大模型在生物学中的应用

以ChatGPT为代表的新兴人工智能技术展现出的卓越表现使“大模型”这个概念真正实现了“破圈”,开始深入到各个行业和生活的各个方面。在生物学领域,计算生物学家们现在可以利用自然语言模型高效地阅读、整理、理解海量的生物学文献。此外,多样的生物学数据构建的生物大模型可以用于解读复杂的生命语言,从而预测多种生物实体的结构与功能。大模型在生物学领域的应用,不仅开启了计算生物学的新篇章,更引领了生物医学研究和健康科技的新潮流,描绘了未来生命科学探索和医疗创新的宏伟蓝图。

Porcine Breeding Management in a Large-scale Piggery with Microbial Fermentation Bed

[Objective] The behavior of eating, drinking, defecating and peeing of 1 500 pigs in a large-scale microbial fermentation bed-equipped piggery was observed. We hoped to find some simple indicators that could reflect the health status of swinery and to provide experience for the swinery performance management in large-scale microbial fermentation bed-equipped piggery. [Method] The body weight （BW）, daily BW gain, feed intake and other indicators of different-day-old pigs were recorded in details. Based on the recorded data, the models between BW, BW gain, average daily feed intake and feed/gain ratio and growth days （d） were established. In addition, the incidences of pox-like macula （dermatitis）, diarrhea （gastrointestinal disease）, cough （respiratory disease）, stiff pig （malnutrition）, conjunctivitis （eye disease） and foot inflection （trauma） among fattening pigs were also investigated. [Result] The BW range, average BW, daily BW gain, breeding days, daily feed intake range, average daily feed intake, staged feed intake, accumulated feed intake, feed/gain ratio and accumulated feed/gain ratio of different-day-old pigs were studied, respectively. Four dynamic models were established for the growth of pigs： （1） the BW （y）-age （x） mod- el： y=0.758 9x-19.883 （3=0.993 7）; （2） the BW gain （y）-age （x） model： y=1.039 5x05051 （F=0.885 4）; （3） the average daily feed intake （y）-age （x） model： y=0.023 5x-0.334 3 （F=0.991 7）; （4） the feed/gain ratio （y）-age （x） model： y=0.022x＋0.427 8 （P=0.988 5）. Based on these models, the corresponding theoretical growth value of pigs at different growth stage could be predicted. The main diseases occurred among the swinery in the large-scale microbial fermentation bed piggery included pox-like macula （dermatitis）, diarrhea （gastrointestinal disease）, cough （respiratory disease）, stiff pig （mal- nutrition）, conjunctivitis （eye disease） and foot inflection （trauma）. The deadly infec- tious diseases had been not found among the pigs. [Conclusion] When the actual BW, BW gain, average daily feed intake and feed/gain ratio were all lower than the theoretical values predicted by the models, the management should be enhanced. The average daily feed intake of 60 to 65-day-old pigs was lower than the theoretic value, indicating that the pigs could not adapt nicely to the fermentation bed at the very early stage. When the pigs grew up to 70 to 75 d old, the average daily feed intake was higher than the theoretical value, indicating that the pigs had adapted to the fermentation bed. In particularly, average daily feed intake of 75-day-old pigs was higher than the theoretical value by 21%. It was suggested the fermentation bed was conducive to the growth of pigs. Considering the occurrence of diseases among pigs, the overall incidence was relatively low. The incidence of each disease was all lower than 10% with little difficulty in treating. If the management of mattress was strength- ened, such as paying attention to feeding and keeping water clean, many diseases could heal by themselves.

Air-Sea Exchange of Volatile Organic Compounds: A New Model with Microlayer Effects

The authors propose a new "three-layer" conceptual model for the air-sea exchange of organic gases, which includes a dynamic surface microlayer with photochemical and biological processes. A parameterization of this three-layer model is presented, which was used to calculate the air-sea fluxes of acetone over the Pacific Ocean. The air-sea fluxes of acetone calculated by the three-layer model are in the same direction but possess half the magnitude of the fluxes calculated by the traditional two-layer model in the absence of photochemical and biological processes. However, photochemical and biological processes impacting acetone in the microlayer can greatly vary the calculated fluxes in the three-layer model, even reversing their direction under favorable conditions. Our model may help explain the discrepancies between measured and calculated acetone fluxes in previous studies. More measurements are needed to validate our conceptual model and provide constraints on the model parameters.

Choice of Beef Herd Adaptation Strategy on Canadian Prairie Mixed Farms Under Extreme Climate Events

Economic impact of climate extremes on beef operation is expected to be significant due to its direct impact on feed production. Impact of such events on farm management and longer term farm financial situation is relatively unstudied in the Canadian Prairie. This study compared three alternative beef herd management strategies in dealing with climate extreme events under reference climate scenario of 1971-2000 and the future scenario of 2041-2070. The study used farm simulation model that integrated the model of cattle herd simulation, pasture model, crop simulation model combined with models of economic decisions. Purchasing feed and maintaining herd size is preferred option in dealing with drought Changes in management such as early weaning combined with limit feeding strategies reduce the feed demand and also reduce the financial burden during the years of extreme event, but it has severe negative consequences on amount of slaughter cattle sold. Cull herd strategy not only reduces feed demand but also increases income from sell of herd during the year/s of extreme event, but it severely impacts the farm＇s long term output supply potential. However, expansion of existing agriculture risk management policy to cover climate risk in beef production is necessary to support farmers in the year/s to extreme events.

Consensus of Flocks under M-Nearest-Neighbor Rules

This paper investigates a class of flocks with an M-nearest-neighbor rule,where each agent's neighbors are determined according to M nearest agents with M being a given integer,rather than all the agents within a fixed metric distance as in the well-known Vicsek's model.Such a neighbor rule has been validated by biologists through experiments and the authors will prove that,similar to the Vicsek's model,such a new neighbor rule can also achieve consensus under some conditions imposed only on the system's speed and the number M,n,without resorting to any priori connectivity assumptions on the trajectory of the system.In particular,the authors will prove that if the number M is proportional to the population size n,then for any speed v,the system will achieve consensus with large probability if the population size is large enough.