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121.
Vincent (2025-02-28 18:53):
#paper https://doi.org/10.1038/s41586-024-08328-6 nature. 2025. Accurate predictions on small data with a tabular foundation model. 过去二十年表格型数据预测一直是梯度提升决策树(gradient boosting decision tree)的天下,这篇文章开发了一种基于生成型transformer的表格基础模型。模型采用统一的嵌入方式来表示数值型和类别型特征,通过自注意力机制捕捉不同特征之间的复杂交互关系,并在数百万个合成数据上进行了大规模预训练,从而显著提升了对新任务的适应能力。实验结果显示,在多个真实小规模数据集上,该模型在预测准确度和训练效率方面都优于传统梯度提升决策树以及其他常见深度学习基线。研究还通过定量、定性和可解释性分析验证了模型在模型微调、数据生成、密度估计及表示学习等方面的多任务能力。尽管该模型在小数据场景中展现出显著优势,但真实数据分布的多样性、扩展到更高维度数据,理解模型的理论基础等问题仍有待进一步研究。
IF:50.500Q1 Nature, 2025-1-9. DOI: 10.1038/s41586-024-08328-6 PMID: 39780007 PMCID:PMC11711098
Abstract:
AbstractTabular data, spreadsheets organized in rows and columns, are ubiquitous across scientific fields, from biomedicine to particle physics to economics and climate science1,2. The fundamental prediction task of filling in … >>>
AbstractTabular data, spreadsheets organized in rows and columns, are ubiquitous across scientific fields, from biomedicine to particle physics to economics and climate science1,2. The fundamental prediction task of filling in missing values of a label column based on the rest of the columns is essential for various applications as diverse as biomedical risk models, drug discovery and materials science. Although deep learning has revolutionized learning from raw data and led to numerous high-profile success stories3–5, gradient-boosted decision trees6–9 have dominated tabular data for the past 20 years. Here we present the Tabular Prior-data Fitted Network (TabPFN), a tabular foundation model that outperforms all previous methods on datasets with up to 10,000 samples by a wide margin, using substantially less training time. In 2.8 s, TabPFN outperforms an ensemble of the strongest baselines tuned for 4 h in a classification setting. As a generative transformer-based foundation model, this model also allows fine-tuning, data generation, density estimation and learning reusable embeddings. TabPFN is a learning algorithm that is itself learned across millions of synthetic datasets, demonstrating the power of this approach for algorithm development. By improving modelling abilities across diverse fields, TabPFN has the potential to accelerate scientific discovery and enhance important decision-making in various domains. <<<
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122.
白鸟 (2025-02-28 17:55):
#paper DOI:10.1126/science.adp2407. Disease diagnostics using machine learning of B cell and T cell receptor sequences.Science387,eadp2407(2025). 作者尝试通过AI模型,利用病人的T/B免疫组库来进行疾病诊断,检测特定感染、自身免疫性疾病、疫苗反应和疾病严重程度差异。斯坦福大学团队开发的Mal-ID人工智能系统,分析593名个体的免疫受体数据集,开发基于机器学习的Mal-ID免疫诊断系统。该系统包括三个基础模型(分别针对BCR和TCR数据进行训练)和一个集合模型(将所有基础模型组合在一起)。 模型1:整体免疫组库,个体的IgH或TRB免疫组库组成差异来预测疾病状态。 模型2:CDR3氨基酸序列相似性,特定疾病公共克隆聚类,计算病人与每种疾病相关的匹配簇数量; 模型3:从蛋白质语言模型中提取的免疫受体序列特征 ; 感兴趣的点,是我们如何利用庞大的免疫组库数据,开发临床应用。
Science, 2025-2-21. DOI: 10.1126/science.adp2407
Abstract:
Clinical diagnosis typically incorporates physical examination, patient history, various laboratory tests, and imaging studies but makes limited use of the human immune system’s own record of antigen exposures encoded by … >>>
Clinical diagnosis typically incorporates physical examination, patient history, various laboratory tests, and imaging studies but makes limited use of the human immune system’s own record of antigen exposures encoded by receptors on B cells and T cells. We analyzed immune receptor datasets from 593 individuals to develop MAchine Learning for Immunological Diagnosis, an interpretive framework to screen for multiple illnesses simultaneously or precisely test for one condition. This approach detects specific infections, autoimmune disorders, vaccine responses, and disease severity differences. Human-interpretable features of the model recapitulate known immune responses to severe acute respiratory syndrome coronavirus 2, influenza, and human immunodeficiency virus, highlight antigen-specific receptors, and reveal distinct characteristics of systemic lupus erythematosus and type-1 diabetes autoreactivity. This analysis framework has broad potential for scientific and clinical interpretation of immune responses. <<<
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123.
前进 (2025-02-28 16:52):
#paper DOI: 10.1109/TMI.2024.3362968. Haiqiao Wang, Dong Ni, and Yi Wang, "Recursive Deformable Pyramid Network for Unsupervised Medical Image Registration," IEEE Transactions on Medical Imaging, vol. 43, no. 6, pp. 2229-2240, Jun. 2024. 这篇论文提出了一种新的无监督医学图像配准方法,即递归可变形金字塔网络(RDP)。该方法采用纯卷积金字塔结构和逐步递归策略,从粗到细地预测变形场,同时整合高层语义信息,以确保变形场的合理性。其创新点在于提出了递归策略,通过多次特征融合,变形估计、变形融合以及跨层融合,能够有效处理大变形,且无需单独的仿射预对齐步骤,这在许多现有的可变形配准网络中是常见的要求。实验结果表明,RDP网络在三个公开的脑部磁共振成像(MRI)数据集上的表现优于多种现有的配准方法,在准确性和效率方面具有显著优势。
124.
燕赵孤侠 (2025-02-28 16:27):
#paper doi:10.1016/j.scitotenv.2023.168081 2024 Combining large-scale investigation and quantum chemical calculation of pharmaceuticals: Spatiotemporal patterns of occurrence and structural insights into removal。提出出了一种新的搞环境治理的模式——环境治理科学化,就是靠数据和计算,搭建起一条完整的线,从观察环境情况,到模拟分析,再到做出治理决策。目的就是要让环境治理从以前那种被动等着污染出现了再去处理,变成主动预防污染;从以前那种比较粗糙、大概的管控,变成精准地去干预。后期把 AI 加进来,能让这个新模式更快地发展。AI 可以通过智能模型,打破数据和计算之间的障碍。比如说,AI 能直接从数据里找出分子行为的规律。这么一来,最后就能搞出一个更高效、花更少钱的污染防控系统。
125.
林海onrush (2025-02-28 16:21):
#paper, Nature, https://doi.org/10.1038/s41586-025-08613-y, Humans in Africa’s wet tropical forests 150 thousand years ago, 本文研究大约 15 万年前人类在非洲西部科特迪瓦湿润热带雨林中的活动,该研究挑战传统观点:热带雨林对早期智人(Homo sapiens)构成了生态障碍。研究通过光释光(OSL)和电子自旋共振(ESR)测年方法,确定 Bété I 遗址的人类占据时间,并结合植物蜡生物标记、稳定同位素、植物硅体和花粉分析,确认当时的环境是湿润的热带森林。这是迄今为止最早的确凿证据,证明智人早在 15 万年前就适应并生活在热带雨林中,非洲雨林在智人演化和迁徙中可能发挥了更重要的作用。
Abstract:
Abstract Humans emerged across Africa shortly before 300 thousand years ago (ka)1–3. Although this pan-African evolutionary process implicates diverse environments in the human story, the role of tropical forests remains … >>>
Abstract Humans emerged across Africa shortly before 300 thousand years ago (ka)1–3. Although this pan-African evolutionary process implicates diverse environments in the human story, the role of tropical forests remains poorly understood. Here we report a clear association between late Middle Pleistocene material culture and a wet tropical forest in southern Côte d’Ivoire, a region of present-day rainforest. Twinned optically stimulated luminescence and electron spin resonance dating methods constrain the onset of human occupations at Bété I to around 150 ka, linking them with Homo sapiens. Plant wax biomarker, stable isotope, phytolith and pollen analyses of associated sediments all point to a wet forest environment. The results represent the oldest yet known clear association between humans and this habitat type. The secure attribution of stone tool assemblages with the wet forest environment demonstrates that Africa’s forests were not a major ecological barrier for H. sapiens as early as around 150 ka. <<<
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126.
尹志 (2025-02-28 15:55):
#paper doi:10.48550/arXiv.2205.15463 Few-Shot Diffusion Models. 文章提出了一种扩散模型及set-based ViT的方式实现few shot生成的技术。实验表明,该模型仅需5个样本就可以完成新类别的生成。
arXiv, 2022-05-30T23:20:33Z. DOI: 10.48550/arXiv.2205.15463
Abstract:
Denoising diffusion probabilistic models (DDPM) are powerful hierarchicallatent variable models with remarkable sample generation quality and trainingstability. These properties can be attributed to parameter sharing in thegenerative hierarchy, as well … >>>
Denoising diffusion probabilistic models (DDPM) are powerful hierarchicallatent variable models with remarkable sample generation quality and trainingstability. These properties can be attributed to parameter sharing in thegenerative hierarchy, as well as a parameter-free diffusion-based inferenceprocedure. In this paper, we present Few-Shot Diffusion Models (FSDM), aframework for few-shot generation leveraging conditional DDPMs. FSDMs aretrained to adapt the generative process conditioned on a small set of imagesfrom a given class by aggregating image patch information using a set-basedVision Transformer (ViT). At test time, the model is able to generate samplesfrom previously unseen classes conditioned on as few as 5 samples from thatclass. We empirically show that FSDM can perform few-shot generation andtransfer to new datasets. We benchmark variants of our method on complex visiondatasets for few-shot learning and compare to unconditional and conditionalDDPM baselines. Additionally, we show how conditioning the model on patch-basedinput set information improves training convergence. <<<
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127.
徐炳祥 (2025-02-28 08:54):
#paper doi:10.1073/pnas.1901423116 Proc Natl Acad Sci USA, 2019, Robust single-cell Hi-C clustering by convolution- and random-walk-based imputation。近年来,单细胞Hi-C技术已经称为三维基因组学研究的新热点。然而受限于单细胞技术的固有缺陷,单细胞Hi-C文库普遍存在严重的测序深度不足和较大的细胞间变异性。因此有必要对原始数据加以修正和填补,本文提出在卷积平滑的基础上附加random walk with restart过程的数据填补,填补后的数据保留了染色质空间构象的各组织特征,同时实现了细胞类型间的更好区分。本文在单细胞Hi-C生物信息学中有重要地位,其提出的思路为后续多项研究所借鉴。
Abstract:
Three-dimensional genome structure plays a pivotal role in gene regulation and cellular function. Single-cell analysis of genome architecture has been achieved using imaging and chromatin conformation capture methods such as … >>>
Three-dimensional genome structure plays a pivotal role in gene regulation and cellular function. Single-cell analysis of genome architecture has been achieved using imaging and chromatin conformation capture methods such as Hi-C. To study variation in chromosome structure between different cell types, computational approaches are needed that can utilize sparse and heterogeneous single-cell Hi-C data. However, few methods exist that are able to accurately and efficiently cluster such data into constituent cell types. Here, we describe scHiCluster, a single-cell clustering algorithm for Hi-C contact matrices that is based on imputations using linear convolution and random walk. Using both simulated and real single-cell Hi-C data as benchmarks, scHiCluster significantly improves clustering accuracy when applied to low coverage datasets compared with existing methods. After imputation by scHiCluster, topologically associating domain (TAD)-like structures (TLSs) can be identified within single cells, and their consensus boundaries were enriched at the TAD boundaries observed in bulk cell Hi-C samples. In summary, scHiCluster facilitates visualization and comparison of single-cell 3D genomes. <<<
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128.
半面阳光 (2025-02-27 14:44):
#paper https://doi.org/10.1038/s41421-022-00457-4. Cell Discovery. 2022. Genetic deconvolution of fetal and maternal cell-free DNA in maternal plasma enables next-generation non-invasive prenatal screening. 这篇文章介绍了一种新的无创产前筛查(NIPS)方法,将NIPT检测范围拓展到了检测单基因遗传病。这种新的NIPT方法基于一种称为COATE-seq(coordinative allele-aware target enrichment sequencing)的测序方法,结合多维基因组分析(测序深度、等位基因频率、SNP连锁分析),克服了传统NIPS难以检测胎儿特异性遗传变异的问题。这个研究对1129例妊娠样本进行了测试,检测到54例胎儿染色体异常(如唐氏综合征T21)、8例微缺失/微重复综合征、8例单基因突变病例,且敏感性达到100%,特异性为99.3%。此外,该研究还揭示了60.3%的染色体非整倍体病例与异常减数分裂重组相关,为理解减数分裂不分离机制提供了重要见解。最终,该方法能够精确解析胎儿基因组,为未来NIPS的扩展和更全面的遗传疾病筛查奠定了基础。
Abstract:
AbstractCurrent non-invasive prenatal screening (NIPS) analyzes circulating fetal cell-free DNA (cfDNA) in maternal peripheral blood for selected aneuploidies or microdeletion/duplication syndromes. Many genetic disorders are refractory to NIPS largely because … >>>
AbstractCurrent non-invasive prenatal screening (NIPS) analyzes circulating fetal cell-free DNA (cfDNA) in maternal peripheral blood for selected aneuploidies or microdeletion/duplication syndromes. Many genetic disorders are refractory to NIPS largely because the maternal genetic material constitutes most of the total cfDNA present in the maternal plasma, which hinders the detection of fetus-specific genetic variants. Here, we developed an innovative sequencing method, termed coordinative allele-aware target enrichment sequencing (COATE-seq), followed by multidimensional genomic analyses of sequencing read depth, allelic fraction, and linked single nucleotide polymorphisms, to accurately separate the fetal genome from the maternal background. Analytical confounders including multiple gestations, maternal copy number variations, and absence of heterozygosity were successfully recognized and precluded for fetal variant analyses. In addition, fetus-specific genomic characteristics, including the cfDNA fragment length, meiotic error origins, meiotic recombination, and recombination breakpoints were identified which reinforced the fetal variant assessment. In 1129 qualified pregnancies tested, 54 fetal aneuploidies, 8 microdeletions/microduplications, and 8 monogenic variants were detected with 100% sensitivity and 99.3% specificity. Using the comprehensive cfDNA genomic analysis tools developed, we found that 60.3% of aneuploidy samples had aberrant meiotic recombination providing important insights into the mechanism underlying meiotic nondisjunctions. Altogether, we show that the genetic deconvolution of the fetal and maternal cfDNA enables thorough and accurate delineation of fetal genome which paves the way for the next-generation prenatal screening of essentially all types of human genetic disorders. <<<
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129.
李翛然 (2025-02-27 12:03):
#paper Biggest-ever AI biology model writes DNA on demand doi:https://doi.org/10.1038/d41586-025-00531-3 evo2 最近非常出名, 主要就是微软的ev2该研究可能开发了当前规模最大的基因组语言模型(Genomic Language Model, GLM),通过深度学习技术实现按需设计功能性DNA序列。其核心思路借鉴了大型语言模型(如ChatGPT)的自监督预训练方法,利用海量基因组数据学习DNA序列的“语法规则”,从而预测或生成具有特定调控功能的序列 。 虽然文章中揭示了bcra基因的突变相关影响基因。但是临床实践上,其实方法很多,暂时没有看出来哪些碾压的存在,倒是twitter讨论的很多,说是可以预测病毒突变,这个我有待观察。论文原文并没有提到这个
130.
刘昊辰 (2025-02-25 22:38):
#paper Playing Hex and Counter Wargames using Reinforcement Learning and Recurrent Neural Networks. 这是一篇关于如何使用强化学习(Reinforcement Learning)和循环神经网络(Recurrent Neural Networks, RNN)来玩六角格战棋游戏(Hex and Counter Wargames)的研究论文。论文提出一种结合AlphaZero强化学习算法和循环神经网络的新系统,以应对六角格战棋游戏的战略复杂性。该系统能够在不同地形和战术情况下进行泛化,并探索其在更大地图上的扩展能力。提出的系统在有限的训练资源和计算能力下,能够在复杂的六角格战棋游戏中取得良好的表现,展示了其在复杂场景中的泛化能力。下载地址:https://arxiv.org/abs/2502.13918
arXiv, 2025-02-19T17:52:45Z. DOI: 10.48550/arXiv.2502.13918
Abstract:
Hex and Counter Wargames are adversarial two-player simulations of realmilitary conflicts requiring complex strategic decision-making. Unlikeclassical board games, these games feature intricate terrain/unit interactions,unit stacking, large maps of varying sizes, … >>>
Hex and Counter Wargames are adversarial two-player simulations of realmilitary conflicts requiring complex strategic decision-making. Unlikeclassical board games, these games feature intricate terrain/unit interactions,unit stacking, large maps of varying sizes, and simultaneous move and combatdecisions involving hundreds of units. This paper introduces a novel systemdesigned to address the strategic complexity of Hex and Counter Wargames byintegrating cutting-edge advancements in Recurrent Neural Networks withAlphaZero, a reliable modern Reinforcement Learning algorithm. The systemutilizes a new Neural Network architecture developed from existing research,incorporating innovative state and action representations tailored to thesespecific game environments. With minimal training, our solution has shownpromising results in typical scenarios, demonstrating the ability to generalizeacross different terrain and tactical situations. Additionally, we explore thesystem's potential to scale to larger map sizes. The developed system is openlyaccessible, facilitating continued research and exploration within thischallenging domain. <<<
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131.
小年 (2025-02-25 18:46):
#paper DOI: 10.1186/s13059-023-03031-7. Yongping Zhang, Shuting Jiang et al.  Genome Biology. Single-cell transcriptomics reveals multiple chemoresistant properties in leukemic stem and progenitor cells in pediatric AML. 该研究依托于儿童AML低剂量化疗联合G-CSF三期随机对照多中心临床试验(CALS III-AML18),通过精细解析患者化疗前后骨髓的异质性细胞群体结合临床大样本队列验证和功能实验,首次刻画了儿童AML化疗后残留肿瘤细胞的单细胞图谱。研究明确了患者体内的白血病干细胞和氧化磷酸化两个耐药特征及其对应的精确细胞亚群,发现了耐药的HSC-like干细胞亚群及其表面标记物CD69,并初步揭示了CD69通过调控mTOR-CCND1-CXCR4轴介导耐药的分子机制。研究还发现该干细胞耐药亚群的细胞比例高低与预后不良的临床表型和基因组特征相关,这些研究为临床诊断和监测提供了重要的理论依据。
Abstract:
Abstract Background Cancer patients can achieve dramatic responses to chemotherapy yet retain resistant tumor cells, which ultimately results in relapse. Although xenograft model studies have identified several cellular and molecular … >>>
Abstract Background Cancer patients can achieve dramatic responses to chemotherapy yet retain resistant tumor cells, which ultimately results in relapse. Although xenograft model studies have identified several cellular and molecular features that are associated with chemoresistance in acute myeloid leukemia (AML), to what extent AML patients exhibit these properties remains largely unknown. Results We apply single-cell RNA sequencing to paired pre- and post-chemotherapy whole bone marrow samples obtained from 13 pediatric AML patients who had achieved disease remission, and distinguish AML clusters from normal cells based on their unique transcriptomic profiles. Approximately 50% of leukemic stem and progenitor populations actively express leukemia stem cell (LSC) and oxidative phosphorylation (OXPHOS) signatures, respectively. These clusters have a higher chance of tolerating therapy and exhibit an enhanced metabolic program in response to treatment. Interestingly, the transmembrane receptor CD69 is highly expressed in chemoresistant hematopoietic stem cell (HSC)-like populations (named the CD69+ HSC-like subpopulation). Furthermore, overexpression of CD69 results in suppression of the mTOR signaling pathway and promotion of cell quiescence and adhesion in vitro. Finally, the presence of CD69+ HSC-like cells is associated with unfavorable genetic mutations, the persistence of residual tumor cells in chemotherapy, and poor outcomes in independent pediatric and adult public AML cohorts. Conclusions Our analysis reveals leukemia stem cell and OXPHOS as two major chemoresistant features in human AML patients. CD69 may serve as a potential biomarker in defining a subpopulation of chemoresistant leukemia stem cells. These findings have important implications for targeting residual chemo-surviving AML cells. <<<
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132.
DeDe宝 (2025-02-25 00:46):
#paper doi:10.1037/rev0000505, Psychol Rev. 2025, Episodic retrieval for model-based evaluation in sequential decision tasks. 长期以来,情景记忆(episodic memory)被认为支持了序列决策。但是,相关实验中的情景记忆确实高度抽象的,缺乏生态效度。在本研究中,研究者提出了一个过程模型TCM-SR以解释情景记忆在序列决策中的作用。 TCM-SR模型由两部分组成。其中,TCM(Temporal Context Model )是一个描述情景检索动态的模型,假设记忆检索受到temporal context的影响(temporal context在此研究中被定义为之前经验的加权平均)。SR(Successor Representation)是强化学习中的概念,用于描述从一个状态到其他所有状态的预期访问次数。TCM-SR假设情景记忆在编码阶段在状态间的转移符合SR,在检索阶段,情景记忆的权重赋值基于TCM模型。研究使用经典序列决策范式“Plinko游戏”检验模型。结果表明TCM-SR模型能够通过情景记忆的检索动态来估计动作的价值,并做出适应性选择。
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颜林林 (2025-02-24 21:06):
#paper doi:10.1038/s41588-024-02050-9, Nature Genetics, 2025, Cell state-dependent allelic effects and contextual Mendelian randomization analysis for human brain phenotypes. 这篇是今年1月份新发表在Nature Genetics的文章,对391例人脑(208患者 vs. 183对照,死后的组织样本)进行snRNA-seq(单核测序)和SNP芯片检测,单核测序能够分析得到不同细胞类型的每个基因的表达量,于是可以鉴别出特定细胞的eQTL,即只在某个细胞类型中才会对基因表达量产生影响的那些突变。这个研究逻辑(鉴别特定细胞的eQTL),在此之前已经有不止一篇文章做过了。本文的重要创新点在于,构建了三个模型(M0、M1、M2),分别表示用临床信息协变量、协变量+基因型、协变量+基因型x疾病来预测表达量,接着,M1 对 M0,M2 对 M1 分别做似然比检验(likelihood ratio test),可以筛选出那些仅影响基因表达量但不直接影响疾病表型的突变,这正好用于后续的孟德尔随机化分析,从而在基因(表达量)与表型之间建立起因果关系(而不仅仅是相关关系)。之后文章还使用大规模的蛋白组数据,在蛋白水平进行了相应验证。
Abstract:
Abstract Gene expression quantitative trait loci are widely used to infer relationships between genes and central nervous system (CNS) phenotypes; however, the effect of brain disease on these inferences is … >>>
Abstract Gene expression quantitative trait loci are widely used to infer relationships between genes and central nervous system (CNS) phenotypes; however, the effect of brain disease on these inferences is unclear. Using 2,348,438 single-nuclei profiles from 391 disease-case and control brains, we report 13,939 genes whose expression correlated with genetic variation, of which 16.7–40.8% (depending on cell type) showed disease-dependent allelic effects. Across 501 colocalizations for 30 CNS traits, 23.6% had a disease dependency, even after adjusting for disease status. To estimate the unconfounded effect of genes on outcomes, we repeated the analysis using nondiseased brains (n = 183) and reported an additional 91 colocalizations not present in the larger mixed disease and control dataset, demonstrating enhanced interpretation of disease-associated variants. Principled implementation of single-cell Mendelian randomization in control-only brains identified 140 putatively causal gene–trait associations, of which 11 were replicated in the UK Biobank, prioritizing candidate peripheral biomarkers predictive of CNS outcomes. <<<
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134.
惊鸿 (2025-02-15 00:02):
#paper DeepSeek-V2: A Strong, Economical, and Efficient Mixture-of-Experts Language Model Pub Date : 2024-05-07 DOI : arxiv-2405.04434 我们提出了 DeepSeek-V2,一种强大的专家混合 (MoE) 语言模型,其特点是经济的训练和高效的推理。它总共包括236B个参数,其中每个令牌激活21B个参数,并支持128K令牌的上下文长度。 DeepSeek-V2采用多头潜在注意力(MLA)和DeepSeekMoE等创新架构。 MLA 通过将键值 (KV) 缓存显着压缩为潜在向量来保证高效推理,而 DeepSeekMoE 则可以通过稀疏计算以经济的成本训练强大的模型。与 DeepSeek 67B 相比,DeepSeek-V2 性能显着增强,同时节省了 42.5% 的训练成本,减少了 93.3% 的 KV 缓存,最大生成吞吐量提升至 5.76 倍。我们在由 8.1T 代币组成的高质量多源语料库上对 DeepSeek-V2 进行预训练,并进一步进行监督微调(SFT)和强化学习(RL)以充分释放其潜力。评估结果表明,即使只有21B个激活参数,DeepSeek-V2及其聊天版本仍然达到了开源模型中顶级的性能。模型检查点位于“https://github.com/deepseek-ai/DeepSeek-V2”。
arXiv, 2024-05-07T15:56:43Z. DOI: 10.48550/arXiv.2405.04434
DeepSeek-AI, Aixin Liu, Bei Feng, Bin Wang, Bingxuan Wang, Bo Liu, Chenggang Zhao, Chengqi Dengr, Chong Ruan, Damai Dai, Daya Guo, Dejian Yang, Deli Chen, Dongjie Ji, Erhang Li, Fangyun Lin, Fuli Luo, Guangbo Hao, Guanting Chen, Guowei Li, H. Zhang, Hanwei Xu, Hao Yang, Haowei Zhang, Honghui Ding, Huajian Xin, Huazuo Gao, Hui Li, Hui Qu, J. L. Cai, Jian Liang, Jianzhong Guo, Jiaqi Ni, Jiashi Li, Jin Chen, Jingyang Yuan, Junjie Qiu, Junxiao Song, Kai Dong, Kaige Gao, Kang Guan, Lean Wang, Lecong Zhang, Lei Xu, Leyi Xia, Liang Zhao, Liyue Zhang, Meng Li, Miaojun Wang, Mingchuan Zhang, Minghua Zhang, Minghui Tang, Mingming Li, Ning Tian, Panpan Huang, Peiyi Wang, Peng Zhang, Qihao Zhu, Qinyu Chen, Qiushi Du, R. J. Chen, R. L. Jin, Ruiqi Ge, Ruizhe Pan, Runxin Xu, Ruyi Chen, S. S. Li, Shanghao Lu, Shangyan Zhou, Shanhuang Chen, Shaoqing Wu, Shengfeng Ye, Shirong Ma, Shiyu Wang, Shuang Zhou, Shuiping Yu, Shunfeng Zhou, Size Zheng, T. Wang, Tian Pei, Tian Yuan, Tianyu Sun, W. L. Xiao, Wangding Zeng, Wei An, Wen Liu, Wenfeng Liang, Wenjun Gao, Wentao Zhang, X. Q. Li, Xiangyue Jin, Xianzu Wang, Xiao Bi, Xiaodong Liu, Xiaohan Wang, Xiaojin Shen, Xiaokang Chen, Xiaosha Chen, Xiaotao Nie, Xiaowen Sun, Xiaoxiang Wang, Xin Liu, Xin Xie, Xingkai Yu, Xinnan Song, Xinyi Zhou, Xinyu Yang, Xuan Lu, Xuecheng Su, Y. Wu, Y. K. Li, Y. X. Wei, Y. X. Zhu, Yanhong Xu, Yanping Huang, Yao Li, Yao Zhao, Yaofeng Sun, Yaohui Li, Yaohui Wang, Yi Zheng, Yichao Zhang, Yiliang Xiong, Yilong Zhao, Ying He, Ying Tang, Yishi Piao, Yixin Dong, Yixuan Tan, Yiyuan Liu, Yongji Wang, Yongqiang Guo, Yuchen Zhu, Yuduan Wang, Yuheng Zou, Yukun Zha, Yunxian Ma, Yuting Yan, Yuxiang You, Yuxuan Liu, Z. Z. Ren, Zehui Ren, Zhangli Sha, Zhe Fu, Zhen Huang, Zhen Zhang, Zhenda Xie, Zhewen Hao, Zhihong Shao, Zhiniu Wen, Zhipeng Xu, Zhongyu Zhang, Zhuoshu Li, Zihan Wang, Zihui Gu, Zilin Li, Ziwei Xie <<<
Abstract:
We present DeepSeek-V2, a strong Mixture-of-Experts (MoE) language modelcharacterized by economical training and efficient inference. It comprises 236Btotal parameters, of which 21B are activated for each token, and supports acontext … >>>
We present DeepSeek-V2, a strong Mixture-of-Experts (MoE) language modelcharacterized by economical training and efficient inference. It comprises 236Btotal parameters, of which 21B are activated for each token, and supports acontext length of 128K tokens. DeepSeek-V2 adopts innovative architecturesincluding Multi-head Latent Attention (MLA) and DeepSeekMoE. MLA guaranteesefficient inference through significantly compressing the Key-Value (KV) cacheinto a latent vector, while DeepSeekMoE enables training strong models at aneconomical cost through sparse computation. Compared with DeepSeek 67B,DeepSeek-V2 achieves significantly stronger performance, and meanwhile saves42.5% of training costs, reduces the KV cache by 93.3%, and boosts the maximumgeneration throughput to 5.76 times. We pretrain DeepSeek-V2 on a high-qualityand multi-source corpus consisting of 8.1T tokens, and further performSupervised Fine-Tuning (SFT) and Reinforcement Learning (RL) to fully unlockits potential. Evaluation results show that, even with only 21B activatedparameters, DeepSeek-V2 and its chat versions still achieve top-tierperformance among open-source models. <<<
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135.
龙海晨 (2025-02-14 17:36):
#paper Ayub Q, Mezzavilla M, Pagani L, Haber M, Mohyuddin A, Khaliq S, Mehdi SQ, Tyler-Smith C. The Kalash genetic isolate: ancient divergence, drift, and selection. Am J Hum Genet. 2015 May 7;96(5):775-83. doi: 10.1016/j.ajhg.2015.03.012. Epub 2015 Apr 30. PMID: 25937445; PMCID: PMC4570283.这是一篇介绍基因与人种的文献,文章通过研究Kalash 基因研究人种的起源。卡拉什人代表了一个神秘的孤立的印欧语系人群,他们已经在今巴基斯坦的兴都库什山脉生活了几个世纪。在马其顿的亚历山大三世入侵该地区后,先前的 Y 染色体和线粒体 DNA 标记没有找到他们有希腊血统的有利证据。为研究该人种的起源。通过与古代狩猎采集者和欧洲农民的已发表数据进行比较表明,卡拉什人与旧石器时代西伯利亚狩猎采集者共享基因漂移遗传漂变,可能代表了一个极度漂移的古代北欧亚人群。自从从其他南亚种群中分离出来以来,卡拉什人一直保持着较低的长期有效种群规模。,并且没有从他们在巴基斯坦的地理邻居或其他现存的欧亚种群中检测到基因流动。 卡拉什人和目前居住在该地区的其他人群之间的平均分化时间估计为 11,800 年前(95% 置信区间 = 10,600−12,600年前)。基因分析表明他们代表了一些最早从西亚进入印度次大陆的移民的后代。
136.
薛定谔的猫 (2025-02-01 00:07):
#paper, doi:10.1001/jama.2024.24438 Pulmonary Vein Isolation With Optimized Linear Ablation vs Pulmonary Vein Isolation Alone for Persistent AF The PROMPT-AF Randomized Clinical Trial PROMPT-AF研究是一项研究者发起的全国多中心、开放标签、随机对照试验,旨在科学验证"改良2C3L"术式(在肺静脉隔离基础上行二尖瓣峡部线、三尖瓣峡部线、顶部线消融)相比传统治疗方案(肺静脉隔离)的优势。研究纳入来自全国12家中心共498例首次消融的持续性房颤患者。所有患者均接受为期12个月的随访,(每周一次24小时的单导联心电贴监测心律),确研究的主要终点为术后12个月(排除术后三个月空白期)、不接受抗心律失常药物治疗的情况下,无>30s的房颤、房扑、房速发生。研究结果表明,“改良2C3L”策略消融术后1年无房性心律失常复发为70.7%,显著优于肺静脉隔离组的61.5%(HR 0.73, 95%CI:0.54 – 0.99)。
JAMA, 2024-11-18. DOI: 10.1001/jama.2024.24438
优化线性消融的肺静脉隔离与单独肺静脉隔离治疗持续性 AF
Abstract:
ImportanceSuccess rates of pulmonary vein isolation (PVI) are modest for persistent atrial fibrillation (AF). Additional linear ablation beyond PVI has not been proved superior to PVI alone in randomized trials. … >>>
ImportanceSuccess rates of pulmonary vein isolation (PVI) are modest for persistent atrial fibrillation (AF). Additional linear ablation beyond PVI has not been proved superior to PVI alone in randomized trials. Ethanol infusion of the vein of Marshall (EIVOM) facilitates ablation at the mitral isthmus and may lead to improved effectiveness of a linear ablation strategy.ObjectiveTo determine whether linear ablation with radiofrequency energy combined with EIVOM added to PVI improves sinus rhythm maintenance compared with PVI alone in patients with persistent AF.Design, Setting, and ParticipantsThe PROMPT-AF trial is an investigator-initiated, multicenter, open-label, randomized trial involving 12 tertiary hospitals in China. A total of 498 patients aged 18 to 80 years, with AF persisting for more than 3 months, undergoing first-time AF ablation, were enrolled and randomized from August 27, 2021, to July 16, 2023.InterventionsPatients were randomized to undergo PVI alone or PVI plus EIVOM and linear ablation (intervention). The latter group first underwent EIVOM, followed by PVI and linear ablation of the left atrial roof, mitral isthmus, and cavotricuspid isthmus.Main Outcomes and MeasuresThe primary end point was freedom from any documented atrial arrhythmias lasting more than 30 seconds, without the use of antiarrhythmic drugs within 12 months. Secondary outcomes included freedom from atrial arrhythmia recurrence, AF, atrial arrhythmia recurrence after multiple procedures, and documented atrial tachycardia or atrial flutter with or without antiarrhythmic drugs; AF burden; and improvement in quality of life. Patients were monitored with wearable single-lead electrocardiographic (ECG) patches, worn for 24 hours a week, supplemented by symptom-triggered ECGs and Holter monitoring.ResultsAmong 498 randomized patients, 495 (99.4%) were included in the primary analysis (mean age, 61.1 years [SD, 9.7] years, 361 male [72.9%]). After 12 months, 174 of 246 patients (70.7%) assigned to undergo PVI plus EIVOM and linear ablation and 153 of 249 patients (61.5%) assigned to undergo PVI alone remained free from atrial arrhythmias without taking antiarrhythmic drugs (hazard ratio, 0.73; 95% CI, 0.54-0.99, P = .045). The intervention effect was consistent across all prespecified subgroups. The comparison of secondary outcomes did not demonstrate significant results.ConclusionAmong patients with persistent AF, linear ablation combined with EIVOM in addition to PVI significantly improved freedom from atrial arrhythmias within 12 months compared with PVI alone.Trial RegistrationClinicalTrials.gov Identifier: NCT04497376 <<<
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137.
林海onrush (2025-01-31 23:53):
#paper, https://doi.org/10.48550/arXiv.2312.01156, Efficient Light Source Placement using Quantum Computing, 这是一个有趣的小问题, 如何利用量子计算解决《我的世界》游戏中的火把放置问题,将形式转化为二次无约束二进制优化(QUBO)问题,通过迭代学习拉格朗日乘子来处理约束条件。实验说明该方法能在合理迭代次数内找到有效的火把放置方案,虽然当前量子硬件存在局限性,经典方法在较大地图上表现更优一些。火把放置问题与集合覆盖问题相联系,展示量子计算在资源优化问题中的价值。
arXiv, 2023-12-02T15:28:59Z. DOI: 10.48550/arXiv.2312.01156
Abstract:
NP-hard problems regularly come up in video games, with interestingconnections to real-world problems. In the game Minecraft, players placetorches on the ground to light up dark areas. Placing them in … >>>
NP-hard problems regularly come up in video games, with interestingconnections to real-world problems. In the game Minecraft, players placetorches on the ground to light up dark areas. Placing them in a way thatminimizes the total number of torches to save resources is far from trivial. Inthis paper, we use Quantum Computing to approach this problem. To this end, wederive a QUBO formulation of the torch placement problem, which we uncover tobe very similar to another NP-hard problem. We employ a solution strategy thatinvolves learning Lagrangian weights in an iterative process, adding to theever growing toolbox of QUBO formulations. Finally, we perform experiments onreal quantum hardware using real game data to demonstrate that our approachyields good torch placements. <<<
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138.
孤舟蓑笠翁 (2025-01-31 23:36):
#paper 10.1186/s12967-023-04576-8。2023。Harnessing large language models (LLMs) for candidate gene prioritization and selection。该论文探讨了用大语言模型以知识驱动的方式对组学数据得到的一大堆基因进行解读、筛选,从而加速获得临床见解的可行性。结果发现OpenAI的GPT-4和Anthropic的Claude表现最佳。我的一个重要收获是发现对于目前的大语言模型的有效使用不是自己原来想的简单的提问就可以的,而是貌似应该是像完成一个项目分解为小的任务,然后逐步推进、整合额外信息,最后得出结论。这提醒我要想用好目前的大语言模型,需要学习如何提问。
Abstract:
AbstractBackgroundFeature selection is a critical step for translating advances afforded by systems-scale molecular profiling into actionable clinical insights. While data-driven methods are commonly utilized for selecting candidate genes, knowledge-driven methods … >>>
AbstractBackgroundFeature selection is a critical step for translating advances afforded by systems-scale molecular profiling into actionable clinical insights. While data-driven methods are commonly utilized for selecting candidate genes, knowledge-driven methods must contend with the challenge of efficiently sifting through extensive volumes of biomedical information. This work aimed to assess the utility of large language models (LLMs) for knowledge-driven gene prioritization and selection.MethodsIn this proof of concept, we focused on 11 blood transcriptional modules associated with an Erythroid cells signature. We evaluated four leading LLMs across multiple tasks. Next, we established a workflow leveraging LLMs. The steps consisted of: (1) Selecting one of the 11 modules; (2) Identifying functional convergences among constituent genes using the LLMs; (3) Scoring candidate genes across six criteria capturing the gene’s biological and clinical relevance; (4) Prioritizing candidate genes and summarizing justifications; (5) Fact-checking justifications and identifying supporting references; (6) Selecting a top candidate gene based on validated scoring justifications; and (7) Factoring in transcriptome profiling data to finalize the selection of the top candidate gene.ResultsOf the four LLMs evaluated, OpenAI's GPT-4 and Anthropic's Claude demonstrated the best performance and were chosen for the implementation of the candidate gene prioritization and selection workflow. This workflow was run in parallel for each of the 11 erythroid cell modules by participants in a data mining workshop. Module M9.2 served as an illustrative use case. The 30 candidate genes forming this module were assessed, and the top five scoring genes were identified as BCL2L1, ALAS2, SLC4A1, CA1, and FECH. Researchers carefully fact-checked the summarized scoring justifications, after which the LLMs were prompted to select a top candidate based on this information. GPT-4 initially chose BCL2L1, while Claude selected ALAS2. When transcriptional profiling data from three reference datasets were provided for additional context, GPT-4 revised its initial choice to ALAS2, whereas Claude reaffirmed its original selection for this module.ConclusionsTaken together, our findings highlight the ability of LLMs to prioritize candidate genes with minimal human intervention. This suggests the potential of this technology to boost productivity, especially for tasks that require leveraging extensive biomedical knowledge. <<<
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139.
Su 0-0 (2025-01-31 23:35):
#paper DOI: 10.1002/smll.202108008 Small. 2022,DNA Logic Circuits for Cancer Theranostics. 这篇文章是一篇综述,DNA逻辑电路具有强大的逻辑判断和信号放大功能,在癌症诊疗方面具有很好的特异性和灵敏性,这篇论文总结了2022年以前DNA逻辑电路在癌症诊断、治疗方面的运用,并提出DNA逻辑电路在实际生物系统中稳定性、时空控制能力等有待提高。
Abstract:
AbstractCancer diagnosis and therapeutics (theranostics) based on the tumor microenvironment (TME) and biomarkers has been an emerging approach for precision medicine. DNA nanotechnology dynamically controls the self‐assembly of DNA molecules … >>>
AbstractCancer diagnosis and therapeutics (theranostics) based on the tumor microenvironment (TME) and biomarkers has been an emerging approach for precision medicine. DNA nanotechnology dynamically controls the self‐assembly of DNA molecules at the nanometer scale to construct intelligent DNA chemical reaction systems. The DNA logic circuit is a particularly emerging approach for computing within the DNA chemical systems. DNA logic circuits can sensitively respond to tumor‐specific markers and the TME through logic operations and signal amplification, to generate detectable signals or to release anti‐cancer agents. In this review, the fundamental concepts of DNA logic circuits are clarified, the basic modules in the circuit are summarized, and how this advanced nano‐assembly circuit responds to tumor‐related molecules, how to perform logic operations, to realize signal amplification, and selectively release drugs through discussing over 30 application examples, are demonstrated. This review shows that DNA logic circuits have powerful logic judgment and signal amplification functions in improving the specificity and sensitivity of cancer diagnosis and making cancer treatment controllable. In the future, researchers are expected to overcome the existing shortcomings of DNA logic circuits and design smarter DNA devices with better biocompatibility and stability, which will further promote the development of cancer theranostics. <<<
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140.
钟鸣 (2025-01-31 23:04):
#paper doi:10.1093/pnasnexus/pgae589 Partner (in)congruence in gender role attitudes and relationship satisfaction 对一万对夫妇(来自美国和德国)进行了为期十余年的跟踪调查,探索夫妻双方对“男主外女主内”的支持度与幸福感之间的关系。结果表明:发现当夫妻双方在强烈的传统或平等态度方面相似时,以及当男性比女性更平等时,他们通常会更幸福。此前类似的研究的局限性在于不够细致,他们使用夫妻间理念的差异分数作为衡量标准,而差异分数的计算迫使人们假设在传统态度上一致的夫妻与在平等态度上一致的夫妻是等同的,同时也限制了对立类型的不匹配是等同的。对结论的解释是:对性别工作与家庭安排抱有漠不关心或矛盾的态度可能会导致一种模糊感,从而阻碍男女混合关系的正常运作,遵守一套明确的传统角色分工的社会脚本可能会给夫妻带来优势,这一规律似乎可以推广到更多的社会议题下。
Abstract:
Abstract The societal shift toward greater gender equality has led to increased variability in people’s gender role attitudes, or the belief that men and women should occupy distinct family roles … >>>
Abstract The societal shift toward greater gender equality has led to increased variability in people’s gender role attitudes, or the belief that men and women should occupy distinct family roles (i.e. men as breadwinners and women as homemakers). Existing evidence on the association between gender role attitudes and relationship well-being remains inconclusive with mixed findings, likely because past research has not adequately considered the direction and degree of (in)congruencies between partners within the relationship. Using longitudinal samples of 1,327 couples from the United States and 5,856 couples from Germany tracked over 2 and 13 years, respectively, we employed dyadic response surface analysis to examine how different patterns of partner (in)congruencies in gender role attitudes predict relationship well-being in mixed-gender relationships. The results showed that, for US men and German men and women, the direction of incongruence between partners’ gender role attitudes mattered: relationship satisfaction was higher when men adopted more egalitarian attitudes than women (or conversely, when women adopted more traditional attitudes than men) compared with the reverse. Relationship satisfaction was also higher when both partners showed congruence in extreme gender role attitudes (either strongly traditional or egalitarian) than when either partner endorsed more neutral attitudes. US women reported higher relationship satisfaction only when either partner endorsed more egalitarian attitudes. Although past research emphasizes the benefits of partner similarity for relationship well-being, our findings highlight the importance of both similarity and complementarity in gender role attitudes, potentially subject to cultural and contextual factors. <<<
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