Re-Benchmarking Pool-Based Active Learning for Binary Classification

Active learning is a paradigm that significantly enhances the performance of machine learning models when acquiring labeled data is expensive. While several benchmarks exist for evaluating active learning strategies, their findings exhibit some misalignment. This discrepancy motivates us to develop a transparent and reproducible benchmark for the community. Our efforts result in an open-sourced implementation (https://github.com/ariapoy/active-learning-benchmark) that is reliable and extensible for future research. By conducting thorough re-benchmarking experiments, we have not only rectified misconfigurations in existing benchmark but also shed light on the under-explored issue of model compatibility, which directly causes the observed discrepancy. Resolving the discrepancy reassures that the uncertainty sampling strategy of active learning remains an effective and preferred choice for most datasets. Our experience highlights the importance of dedicating research efforts towards re-benchmarking existing benchmarks to produce more credible results and gain deeper insights

BioRED: A Comprehensive Biomedical Relation Extraction Dataset

Automated relation extraction (RE) from biomedical literature is critical for many downstream text mining applications in both research and real-world settings. However, most existing benchmarking datasets for bio-medical RE only focus on relations of a single type (e.g., protein-protein interactions) at the sentence level, greatly limiting the development of RE systems in biomedicine. In this work, we first review commonly used named entity recognition (NER) and RE datasets. Then we present BioRED, a first-of-its-kind biomedical RE corpus with multiple entity types (e.g., gene/protein, disease, chemical) and relation pairs (e.g., gene-disease; chemical-chemical), on a set of 600 PubMed articles. Further, we label each relation as describing either a novel finding or previously known background knowledge, enabling automated algorithms to differentiate between novel and background information. We assess the utility of BioRED by benchmarking several existing state-of-the-art methods, including BERT-based models, on the NER and RE tasks. Our results show that while existing approaches can reach high performance on the NER task (F-score of 89.3%), there is much room for improvement for the RE task, especially when extracting novel relations (F-score of 47.7%). Our experiments also demonstrate that such a comprehensive dataset can successfully facilitate the development of more accurate, efficient, and robust RE systems for biomedicine

Comparative efficacy of Chinese herbal medicines for dialysis patients with uremic pruritus: A systematic review and network meta-analysis

Introduction: Uremic pruritus is common in dialysis patients and reduces their quality of life. Chinese herbal medicine has been effective in patients with this condition.Methods: We conducted a random-effects network meta-analysis to compare the efficacies of different Chinese herbal medicine treatments for uremic pruritus. Outcome measures including the overall effective rates, visual analog scale scores, C-reactive protein levels, and adverse drug reactions were analyzed.Results: The network meta-analysis retrieved 25 randomized controlled trials. Compared with conventional treatments alone, combination treatments with Xiao-Yang-Ke-Li was the most effective intervention in decreasing visual analog scale scores (mean difference −2.98, 95% mean difference −5.05 to −0.91) and levels of C-reactive protein (mean difference −5.01, 95% mean difference −7.27 to −2.75). Conventional treatment combined with Si-Wu Tang was superior to other therapeutic combinations when overall effective rates were determined. The best visual analog scale scores and overall effective rates were achieved by adjunctive treatment with the Touxie-Jiedu-Zhiyang decoction followed by uremic clearance granules; these treatments were the most beneficial for uremic pruritis.Conclusion: Our network meta-analysis provided the relative efficacies of different adjunctive Chinese herbal formulas. Adjunctive treatment with the Touxie-Jiedu-Zhiyang decoction was the best treatment for improving overall effective rates and reducing visual analog scores of uremic pruritus in dialysis patients.Systematic Review Registration:https://www.crd.york.ac.uk/prospero/display_record.php?RecordID=357656; Identifier: CRD42022357656

Shared Representational Geometry Across Neural Networks

Different neural networks trained on the same dataset often learn similar input-output mappings with very different weights. Is there some correspondence between these neural network solutions? For linear networks, it has been shown that different instances of the same network architecture encode the same representational similarity matrix, and their neural activity patterns are connected by orthogonal transformations. However, it is unclear if this holds for non-linear networks. Using a shared response model, we show that different neural networks encode the same input examples as different orthogonal transformations of an underlying shared representation. We test this claim using both standard convolutional neural networks and residual networks on CIFAR10 and CIFAR100.Comment: Integration of Deep Learning Theories workshop, NeurIPS 201

Microstructure and superelastic properties of FeNiCoAlTi single crystals with the <100> orientation under tension

The microstructure and superelastic response of an Fe41 Ni28 Co17 Al11.5 Ti2.5 (at.%) single crystal along the [removed] orientation was investigated under tension at room temperature after aging at 600◦ C for 24 h. From the superelastic results, the samples aged at 600◦ C for 24 h exhibited 4.5% recoverable strain at room temperature. The digital image correlation (DIC) method was used to observe the strain distribution during the 6.5% applied strain loading. The DIC results showed that the strain was uniformly distributed during the loading and unloading cycles. Only one martensite variant was observed from the DIC results. This was related to the aging heat treatment times. The martensite morphology became a single variant with a longer aging time. The thermo-magnetization results indicated that the phase transformation and temperature hysteresis was around 36◦ C. Increasing the magnetic field from 0.05 to 7 Tesla, the transformation temperatures increased. The maximum magnetization was 160 emu/g under the magnetic field of 7 Tesla. From the transmission electron microscopy results, the L12 precipitates were around 10 nm in size, and they were high in Ni content and low in Fe content

Neoadjuvant Carboplatin/Paclitaxel versus 5-Fluorouracil/Cisplatin in Combination with Radiotherapy for Locally Advanced Esophageal Squamous Cell Carcinoma:A Multicenter Comparative Study

SIMPLE SUMMARY: The most beneficial neoadjuvant chemoradiotherapy for Asian patients with esophageal squamous cell carcinoma remains uncertain. Using propensity score matching by inverse probability of treatment weighting to balance the baseline variables, the neoadjuvant carboplatin/paclitaxel (CROSS) regimen versus the cisplatin/5-fluorouracil (PF) regimen in combination with 41.4–50.4 Gy of radiotherapy were compared. We found that Taiwanese patients treated with the CROSS regimen (Carboplatin + Paclitaxel + 41.4–45.0 Gy) had less treatment-related complications and more favorable survival figures. Collectively, these results suggest that CROSS is safe and effective. ABSTRACT: Background: The most beneficial neoadjuvant chemoradiotherapy (nCRT) combination for esophageal squamous cell carcinoma (ESCC) in Asia remains uncertain. Herein, we compared the neoadjuvant carboplatin/paclitaxel (CROSS) regimen versus the cisplatin/5-fluorouracil (PF) regimen in combination with 41.4–50.4 Gy of radiotherapy. Methods: Patients were stratified according to their nCRT regimen: CROSS + 41.4–45.0 Gy (CROSS), PF + 45.0 Gy (PF4500) or PF + 50.4 Gy (PF5040). Propensity score matching by inverse probability of treatment weighting (IPTW) was used to balance the baseline variables. Results: Before IPTW, a total of 334 patients were included. The lowest chemotherapy completion rate was observed in the PF5040 group (76.2% versus 89.4% and 92.0% in the remaining two groups, respectively). Compared with CROSS, both PF groups showed more severe weight loss during nCRT and a higher frequency of post-esophagectomy anastomotic leaks. The use of PF5040 was associated with the highest rate of pathological complete response (45.3%). While CROSS conferred a significant overall survival benefit over PF4500 (hazard ratio [HR] = 1.30, 95% CI = 1.05 to 1.62, p = 0.018), similar survival figures were observed when compared with PF5040 (HR = 1.17, 95% CI = 0.94 to 1.45, p = 0.166). Conclusions: The CROSS regimen conferred a significant survival benefit over PF4500, although the similar survival figures were similar to those observed with PF5040. Considering the lower incidences of severe weight loss and post-esophagectomy anastomotic leaks, CROSS represents a safe and effective neoadjuvant treatment for Taiwanese patients with ESCC

Structural and cognitive deficits in chronic carbon monoxide intoxication: a voxel-based morphometry study

BACKGROUND: Patients with carbon monoxide (CO) intoxication may develop ongoing neurological and psychiatric symptoms that ebb and flow, a condition often called delayed encephalopathy (DE). The association between morphologic changes in the brain and neuropsychological deficits in DE is poorly understood. METHODS: Magnetic resonance imaging and neuropsychological tests were conducted on 11 CO patients with DE, 11 patients without DE, and 15 age-, sex-, and education-matched healthy subjects. Differences in gray matter volume (GMV) between the subgroups were assessed and further correlated with diminished cognitive functioning. RESULTS: As a group, the patients had lower regional GMV compared to controls in the following regions: basal ganglia, left claustrum, right amygdala, left hippocampus, parietal lobes, and left frontal lobe. The reduced GMV in the bilateral basal ganglia, left post-central gyrus, and left hippocampus correlated with decreased perceptual organization and processing speed function. Those CO patients characterized by DE patients had a lower GMV in the left anterior cingulate and right amygdala, as well as lower levels of cognitive function, than the non-DE patients. CONCLUSIONS: Patients with CO intoxication in the chronic stage showed a worse cognitive and morphologic outcome, especially those with DE. This study provides additional evidence of gray matter structural abnormalities in the pathophysiology of DE in chronic CO intoxicated patients

Realization of Polarization Control in High-Order Harmonic Generation

The nature of high-order harmonic generation process limits the harmonics emission to linear polarization. In this paper, we review the recent progress to generate elliptically or circularly polarized high-harmonic EUV pulses. We further demonstrate how complete control of polarization state of isolated high-harmonic pulse can be realized today by noncollinear focusing of two driving pulses with identical ellipticity but counter-rotating helicity. This paper opens a path towards the study of the fastest dynamics--down to attosecond time scales--in circular dichroism of magnetic materials, chiral molecules, and electronic spin motion.Taiwan Ministry of Science and Technology; Academia Sinica; Junta de Castilla y León; Ministerio de Economía y Competitividad; Leonardo Grant for Researchers and Cultural Creators, BBVA Foundation; Ministerio de Ciencia, Innovación y Universidades for a Ramón y Cajal; European Social Fund; Ministerio de Educación, Cultura y Deporte

The Implementation of NEMS GFS Aerosol Component (NGAC) Version 1.0 for Global Dust Forecasting at NOAA NCEP

The NOAA National Centers for Environmental Prediction (NCEP) implemented the NOAA Environmental Modeling System (NEMS) Global Forecast System (GFS) Aerosol Component (NGAC) for global dust forecasting in collaboration with NASA Goddard Space Flight Center (GSFC). NGAC Version 1.0 has been providing 5-day dust forecasts at 1deg x 1deg resolution on a global scale, once per day at 00:00 Coordinated Universal Time (UTC), since September 2012. This is the first global system capable of interactive atmosphere aerosol forecasting at NCEP. The implementation of NGAC V1.0 reflects an effective and efficient transitioning of NASA research advances to NCEP operations, paving the way for NCEP to provide global aerosol products serving a wide range of stakeholders, as well as to allow the effects of aerosols on weather forecasts and climate prediction to be considered

Memory Impairment and Plasma BDNF Correlates of the BDNF Val66Met Polymorphism in Patients With Bipolar II Disorder

Studies suggest that a functional polymorphism of brain-derived neurotrophic factor (BDNF), polymorphism BDNF Val66Met affects cognitive functions, however, the effect is unclear in bipolar II (BD-II) disorder. We used the Wechsler Memory Scale-third edition (WMS-III), the presence of the BDNF Val66Met polymorphism, and plasma concentrations of BDNF to investigate the association between memory impairment and BDNF in BD-II disorder. We assessed the memory functions of 228 BD-II patients and 135 healthy controls (HCs). BD-II patients had significantly lower scores on five of the eight WMS-III subscales. In addition to education, the BDNF polymorphism were associated with the following subscales of WMS-III, auditory delayed memory, auditory delayed recognition memory and general memory scores in BD-II patients, but not in HC. Moreover, BD-II patients with the Val-homozygote scored significantly higher on the visual immediate memory subscale than did those with the Met/Met and Val/Met polymorphisms. The significantly positive effect of the Val-homozygote did not have a significantly positive effect on memory in the HC group, however. We found no significant association between BDNF polymorphisms and plasma concentrations of BDNF. The plasma BDNF was more likely to be associated with clinical characteristics than it was with memory indices in the BD-II group. The impaired memory function in BD-II patients might be dependent upon the association between the BDNF Val66Met polymorphism and peripheral BDNF levels