scholarly journals Embedding Symbolic Temporal Knowledge into Deep Sequential Models

Author(s):  
Yaqi Xie ◽  
Fan Zhou ◽  
Harold Soh
Keyword(s):  
IEEE Access ◽  
2021 ◽  
pp. 1-1
Author(s):  
Abdul Wahab ◽  
Muhammad Anas Tahir ◽  
Naveed Iqbal ◽  
Adnan Ul-Hasan ◽  
Faisal Shafiat ◽  
...  

2019 ◽  
pp. 415-446
Author(s):  
Hisham El-Amir ◽  
Mahmoud Hamdy
Keyword(s):  

2004 ◽  
Author(s):  
Mikkel B. Stegmann ◽  
Rhodri H. Davies ◽  
Charlotte Ryberg

2021 ◽  
Vol 3 (4) ◽  
pp. 922-945
Author(s):  
Shaw-Hwa Lo ◽  
Yiqiao Yin

Text classification is a fundamental language task in Natural Language Processing. A variety of sequential models are capable of making good predictions, yet there is a lack of connection between language semantics and prediction results. This paper proposes a novel influence score (I-score), a greedy search algorithm, called Backward Dropping Algorithm (BDA), and a novel feature engineering technique called the “dagger technique”. First, the paper proposes to use the novel influence score (I-score) to detect and search for the important language semantics in text documents that are useful for making good predictions in text classification tasks. Next, a greedy search algorithm, called the Backward Dropping Algorithm, is proposed to handle long-term dependencies in the dataset. Moreover, the paper proposes a novel engineering technique called the “dagger technique” that fully preserves the relationship between the explanatory variable and the response variable. The proposed techniques can be further generalized into any feed-forward Artificial Neural Networks (ANNs) and Convolutional Neural Networks (CNNs), and any neural network. A real-world application on the Internet Movie Database (IMDB) is used and the proposed methods are applied to improve prediction performance with an 81% error reduction compared to other popular peers if I-score and “dagger technique” are not implemented.


eLife ◽  
2020 ◽  
Vol 9 ◽  
Author(s):  
Xue Fei ◽  
Tristan A Bell ◽  
Simon Jenni ◽  
Benjamin M Stinson ◽  
Tania A Baker ◽  
...  

ClpXP is an ATP-dependent protease in which the ClpX AAA+ motor binds, unfolds, and translocates specific protein substrates into the degradation chamber of ClpP. We present cryo-EM studies of the E. coli enzyme that show how asymmetric hexameric rings of ClpX bind symmetric heptameric rings of ClpP and interact with protein substrates. Subunits in the ClpX hexamer assume a spiral conformation and interact with two-residue segments of substrate in the axial channel, as observed for other AAA+ proteases and protein-remodeling machines. Strictly sequential models of ATP hydrolysis and a power stroke that moves two residues of the substrate per translocation step have been inferred from these structural features for other AAA+ unfoldases, but biochemical and single-molecule biophysical studies indicate that ClpXP operates by a probabilistic mechanism in which five to eight residues are translocated for each ATP hydrolyzed. We propose structure-based models that could account for the functional results.


2020 ◽  
Vol 117 (41) ◽  
pp. 25455-25463 ◽  
Author(s):  
Kristin L. Zuromski ◽  
Robert T. Sauer ◽  
Tania A. Baker

ClpA is a hexameric double-ring AAA+ unfoldase/translocase that functions with the ClpP peptidase to degrade proteins that are damaged or unneeded. How the 12 ATPase active sites of ClpA, 6 in the D1 ring and 6 in the D2 ring, work together to fuel ATP-dependent degradation is not understood. We use site-specific cross-linking to engineer ClpA hexamers with alternating ATPase-active and ATPase-inactive modules in the D1 ring, the D2 ring, or both rings to determine if these active sites function together. Our results demonstrate that D2 modules coordinate with D1 modules and ClpP during mechanical work. However, there is no requirement for adjacent modules in either ring to be active for efficient enzyme function. Notably, ClpAP variants with just three alternating active D2 modules are robust protein translocases and function with double the energetic efficiency of ClpAP variants with completely active D2 rings. Although D2 is the more powerful motor, three or six active D1 modules are important for high enzyme processivity, which depends on D1 and D2 acting coordinately. These results challenge sequential models of ATP hydrolysis and coupled mechanical work by ClpAP and provide an engineering strategy that will be useful in testing other aspects of ClpAP mechanism.


Author(s):  
Jean-Pierre Florens ◽  
Velayoudom Marimoutou ◽  
Anne Peguin-Feissolle ◽  
Josef Perktold ◽  
Marine Carrasco
Keyword(s):  

2019 ◽  
Vol 26 (12) ◽  
pp. 1493-1504 ◽  
Author(s):  
Jihyun Park ◽  
Dimitrios Kotzias ◽  
Patty Kuo ◽  
Robert L Logan IV ◽  
Kritzia Merced ◽  
...  

Abstract Objective Amid electronic health records, laboratory tests, and other technology, office-based patient and provider communication is still the heart of primary medical care. Patients typically present multiple complaints, requiring physicians to decide how to balance competing demands. How this time is allocated has implications for patient satisfaction, payments, and quality of care. We investigate the effectiveness of machine learning methods for automated annotation of medical topics in patient-provider dialog transcripts. Materials and Methods We used dialog transcripts from 279 primary care visits to predict talk-turn topic labels. Different machine learning models were trained to operate on single or multiple local talk-turns (logistic classifiers, support vector machines, gated recurrent units) as well as sequential models that integrate information across talk-turn sequences (conditional random fields, hidden Markov models, and hierarchical gated recurrent units). Results Evaluation was performed using cross-validation to measure 1) classification accuracy for talk-turns and 2) precision, recall, and F1 scores at the visit level. Experimental results showed that sequential models had higher classification accuracy at the talk-turn level and higher precision at the visit level. Independent models had higher recall scores at the visit level compared with sequential models. Conclusions Incorporating sequential information across talk-turns improves the accuracy of topic prediction in patient-provider dialog by smoothing out noisy information from talk-turns. Although the results are promising, more advanced prediction techniques and larger labeled datasets will likely be required to achieve prediction performance appropriate for real-world clinical applications.


1997 ◽  
Vol 14 ◽  
pp. 109-122
Author(s):  
Els van der Kooij

Abstract In early, simultaneous analyses of signs, [a_contact] is a multivalent feature pertaining to the movement parameter (cf. Friedman 1976). In models that make use of sequential units (Liddell and Johnson 1989, Sandler 1989, Perlmutter 1989, van der Hulst 1993) the valence of [contact] can be reduced to one. In comparing two types of sequential models I will show that one of them - the No-Movement model -is more adequate in accounting for the contact types proposed in Friedman (1976). By examining the consequences of the representation of the contact types in the No-Movement model of van der Hulst (1993) and further developments thereof (Crasborn 1995,1996; van der Hulst 1995, 1996; van der Kooij 1994, 1996; van der Kooij and Crasborn 1996). I will show that contact is a redundant property, predictable from the place specification of the sign. Being phonologically redundant, variation and non-distinctiveness of contact is correctly predicted.


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