Did You Read the Instructions? Rethinking the Effectiveness of Task Definitions in Instruction Learning

Large language models (LLMs) have shown impressive performance in following natural language instructions to solve unseen tasks. However, it remains unclear whether models truly understand task definitions and whether the human-written definitions are optimal. In this paper, we systematically study the role of task definitions in instruction learning. We first conduct an ablation analysis informed by human annotations to understand which parts of a task definition are most important, and find that model performance only drops substantially when removing contents describing the task output, in particular label information. Next, we propose an automatic algorithm to compress task definitions to a minimal supporting set of tokens, and find that 60\% of tokens can be removed while maintaining or even improving model performance. Based on these results, we propose two strategies to help models better leverage task instructions: (1) providing only key information for tasks in a common structured format, and (2) adding a meta-tuning stage to help the model better understand the definitions. With these two strategies, we achieve a 4.2 Rouge-L improvement over 119 unseen test tasks.Comment: ACL 2023, camera-ready; 10 page

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Genome-wide association study of lung adenocarcinoma in East Asia and comparison with a European population

Lung adenocarcinoma is the most common type of lung cancer. Known risk variants explain only a small fraction of lung adenocarcinoma heritability. Here, we conducted a two-stage genome-wide association study of lung adenocarcinoma of East Asian ancestry (21,658 cases and 150,676 controls; 54.5% never-smokers) and identified 12 novel susceptibility variants, bringing the total number to 28 at 25 independent loci. Transcriptome-wide association analyses together with colocalization studies using a Taiwanese lung expression quantitative trait loci dataset (n = 115) identified novel candidate genes, including FADS1 at 11q12 and ELF5 at 11p13. In a multi-ancestry meta-analysis of East Asian and European studies, four loci were identified at 2p11, 4q32, 16q23, and 18q12. At the same time, most of our findings in East Asian populations showed no evidence of association in European populations. In our studies drawn from East Asian populations, a polygenic risk score based on the 25 loci had a stronger association in never-smokers vs. individuals with a history of smoking (P interaction  = 0.0058). These findings provide new insights into the etiology of lung adenocarcinoma in individuals from East Asian populations, which could be important in developing translational applications

Genome-wide association study of lung adenocarcinoma in East Asia and comparison with a European population.

Lung adenocarcinoma is the most common type of lung cancer. Known risk variants explain only a small fraction of lung adenocarcinoma heritability. Here, we conducted a two-stage genome-wide association study of lung adenocarcinoma of East Asian ancestry (21,658 cases and 150,676 controls; 54.5% never-smokers) and identified 12 novel susceptibility variants, bringing the total number to 28 at 25 independent loci. Transcriptome-wide association analyses together with colocalization studies using a Taiwanese lung expression quantitative trait loci dataset (n = 115) identified novel candidate genes, including FADS1 at 11q12 and ELF5 at 11p13. In a multi-ancestry meta-analysis of East Asian and European studies, four loci were identified at 2p11, 4q32, 16q23, and 18q12. At the same time, most of our findings in East Asian populations showed no evidence of association in European populations. In our studies drawn from East Asian populations, a polygenic risk score based on the 25 loci had a stronger association in never-smokers vs. individuals with a history of smoking (Pinteraction = 0.0058). These findings provide new insights into the etiology of lung adenocarcinoma in individuals from East Asian populations, which could be important in developing translational applications

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Modified Separator Performing Dual Physical/Chemical Roles to Inhibit Polysulfide Shuttle Resulting in Ultrastable Li–S Batteries

In this paper we describe a modified (AEG/CH) coated separator for Li–S batteries in which the shuttling phenomenon of the lithium polysulfides is restrained through two types of interactions: activated expanded graphite (AEG) flakes interacted physically with the lithium polysulfides, while chitosan (CH), used to bind the AEG flakes on the separator, interacted chemically through its abundance of amino and hydroxyl functional groups. Moreover, the AEG flakes facilitated ionic and electronic transfer during the redox reaction. Live H-cell discharging experiments revealed that the modified separator was effective at curbing polysulfide shuttling; moreover, X-ray photoelectron spectroscopy analysis of the cycled separator confirmed the presence of lithium polysulfides in the AEG/CH matrix. Using this dual functional interaction approach, the lifetime of the pure sulfur-based cathode was extended to 3000 cycles at 1C-rate (1C = 1670 mA/g), decreasing the decay rate to 0.021% per cycle, a value that is among the best reported to date. A flexible battery based on this modified separator exhibited stable performance and could turn on multiple light-emitting diodes. Such modified membranes with good mechanical strength, high electronic conductivity, and anti-self-discharging shield appear to be a scalable solution for future high-energy battery systems

Modified Separator Performing Dual Physical/Chemical Roles to Inhibit Polysulfide Shuttle Resulting in Ultrastable Li–S Batteries

In this paper we describe a modified (AEG/CH) coated separator for Li–S batteries in which the shuttling phenomenon of the lithium polysulfides is restrained through two types of interactions: activated expanded graphite (AEG) flakes interacted physically with the lithium polysulfides, while chitosan (CH), used to bind the AEG flakes on the separator, interacted chemically through its abundance of amino and hydroxyl functional groups. Moreover, the AEG flakes facilitated ionic and electronic transfer during the redox reaction. Live H-cell discharging experiments revealed that the modified separator was effective at curbing polysulfide shuttling; moreover, X-ray photoelectron spectroscopy analysis of the cycled separator confirmed the presence of lithium polysulfides in the AEG/CH matrix. Using this dual functional interaction approach, the lifetime of the pure sulfur-based cathode was extended to 3000 cycles at 1C-rate (1C = 1670 mA/g), decreasing the decay rate to 0.021% per cycle, a value that is among the best reported to date. A flexible battery based on this modified separator exhibited stable performance and could turn on multiple light-emitting diodes. Such modified membranes with good mechanical strength, high electronic conductivity, and anti-self-discharging shield appear to be a scalable solution for future high-energy battery systems

Modified Separator Performing Dual Physical/Chemical Roles to Inhibit Polysulfide Shuttle Resulting in Ultrastable Li–S Batteries

In this paper we describe a modified (AEG/CH) coated separator for Li–S batteries in which the shuttling phenomenon of the lithium polysulfides is restrained through two types of interactions: activated expanded graphite (AEG) flakes interacted physically with the lithium polysulfides, while chitosan (CH), used to bind the AEG flakes on the separator, interacted chemically through its abundance of amino and hydroxyl functional groups. Moreover, the AEG flakes facilitated ionic and electronic transfer during the redox reaction. Live H-cell discharging experiments revealed that the modified separator was effective at curbing polysulfide shuttling; moreover, X-ray photoelectron spectroscopy analysis of the cycled separator confirmed the presence of lithium polysulfides in the AEG/CH matrix. Using this dual functional interaction approach, the lifetime of the pure sulfur-based cathode was extended to 3000 cycles at 1C-rate (1C = 1670 mA/g), decreasing the decay rate to 0.021% per cycle, a value that is among the best reported to date. A flexible battery based on this modified separator exhibited stable performance and could turn on multiple light-emitting diodes. Such modified membranes with good mechanical strength, high electronic conductivity, and anti-self-discharging shield appear to be a scalable solution for future high-energy battery systems

Management consensus guideline for hepatocellular carcinoma: 2016 updated by the Taiwan Liver Cancer Association and the Gastroenterological Society of Taiwan

Background: Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related mortality in Taiwan. To help clinical physicians to manage patients with HCC, the Taiwan Liver Cancer Association and the Gastroenterological Society of Taiwan produced the management consensus guideline for HCC. Methods: The recommendations focus on nine important issues on management of HCC, including surveillance, diagnosis, staging, surgery, local ablation, transarterial chemoembolization/transarterial radioembolization/hepatic arterial infusion chemotherapy, systemic therapy, radiotherapy, and prevention. Results: The consensus statements were discussed, debated and got consensus in each expert team. And then the statements were sent to all of the experts for further discussion and refinement. Finally, all of the experts were invited to vote for the statements, including the level of evidence and recommendation. Conclusion: With the development of the management consensus guideline, HCC patients could benefit from the optimal therapeutic modality. Keywords: Diagnosis, Hepatocellular carcinoma, Staging, Surveillance, Treatmen