Baichuan 2: Open Large-scale Language Models

Large language models (LLMs) have demonstrated remarkable performance on a variety of natural language tasks based on just a few examples of natural language instructions, reducing the need for extensive feature engineering. However, most powerful LLMs are closed-source or limited in their capability for languages other than English. In this technical report, we present Baichuan 2, a series of large-scale multilingual language models containing 7 billion and 13 billion parameters, trained from scratch, on 2.6 trillion tokens. Baichuan 2 matches or outperforms other open-source models of similar size on public benchmarks like MMLU, CMMLU, GSM8K, and HumanEval. Furthermore, Baichuan 2 excels in vertical domains such as medicine and law. We will release all pre-training model checkpoints to benefit the research community in better understanding the training dynamics of Baichuan 2.Comment: Baichuan 2 technical report. Github: https://github.com/baichuan-inc/Baichuan

Challenges in QCD matter physics - The Compressed Baryonic Matter experiment at FAIR

Substantial experimental and theoretical efforts worldwide are devoted to explore the phase diagram of strongly interacting matter. At LHC and top RHIC energies, QCD matter is studied at very high temperatures and nearly vanishing net-baryon densities. There is evidence that a Quark-Gluon-Plasma (QGP) was created at experiments at RHIC and LHC. The transition from the QGP back to the hadron gas is found to be a smooth cross over. For larger net-baryon densities and lower temperatures, it is expected that the QCD phase diagram exhibits a rich structure, such as a first-order phase transition between hadronic and partonic matter which terminates in a critical point, or exotic phases like quarkyonic matter. The discovery of these landmarks would be a breakthrough in our understanding of the strong interaction and is therefore in the focus of various high-energy heavy-ion research programs. The Compressed Baryonic Matter (CBM) experiment at FAIR will play a unique role in the exploration of the QCD phase diagram in the region of high net-baryon densities, because it is designed to run at unprecedented interaction rates. High-rate operation is the key prerequisite for high-precision measurements of multi-differential observables and of rare diagnostic probes which are sensitive to the dense phase of the nuclear fireball. The goal of the CBM experiment at SIS100 (sqrt(s_NN) = 2.7 - 4.9 GeV) is to discover fundamental properties of QCD matter: the phase structure at large baryon-chemical potentials (mu_B > 500 MeV), effects of chiral symmetry, and the equation-of-state at high density as it is expected to occur in the core of neutron stars. In this article, we review the motivation for and the physics programme of CBM, including activities before the start of data taking in 2022, in the context of the worldwide efforts to explore high-density QCD matter.Comment: 15 pages, 11 figures. Published in European Physical Journal

Assessing Reproducibility of Inherited Variants Detected With Short-Read Whole Genome Sequencing

Background: Reproducible detection of inherited variants with whole genome sequencing (WGS) is vital for the implementation of precision medicine and is a complicated process in which each step affects variant call quality. Systematically assessing reproducibility of inherited variants with WGS and impact of each step in the process is needed for understanding and improving quality of inherited variants from WGS. Results: To dissect the impact of factors involved in detection of inherited variants with WGS, we sequence triplicates of eight DNA samples representing two populations on three short-read sequencing platforms using three library kits in six labs and call variants with 56 combinations of aligners and callers. We find that bioinformatics pipelines (callers and aligners) have a larger impact on variant reproducibility than WGS platform or library preparation. Single-nucleotide variants (SNVs), particularly outside difficult-to-map regions, are more reproducible than small insertions and deletions (indels), which are least reproducible when \u3e 5 bp. Increasing sequencing coverage improves indel reproducibility but has limited impact on SNVs above 30×. Conclusions: Our findings highlight sources of variability in variant detection and the need for improvement of bioinformatics pipelines in the era of precision medicine with WGS

Assessing reproducibility of inherited variants detected with short-read whole genome sequencing

Background: Reproducible detection of inherited variants with whole genome sequencing (WGS) is vital for the implementation of precision medicine and is a complicated process in which each step affects variant call quality. Systematically assessing reproducibility of inherited variants with WGS and impact of each step in the process is needed for understanding and improving quality of inherited variants from WGS. Results: To dissect the impact of factors involved in detection of inherited variants with WGS, we sequence triplicates of eight DNA samples representing two populations on three short-read sequencing platforms using three library kits in six labs and call variants with 56 combinations of aligners and callers. We find that bioinformatics pipelines (callers and aligners) have a larger impact on variant reproducibility than WGS platform or library preparation. Single-nucleotide variants (SNVs), particularly outside difficult-to-map regions, are more reproducible than small insertions and deletions (indels), which are least reproducible when > 5 bp. Increasing sequencing coverage improves indel reproducibility but has limited impact on SNVs above 30x. Conclusions: Our findings highlight sources of variability in variant detection and the need for improvement of bioinformatics pipelines in the era of precision medicine with WGS.Peer reviewe

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

Automatisk mätning av maximal ljudtrycksnivå i bilar

With a growing interest in technical specifications among consumers, there is a need for accessible measurement tools that enable individuals to evaluate the performance of their equipment, including common speakers and car audio systems, beyond what the manufacturer provides. However, the existing measurement systems are often geared towards professionals. This thesis aims to address this gap by designing and developing a user-friendly measurement tool that empowers individuals to easily measure and evaluate the performance of their devices. The work started with identifying the key technical specifications that users are interested in, and three parameters were selected for estimation: the maximum sound pressure level the system can provide, the corresponding multi-tone distortion and total harmonic distortion. Each parameter's measurement method varies, particularly in the choice of test stimuli and data processing. The methods in this thesis were determined after comparing existing standards for acoustical output-based measurement. Furthermore, some problems in terms of measurement capabilities and accuracy when implementing measurements within the defined application scenarios were also discussed. Ideally, the tool can finally provide users with detailed insights into chosen technical specifications, allowing them to know their audio systems better and make informed decisions. The automatic control of playback and recording as well as the processing afterwards was implemented in Python with the help of some existing packages. A graphic user interface based on PyQt was also developed to improve the manipulation of the measurement. Thus, the functionality that the tool is supposed to have is initially fulfilled, although its accuracy needs further verifying and improvement and the scope of the tool can be extended.Med ett växande intresse för tekniska specifikationer bland konsumenter finns det ett behov av tillgängliga mätverktyg som gör det möjligt för privatpersoner att utvärdera prestandan hos sin utrustning, inklusive vanliga högtalare och bilstereosystem, utöver vad tillverkaren tillhandahåller. De befintliga mätsystemen är dock ofta inriktade på professionella användare. Denna avhandling syftar till att åtgärda denna brist genom att utforma och utveckla ett användarvänligt mätverktyg som gör det möjligt för privatpersoner att enkelt mäta och utvärdera prestandan hos sina enheter. Arbetet inleddes med att identifiera de viktigaste tekniska specifikationerna som användarna är intresserade av, och tre parametrar valdes ut för uppskattning: den maximala ljudtrycksnivå som systemet kan ge, motsvarande multitondistorsion och total harmonisk distorsion. Mätmetoden för varje parameter varierar, särskilt när det gäller valet av teststimuli och databehandling. Metoderna i denna avhandling fastställdes efter jämförelse av befintliga standarder för akustisk effektbaserad mätning. Dessutom diskuterades vissa problem när det gäller mätkapacitet och noggrannhet vid implementering av mätningar inom de definierade tillämpningsscenarierna. I bästa fall kan verktyget slutligen ge användarna detaljerade insikter i valda tekniska specifikationer, så att de kan lära känna sina ljudsystem bättre och fatta välgrundade beslut. Den automatiska styrningen av uppspelning och inspelning samt bearbetningen i efterhand implementerades i Python med hjälp av några befintliga paket. Ett grafiskt användargränssnitt baserat på PyQt utvecklades också för att förbättra hanteringen av mätningen. Den funktionalitet som verktyget är tänkt att ha är således initialt uppfylld, även om dess noggrannhet behöver verifieras och förbättras ytterligare och verktygets omfattning kan utökas

Automatisk mätning av maximal ljudtrycksnivå i bilar

With a growing interest in technical specifications among consumers, there is a need for accessible measurement tools that enable individuals to evaluate the performance of their equipment, including common speakers and car audio systems, beyond what the manufacturer provides. However, the existing measurement systems are often geared towards professionals. This thesis aims to address this gap by designing and developing a user-friendly measurement tool that empowers individuals to easily measure and evaluate the performance of their devices. The work started with identifying the key technical specifications that users are interested in, and three parameters were selected for estimation: the maximum sound pressure level the system can provide, the corresponding multi-tone distortion and total harmonic distortion. Each parameter's measurement method varies, particularly in the choice of test stimuli and data processing. The methods in this thesis were determined after comparing existing standards for acoustical output-based measurement. Furthermore, some problems in terms of measurement capabilities and accuracy when implementing measurements within the defined application scenarios were also discussed. Ideally, the tool can finally provide users with detailed insights into chosen technical specifications, allowing them to know their audio systems better and make informed decisions. The automatic control of playback and recording as well as the processing afterwards was implemented in Python with the help of some existing packages. A graphic user interface based on PyQt was also developed to improve the manipulation of the measurement. Thus, the functionality that the tool is supposed to have is initially fulfilled, although its accuracy needs further verifying and improvement and the scope of the tool can be extended.Med ett växande intresse för tekniska specifikationer bland konsumenter finns det ett behov av tillgängliga mätverktyg som gör det möjligt för privatpersoner att utvärdera prestandan hos sin utrustning, inklusive vanliga högtalare och bilstereosystem, utöver vad tillverkaren tillhandahåller. De befintliga mätsystemen är dock ofta inriktade på professionella användare. Denna avhandling syftar till att åtgärda denna brist genom att utforma och utveckla ett användarvänligt mätverktyg som gör det möjligt för privatpersoner att enkelt mäta och utvärdera prestandan hos sina enheter. Arbetet inleddes med att identifiera de viktigaste tekniska specifikationerna som användarna är intresserade av, och tre parametrar valdes ut för uppskattning: den maximala ljudtrycksnivå som systemet kan ge, motsvarande multitondistorsion och total harmonisk distorsion. Mätmetoden för varje parameter varierar, särskilt när det gäller valet av teststimuli och databehandling. Metoderna i denna avhandling fastställdes efter jämförelse av befintliga standarder för akustisk effektbaserad mätning. Dessutom diskuterades vissa problem när det gäller mätkapacitet och noggrannhet vid implementering av mätningar inom de definierade tillämpningsscenarierna. I bästa fall kan verktyget slutligen ge användarna detaljerade insikter i valda tekniska specifikationer, så att de kan lära känna sina ljudsystem bättre och fatta välgrundade beslut. Den automatiska styrningen av uppspelning och inspelning samt bearbetningen i efterhand implementerades i Python med hjälp av några befintliga paket. Ett grafiskt användargränssnitt baserat på PyQt utvecklades också för att förbättra hanteringen av mätningen. Den funktionalitet som verktyget är tänkt att ha är således initialt uppfylld, även om dess noggrannhet behöver verifieras och förbättras ytterligare och verktygets omfattning kan utökas

Trait-Based Models of Decomposition with Interspecific and Environmental Interactions

Most saprotrophic fungi are dominant decomposers, and they play a vital role in the carbon cycle and stability of ecosystem. Previous researchers examined that how traits and environments influence the decomposition rate(DR), but few studies last long enough to scale short-term results up to long-term trends. In this paper, we build several trait-based models of decomposition with interspecific and environmental interactions to describe both short- and long-term trends. First, we build the model of decomposition ratio versus time with covariates – hyphal extension ratio and moisture tolerance for each species. Second, we define Interspecific Interference Ratio (IIR) to reflect interactions between fungi species and rank the relative competitiveness based on Grey System Theory with four evaluation indices: hyphal extension rate, moisture niche width, the hyphal density and thermal niche width. Then, we predict the relative advantages and disadvantages for different species by IIR and analyze the impact of biodiversity. Finally, we perform sensitivity and robustness analysis of our models, which exhibits the wide prospects and a deeper understanding of the role of fungi in the ecosystem

Impacts of the COVID-19 Pandemic on Anxiety and Depressive Symptoms in Pregnant Women and Related Perinatal Outcomes

To evaluate the impacts of the COVID-19 pandemic on anxiety and depression symptoms in pregnant women and their relationship with pregnancy outcomes, 1087 pregnant women completed online questionnaires. Anxiety symptoms were measured using the Self-Rating Anxiety Scale (SAS). Depression was assessed using the Edinburgh Postnatal Depression Scale (EPDS), and the Pittsburgh Sleep Quality Index (PSQI) was used to assess sleep quality. Univariate analysis and logistic regression analysis were used to determine the association between depression and anxiety symptoms, participants’ characteristics, and pregnancy outcomes. Of the 986 pregnant women who were included in this study, the rates of anxiety symptoms and depressive tendencies were 13.4% and 18.3%, respectively. Sleep disorder ((Adjusted odds ratio, AOR = 4.166; 95% confidence interval, CI: 2.797–6.205), time spent paying attention to the epidemic per day (≥1 h/d AOR = 1.568; 95% CI: 1.052–2.338), and the time spent with their spouses (Increase AOR = 0.629; 95% CI: 0.409–0.967) were associated with the risk of anxiety. Sleep disorder (AOR = 3.839; 95% CI: 2.718–5.432) and educational level (bachelor’s degree or above AOR = 1.833; 95% CI: 1.004–3.345) were associated with the risk of depression. Psychological status was not correlated with the pregnancy outcomes (p > 0.05). Anxiety and depression symptoms were common among pregnant women during the COVID-19 pandemic. Special attention should be paid to manage their risk factors