Recent Advances in Open Set Recognition: A Survey Geng, Chuanxing; Huang, Sheng-Jun; Chen, Songcan
IEEE transactions on pattern analysis and machine intelligence,
10/2021, Letnik:
43, Številka:
10
Journal Article
Recenzirano
Odprti dostop
In real-world recognition/classification tasks, limited by various objective factors, it is usually difficult to collect training samples to exhaust all classes when training a recognizer or ...classifier. A more realistic scenario is open set recognition (OSR), where incomplete knowledge of the world exists at training time, and unknown classes can be submitted to an algorithm during testing, requiring the classifiers to not only accurately classify the seen classes, but also effectively deal with unseen ones. This paper provides a comprehensive survey of existing open set recognition techniques covering various aspects ranging from related definitions, representations of models, datasets, evaluation criteria, and algorithm comparisons. Furthermore, we briefly analyze the relationships between OSR and its related tasks including zero-shot, one-shot (few-shot) recognition/learning techniques, classification with reject option, and so forth. Additionally, we also review the open world recognition which can be seen as a natural extension of OSR. Importantly, we highlight the limitations of existing approaches and point out some promising subsequent research directions in this field.
The HDOCK server (http://hdock.phys.hust.edu.cn/) is a highly integrated suite of homology search, template-based modeling, structure prediction, macromolecular docking, biological information ...incorporation and job management for robust and fast protein-protein docking. With input information for receptor and ligand molecules (either amino acid sequences or Protein Data Bank structures), the server automatically predicts their interaction through a hybrid algorithm of template-based and template-free docking. The HDOCK server distinguishes itself from similar docking servers in its ability to support amino acid sequences as input and a hybrid docking strategy in which experimental information about the protein-protein binding site and small-angle X-ray scattering can be incorporated during the docking and post-docking processes. Moreover, HDOCK also supports protein-RNA/DNA docking with an intrinsic scoring function. The server delivers both template- and docking-based binding models of two molecules and allows for download and interactive visualization. The HDOCK server is user friendly and has processed >30,000 docking jobs since its official release in 2017. The server can normally complete a docking job within 30 min.
Abstract
On 2022 July 13, NASA released to the whole world the data obtained by the James Webb Space Telescope (JWST) Early Release Observations (ERO). These are the first set of science-grade data ...from this long-awaited facility, marking the beginning of a new era in astronomy. In the study of the early universe, JWST will allow us to push far beyond
z
≈ 11, the redshift boundary previously imposed by the 1.7
μ
m red cutoff of the Hubble Space Telescope (HST). In contrast, JWST’s NIRCam reaches ∼5
μ
m. Among the JWST ERO targets there is a nearby galaxy cluster SMACS 0723-73, which is a massive cluster and has been long recognized as a potential “cosmic telescope” in amplifying background galaxies. The ERO six-band NIRCam observations on this target have covered an additional flanking field not boosted by gravitational lensing, which also sees far beyond HST. Here we report the result from our search of candidate objects at
z
> 11 using these ERO data. In total, there are 87 such objects identified by using the standard “dropout” technique. These objects are all detected in multiple bands and therefore cannot be spurious. For most of them, their multiband colors are inconsistent with known types of contaminants. If the detected dropout signature is interpreted as the expected Lyman break, it implies that these objects are at
z
≈ 11–20. The large number of such candidate objects at such high redshifts is not expected from the previously favored predictions and demands further investigations. JWST spectroscopy on such objects will be critical.
To evaluate the effects of post-acute care (PAC) on frail older adults after acute hospitalization in Taiwan.
This was a multicenter interventional study. Frail patients aged ≥ 75 were recruited and ...divided into PAC or control group. The PAC group received comprehensive geriatric assessment (CGA) and multifactorial intervention including exercise, nutrition education, and medicinal adjustments for two to four weeks, while the control group received only CGA. Outcome measures included emergency room (ER) visits, readmissions, and mortality within 90 days after PAC.
Among 254 participants, 205 (87.6±6.0 years) were in the PAC and 49 (85.2±6.0 years) in the control group. PAC for more than two weeks significantly decreased 90-day ER visits (odds ratio OR 0.21, 95% confidence interval CI 0.10-0.43; p = 0.024), readmissions (OR 0.30, 95% CI 0.16-0.56; p < 0.001), and mortality (OR 0.20, 95% CI 0.04-0.87; p = 0.032). Having problems in self-care was an independent risk factor for 90-day ER visits (OR 2.11, 95% CI 1.17-3.78; p = 0.012), and having problems in usual activities was an independent risk factor for 90-day readmissions (OR 2.69, 95% CI 1.53-4.72; p = 0.001) and mortality (OR 3.16, 95% CI 1.16-8.63; p = 0.024).
PAC program for more than two weeks could have beneficial effects on decreasing ER visits, readmissions, and mortality after an acute illness in frail older patients. Those who perceived severe problems in self-care and usual activities had a higher risk of subsequent adverse outcomes.
ClinicalTrials.gov NCT Identifier: NCT05452395.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
We consider symmetry-protected topological (SPT) phases with crystalline point group symmetry, dubbed point group SPT (pgSPT) phases. We show that such phases can be understood in terms of ...lower-dimensional topological phases with on-site symmetry and that they can be constructed as stacks and arrays of these lower-dimensional states. This provides the basis for a general framework to classify and characterize bosonic and fermionic pgSPT phases, which can be applied for arbitrary crystalline point group symmetry and in arbitrary spatial dimensions. We develop and illustrate this framework by means of a few examples, focusing on three-dimensional states. We classify bosonic pgSPT phases and fermionic topological crystalline superconductors with Z2P (reflection) symmetry, electronic topological crystalline insulators (TCIs) with U(1)×Z2P symmetry, and bosonic pgSPT phases with C2v symmetry, which is generated by two perpendicular mirror reflections. We also study surface properties, with a focus on gapped, topologically ordered surface states. For electronic TCIs, we find a Z8×Z2 classification, where the Z8 corresponds to known states obtained from noninteracting electrons, and the Z2 corresponds to a “strongly correlated” TCI that requires strong interactions in the bulk. Our approach may also point the way toward a general theory of symmetry-enriched topological phases with crystalline point group symmetry.
Protein-protein and protein-DNA/RNA interactions play a fundamental role in a variety of biological processes. Determining the complex structures of these interactions is valuable, in which molecular ...docking has played an important role. To automatically make use of the binding information from the PDB in docking, here we have presented HDOCK, a novel web server of our hybrid docking algorithm of template-based modeling and free docking, in which cases with misleading templates can be rescued by the free docking protocol. The server supports protein-protein and protein-DNA/RNA docking and accepts both sequence and structure inputs for proteins. The docking process is fast and consumes about 10-20 min for a docking run. Tested on the cases with weakly homologous complexes of <30% sequence identity from five docking benchmarks, the HDOCK pipeline tied with template-based modeling on the protein-protein and protein-DNA benchmarks and performed better than template-based modeling on the three protein-RNA benchmarks when the top 10 predictions were considered. The performance of HDOCK became better when more predictions were considered. Combining the results of HDOCK and template-based modeling by ranking first of the template-based model further improved the predictive power of the server. The HDOCK web server is available at http://hdock.phys.hust.edu.cn/.
•Search strategies of current protein–protein docking algorithms were reviewed.•Challenges and future directions of established approaches were discussed.•Post-docking approaches have been ...increasingly used in reranking docking solutions.•Evaluations depend on docking benchmarks, criteria and an objective platform.•The web server is one of the future trends for automatic protein–protein docking.
Protein–protein docking is attracting increasing attention in drug discovery research targeting protein–protein interactions, owing to its potential in predicting protein–protein interactions and identifying ‘hot spot’ residues at the protein–protein interface. Given the relative lack of information about binding sites and the fact that proteins are generally larger than ligand, the search algorithms and evaluation methods for protein–protein docking differ somewhat from those for protein–ligand docking and, hence, require different research strategies. Here, we review the basic concepts, principles and advances of current search strategies and evaluation methods for protein–protein docking. We also discuss the current challenges and limitations, as well as future directions, of established approaches.
This review discusses current search strategies and evaluation methods for investigating protein–protein docking, two important issues that are quite different from those of protein–ligand docking.
The outbreak of a novel coronavirus, which was later formally named the severe acute respiratory coronavirus 2 (SARS-CoV-2), has caused a worldwide public health crisis. Previous studies showed that ...SARS-CoV-2 is highly homologous to SARS-CoV and infects humans through the binding of the spike protein to ACE2. Here, we have systematically studied the molecular mechanisms of human infection with SARS-CoV-2 and SARS-CoV by protein-protein docking and MD simulations. It was found that SARS-CoV-2 binds ACE2 with a higher affinity than SARS-CoV, which may partly explain that SARS-CoV-2 is much more infectious than SARS-CoV. In addition, the spike protein of SARS-CoV-2 has a significantly lower free energy than that of SARS-CoV, suggesting that SARS-CoV-2 is more stable and may survive a higher temperature than SARS-CoV. This provides insights into the evolution of SARS-CoV-2 because SARS-like coronaviruses have originated in bats. Our computation also suggested that the RBD-ACE2 binding for SARS-CoV-2 is much more temperature-sensitive than that for SARS-CoV. Thus, it is expected that SARS-CoV-2 would decrease its infection ability much faster than SARS-CoV when the temperature rises. These findings would be beneficial for the disease prevention and drug/vaccine development of SARS-CoV-2.
Palladium diselenide (PdSe2), a thus far scarcely studied group‐10 transition metal dichalcogenide has exhibited promising potential in future optoelectronic and electronic devices due to unique ...structures and electrical properties. Here, the controllable synthesis of wafer‐scale and homogeneous 2D PdSe2 film is reported by a simple selenization approach. By choosing different thickness of precursor Pd layer, 2D PdSe2 with thickness of 1.2–20 nm can be readily synthesized. Interestingly, with the increase in thickness, obvious redshift in wavenumber is revealed by Raman spectroscopy. Moreover, in accordance with density functional theory (DFT) calculation, optical absorption and ultraviolet photoemission spectroscopy (UPS) analyses confirm that the PdSe2 exhibits an evolution from a semiconductor (monolayer) to semimetal (bulk). Further combination of the PdSe2 layer with Si leads to a highly sensitive, fast, and broadband photodetector with a high responsivity (300.2 mA W−1) and specific detectivity (≈1013 Jones). By decorating the device with black phosphorus quantum dots, the device performance can be further optimized. These results suggest the as‐selenized PdSe2 is a promising material for optoelectronic application.
This study reports on the wafer‐area synthesis of a high‐quality 2D palladium diselenide (PdSe2) layer through a simple selenization method. Both experimental analysis and theoretical simulation reveal that the PdSe2 film exhibits a gradual transition from a semiconductor (monolayer) to semimetal (bulk). Further combination of PdSe2 with Si leads to a fast and sensitive broadband photodiode, with a high responsivity and specific detectivity.
Group‐10 layered transitional metal dichalcogenides including PtS2, PtSe2, and PtTe2 are excellent potential candidates for optoelectronic devices due to their unique properties such as high carrier ...mobility, tunable bandgap, stability, and flexibility. Large‐area platinum diselenide (PtSe2) with semiconducting characteristics is far scarcely investigated. Here, the development of a high‐performance photodetector based on vertically aligned PtSe2‐GaAs heterojunction which exhibits a broadband sensitivity from deep ultraviolet to near‐infrared light, with peak sensitivity from 650 to 810 nm, is reported. The Ilight/Idark ratio and responsivity of photodetector are 3 × 104 and 262 mA W−1 measured at 808 nm under zero bias voltage. The response speed of τr/τf is 5.5/6.5 µs, which represents the best result achieved for Group‐10 TMDs based optoelectronic device thus far. According to first‐principle density functional theory, the broad photoresponse ranging from visible to near‐infrared region is associated with the semiconducting characteristics of PtSe2 which has interstitial Se atoms within the PtSe2 layers. It is also revealed that the PtSe2/GaAs photodetector does not exhibit performance degradation after six weeks in air. The generality of the above good results suggests that the vertically aligned PtSe2 is an ideal material for high‐performance optoelectronic systems in the future.
This work shows the large‐area growth of high‐quality vertically aligned PtSe2, and its application to photodetectors based on PtSe2‐GaAs heterojunctions which exhibit a broadband sensitivity to illumination ranging from deep ultraviolet to near‐infrared light, with a peak sensitivity in the region from 650 to 810 nm. The high‐performance broadband photodetector will develop the next‐generation 2D Group‐10 materials based optoelectronic devices.
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