Conformal Prediction for Deep Classifier via Label Ranking

Conformal prediction is a statistical framework that generates prediction sets containing ground-truth labels with a desired coverage guarantee. The predicted probabilities produced by machine learning models are generally miscalibrated, leading to large prediction sets in conformal prediction. In this paper, we empirically and theoretically show that disregarding the probabilities' value will mitigate the undesirable effect of miscalibrated probability values. Then, we propose a novel algorithm named $\textit{Sorted Adaptive prediction sets}$ (SAPS), which discards all the probability values except for the maximum softmax probability. The key idea behind SAPS is to minimize the dependence of the non-conformity score on the probability values while retaining the uncertainty information. In this manner, SAPS can produce sets of small size and communicate instance-wise uncertainty. Theoretically, we provide a finite-sample coverage guarantee of SAPS and show that the expected value of set size from SAPS is always smaller than APS. Extensive experiments validate that SAPS not only lessens the prediction sets but also broadly enhances the conditional coverage rate and adaptation of prediction sets

Modeling impacts of carbon sequestration on net greenhouse gas emissions from agricultural soils in China

Soil organic carbon (SOC) contents in many farmlands have been depleted because of the long-term history of intensive cultivation in China. Chinese farmers are encouraged to adopt alternative management practices on their farms to sequester SOC. On the basis of the availability of carbon (C) resources in the rural areas in China, the most promising practices are (1) incorporating more crop residue in the soils and (2) resuming traditional manure fertilizer. By implementing the alternative practices, increase in SOC content has been observed in some fields. This paper investigates how the C sequestration strategies could affect nitrous oxide (N2O) and methane (CH4) emissions from the agricultural soils in six selected sites across China. A process-based model, denitrification-decomposition or DNDC, which has been widely validated against data sets of SOC dynamics and N2O and CH4 fluxes observed in China, was adopted in the study to quantify the greenhouse gas impacts of enhanced crop residue incorporation and manure amendment under the diverse climate, soil, and crop rotation conditions across the six agroecosystems. Model results indicated that (1) when the alternative management practices were employed C sequestration rates increased, however, N2O or CH4 emissions were also increased for these practices; and (2) reducing the application rates of synthetic fertilizer in conjunction with the alternative practices could decrease N2O emissions while at the same time maintaining existing crop yields and C sequestration rates. The modeling approach could help with development of spatially differentiated best management practices at large regional scales

Aroma precursors of cigars from different tobacco parts and origins, and their correlations with sensory characteristics

Cigars are developing rapidly around the world, but the content characteristics of aroma precursors and their contribution to sensory perception have not been fully elucidated. In this study, 69 aroma precursors from 61 tobaccos of different parts and origins were systematically determined, and the sensory characteristics of middle leaves from different origins and their correlation with aroma precursors were evaluated. The results showed that tobacco parts mainly affected amino acid content, and contents of nicotine, oxalic acid, malic acid, isovaleric acid, cystine, glutarnine, glycine, isoleucine, glutamicacid, asparticacid, and fructose-proline were significantly changed. Tobacco origins mainly influenced the contents of amino acids, polyacids and high fatty acids, and sugar alcohols, and significantly affected the contents of myosmine, anabasine, nonanoic acid, propanetriol, mannitol, mannose, glucose, alanine, arginine, glutarnine, glutamicacid, histidine, serine, threonine, tryptophan, fructose-alanine, and fructose-asparagine. The flavor characteristics were prominent by wood aroma, and the style and quality characteristics varied greatly among different origins of middle leaves. There were 34, 21, and 22 aroma precursors with high correlations with flavor, style, and quality characteristics. This study provides support for regulating the content and coordination of aroma precursors in different tobacco parts and origins to improve sensory characteristics

Agents: An Open-source Framework for Autonomous Language Agents

Recent advances on large language models (LLMs) enable researchers and developers to build autonomous language agents that can automatically solve various tasks and interact with environments, humans, and other agents using natural language interfaces. We consider language agents as a promising direction towards artificial general intelligence and release Agents, an open-source library with the goal of opening up these advances to a wider non-specialist audience. Agents is carefully engineered to support important features including planning, memory, tool usage, multi-agent communication, and fine-grained symbolic control. Agents is user-friendly as it enables non-specialists to build, customize, test, tune, and deploy state-of-the-art autonomous language agents without much coding. The library is also research-friendly as its modularized design makes it easily extensible for researchers. Agents is available at https://github.com/aiwaves-cn/agents.Comment: Code available at https://github.com/aiwaves-cn/agent

Reply to: Mobility overestimation in MoS2_2 transistors due to invasive voltage probes

In this reply, we include new experimental results and verify that the observed non-linearity in rippled-MoS$_2$ (leading to mobility kink) is an intrinsic property of a disordered system, rather than contact effects (invasive probes) or other device issues. Noting that Peng Wu's hypothesis is based on a highly ordered ideal system, transfer curves are expected to be linear, and the carrier density is assumed be constant. Wu's model is therefore oversimplified for disordered systems and neglects carrier-density dependent scattering physics. Thus, it is fundamentally incompatible with our rippled-MoS$_2$, and leads to the wrong conclusion

Understanding and exploring the diversity of soil microorganisms in tea (Camellia sinensis) gardens: toward sustainable tea production

Leaves of Camellia sinensis plants are used to produce tea, one of the most consumed beverages worldwide, containing a wide variety of bioactive compounds that help to promote human health. Tea cultivation is economically important, and its sustainable production can have significant consequences in providing agricultural opportunities and lowering extreme poverty. Soil parameters are well known to affect the quality of the resultant leaves and consequently, the understanding of the diversity and functions of soil microorganisms in tea gardens will provide insight to harnessing soil microbial communities to improve tea yield and quality. Current analyses indicate that tea garden soils possess a rich composition of diverse microorganisms (bacteria and fungi) of which the bacterial Proteobacteria, Actinobacteria, Acidobacteria, Firmicutes and Chloroflexi and fungal Ascomycota, Basidiomycota, Glomeromycota are the prominent groups. When optimized, these microbes’ function in keeping garden soil ecosystems balanced by acting on nutrient cycling processes, biofertilizers, biocontrol of pests and pathogens, and bioremediation of persistent organic chemicals. Here, we summarize research on the activities of (tea garden) soil microorganisms as biofertilizers, biological control agents and as bioremediators to improve soil health and consequently, tea yield and quality, focusing mainly on bacterial and fungal members. Recent advances in molecular techniques that characterize the diverse microorganisms in tea gardens are examined. In terms of viruses there is a paucity of information regarding any beneficial functions of soil viruses in tea gardens, although in some instances insect pathogenic viruses have been used to control tea pests. The potential of soil microorganisms is reported here, as well as recent techniques used to study microbial diversity and their genetic manipulation, aimed at improving the yield and quality of tea plants for sustainable production

A multicentre single arm phase 2 trial of neoadjuvant pyrotinib and letrozole plus dalpiciclib for triple-positive breast cancer.

peer reviewedCurrent therapies for HER2-positive breast cancer have limited efficacy in patients with triple-positive breast cancer (TPBC). We conduct a multi-center single-arm phase 2 trial to test the efficacy and safety of an oral neoadjuvant therapy with pyrotinib, letrozole and dalpiciclib (a CDK4/6 inhibitor) in patients with treatment-naïve, stage II-III TPBC with a Karnofsky score of ≥70 (NCT04486911). The primary endpoint is the proportion of patients with pathological complete response (pCR) in the breast and axilla. The secondary endpoints include residual cancer burden (RCB)-0 or RCB-I, objective response rate (ORR), breast pCR (bpCR), safety and changes in molecular targets (Ki67) from baseline to surgery. Following 5 cycles of 4-week treatment, the results meet the primary endpoint with a pCR rate of 30.4% (24 of 79; 95% confidence interval (CI), 21.3-41.3). RCB-0/I is 55.7% (95% CI, 44.7-66.1). ORR is 87.4%, (95% CI, 78.1-93.2) and bpCR is 35.4% (95% CI, 25.8-46.5). The mean Ki67 expression reduces from 40.4% at baseline to 17.9% (P < 0.001) at time of surgery. The most frequent grade 3 or 4 adverse events are neutropenia, leukopenia, and diarrhoea. There is no serious adverse event- or treatment-related death. This fully oral, chemotherapy-free, triplet combined therapy has the potential to be an alternative neoadjuvant regimen for patients with TPBC

Retracted article : nanoporous PtFe surface alloy architecture for enhanced methanol electro-oxidation

By selectively dealloying PtFeAl ternary alloy in 0.5 M NaOH solution, a novel nanoporous PtFe (npPtFe) alloy with nanorod-like morphology and inherent three-dimensional bicontinuous ligament-pore structure was successfully fabricated. X-Ray diffraction and electron microscope characterization demonstrated the crystal nature of the alloy ligament with ligament size down to 3 nm. NaOH concentration plays a key role in the formation of a uniform PtFe alloy structure. Dealloying solution with a low NaOH concentration (0.5 M) is suitable for the formation of a pure PtFe alloy structure, while Fe3 O4/np-PtFe nanocomposite is obtained when using a high NaOH concentration ($2 M). The np-PtFe alloy can be facilely converted into a nanoporous near-surface alloy structure with a Pt-rich surface and PtFe alloy core by a second dealloying process in dilute HNO3 solution. Electrochemical measurements show that the nanoporous near-surface alloy has greatly enhanced catalytic activity and durability towards methanol electro-oxidation compared with the state-of-the-art Pt/C catalyst. The peak current density of methanol electro-oxidation on the nanoporous surface alloy is about five times that on Pt/C. More importantly, continuous potential cycling from 0.6 to 0.9 V (vs. RHE) in 0.5 M H2 SO4 aqueous solution demonstrates that the np-PtFe surface alloy has a better structural stability than commercial Pt/C. With evident advantages of facile preparation and enhanced electrocatalytic activity and durability, the np-PtFe surface alloy holds great potential as an anode catalyst in direct methanol fuel cells