceae for the first time

Study on species diversity of Akanthomyces (Cordycipitaceae, Hypocreales) in the Jinyun Mountains, Chongqing, China

Akanthomyces species have only been reported from Guizhou and Qinghai Province, with few reports from other regions in China. In this research, the species diversity of Akanthomyces in the Jinyun Mountains, Chongqing was investigated. Fourteen infected spider specimens were collected and two new species (A. bashanensis and A. beibeiensis) and a known species (A. tiankengensis) were established and described according to a multi-locus phylogenetic analysis and the morphological characteristics. Our results reveal abundant Akanthomyces specimens and three species were found at Jinyun Mountain. Due to its being an important kind of entomopathogenic fungi, further attention needs to be paid to the diversity of other entomopathogenic fungi in Chongqing, China

Additions to Thelebolales (Leotiomycetes, Ascomycota): Pseudogeomyces lindneri gen. et sp. nov. and Pseudogymnoascus campensis sp. nov.

Thelebolales are globally distributed fungi with diverse ecological characteristics. The classification of Thelebolales remains controversial to date and this study introduces two new taxa, based on morphological and phylogenetic analyses. The results of phylogenetic analyses indicated that the new taxa formed distinct lineages with strong support that were separated from the other members of Thelebolales. The new taxa described herein did not form sexual structures. The phylogenetic relationships of the new taxa and the morphological differences between these taxa and the other species under Thelebolales are also discussed

Culturable fungi from urban soils in China II, with the description of 18 novel species in Ascomycota (Dothideomycetes, Eurotiomycetes, Leotiomycetes and Sordariomycetes)

As China’s urbanisation continues to advance, more people are choosing to live in cities. However, this trend has a significant impact on the natural ecosystem. For instance, the accumulation of keratin-rich substrates in urban habitats has led to an increase in keratinophilic microbes. Despite this, there is still a limited amount of research on the prevalence of keratinophilic fungi in urban areas. Fortunately, our group has conducted in-depth investigations into this topic since 2015. Through our research, we have discovered a significant amount of keratinophilic fungi in soil samples collected from various urban areas in China. In this study, we have identified and characterised 18 new species through the integration of morphological and phylogenetic analyses. These findings reveal the presence of numerous unexplored fungal taxa in urban habitats, emphasising the need for further taxonomic research in urban China

Morphological and phylogenetic characterisations reveal three new species of Samsoniella (Cordycipitaceae, Hypocreales) from Guizhou, China

Samsoniella species have been found on lepidopteran larvae or pupae buried in soil or leaf litter. Three new species, Samsoniella hymenopterorum, S. coleopterorum and S. lepidopterorum, parasitic on hymenopteran larvae, coleopteran larvae and lepidopteran pupae, respectively, are reported. Morphological comparisons with extant species and DNA-based phylogenies from analysis of a multigene (ITS, RPB1, RPB2 and TEF) dataset supported the establishment of the new species. Unusually, all three new species have mononematous conidiophores. The new species are clearly distinct from other species in Samsoniella occurring in separate subclades

Two new species of Samsoniella (Cordycipitaceae, Hypocreales) from the Mayao River Valley, Guizhou, China

Samsoniella species have been often found in the forest habitat and rarely found in special karst eco-environments, such as Tiankeng, valleys and caves. In this research, eleven cordyceps specimens were collected from Mayao River Valley. A known species (S. haniana) and two new species (S. duyunensis and S. vallis) were established and described according to a multilocus phylogenetic analysis and morphological characteristics. Our results provide insight that the richness of Samsoniella species in karst eco-environments and further attention should be paid to entomopathogenic fungi in such habitats

Phylogenetic, ecological and morphological characteristics reveal two new spider-associated genera in Clavicipitaceae

Clavicipitaceous fungi are pathogenic to scale insects, white flies and other insect orders. However, a few species are spider-associated. Two new genera from China, Neoaraneomyces and Pseudometarhizium, are described based on phylogenetic, ecological and morphological characteristics. Two spider-associated species, Neoaraneomyces araneicola, Pseudometarhizium araneogenum, and an insect-associated species Pseudometarhizium lepidopterorum are included. The morphological characteristics of paecilomyces-like conidiogenous structures, present in many insect/spiders associated species make species-level identifications difficult. A phylogenetic analysis of the combined dataset (ITS, LSU, RPB2 and TEF), placed the two new genera in Clavicipitaceae. The new spider-associated species may be the result of convergent evolution to adapt to the ecological environment and may have undergone host jumping or altered their nutritional preferences

Phylogeny and taxonomy of two new Plectosphaerella (Plectosphaerellaceae, Glomerellales) species from China

Volume: 57Start Page: 47End Page: 6

Table_1_Multigene phylogeny, phylogenetic network, and morphological characterizations reveal four new arthropod-associated Simplicillium species and their evolutional relationship.docx

Simplicillium species are widely distributed and commonly found on various substrates. A minority of species are associated with arthropods. A spider-associated species Simplicillium araneae, and three insect-associated species, Simplicillium coleopterorum, Simplicillium guizhouense, and Simplicillium larvatum, are proposed as novel species based on a multi-locus phylogenetic analysis and morphological characteristics. These Simplicillium species completely fit the nutritional model of Hypocreales fungi and could be used as a model to study their evolutionary relationship. A phylogenetic network analysis based on ITS sequences suggests that a host jump was common among Simplicillium species, and S. araneae may have originally come from an insect host and then jumped to a spider host. However, the evolutionary relationship of S. coleopterorum, S. guizhouense, and S. larvatum was not clear in the phylogenetic network and more sequencing information should be added to the network. In addition, strain CBS 101267 was identified as Simplicillium subtropicum.</p