arXiv - QuanBio - Molecular Networks最新文献_第6页

Data-Efficient Molecular Generation with Hierarchical Textual Inversion 利用层次化文本反演进行高效数据分子生成

arXiv - QuanBio - Molecular Networks Pub Date : 2024-05-05 DOI: arxiv-2405.02845

Seojin Kim, Jaehyun Nam, Sihyun Yu, Younghoon Shin, Jinwoo Shin

{"title":"Data-Efficient Molecular Generation with Hierarchical Textual Inversion","authors":"Seojin Kim, Jaehyun Nam, Sihyun Yu, Younghoon Shin, Jinwoo Shin","doi":"arxiv-2405.02845","DOIUrl":"https://doi.org/arxiv-2405.02845","url":null,"abstract":"Developing an effective molecular generation framework even with a limited\u0000number of molecules is often important for its practical deployment, e.g., drug\u0000discovery, since acquiring task-related molecular data requires expensive and\u0000time-consuming experimental costs. To tackle this issue, we introduce\u0000Hierarchical textual Inversion for Molecular generation (HI-Mol), a novel\u0000data-efficient molecular generation method. HI-Mol is inspired by the\u0000importance of hierarchical information, e.g., both coarse- and fine-grained\u0000features, in understanding the molecule distribution. We propose to use\u0000multi-level embeddings to reflect such hierarchical features based on the\u0000adoption of the recent textual inversion technique in the visual domain, which\u0000achieves data-efficient image generation. Compared to the conventional textual\u0000inversion method in the image domain using a single-level token embedding, our\u0000multi-level token embeddings allow the model to effectively learn the\u0000underlying low-shot molecule distribution. We then generate molecules based on\u0000the interpolation of the multi-level token embeddings. Extensive experiments\u0000demonstrate the superiority of HI-Mol with notable data-efficiency. For\u0000instance, on QM9, HI-Mol outperforms the prior state-of-the-art method with 50x\u0000less training data. We also show the effectiveness of molecules generated by\u0000HI-Mol in low-shot molecular property prediction.","PeriodicalId":501325,"journal":{"name":"arXiv - QuanBio - Molecular Networks","volume":"27 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140885702","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Stress-induced Eukaryotic Translational Regulatory Mechanisms 压力诱导的真核生物转化调控机制

arXiv - QuanBio - Molecular Networks Pub Date : 2024-05-02 DOI: arxiv-2405.01664

Dilawar Ahmad Mir, Zhengxin Ma, Jordan Horrocks, Aric N Rogers

{"title":"Stress-induced Eukaryotic Translational Regulatory Mechanisms","authors":"Dilawar Ahmad Mir, Zhengxin Ma, Jordan Horrocks, Aric N Rogers","doi":"arxiv-2405.01664","DOIUrl":"https://doi.org/arxiv-2405.01664","url":null,"abstract":"The eukaryotic protein synthesis process entails intricate stages governed by\u0000diverse mechanisms to tightly regulate translation. Translational regulation\u0000during stress is pivotal for maintaining cellular homeostasis, ensuring the\u0000accurate expression of essential proteins crucial for survival. This selective\u0000translational control mechanism is integral to cellular adaptation and\u0000resilience under adverse conditions. This review manuscript explores various\u0000mechanisms involved in selective translational regulation, focusing on\u0000mRNA-specific and global regulatory processes. Key aspects of translational\u0000control include translation initiation, which is often a rate-limiting step,\u0000and involves the formation of the eIF4F complex and recruitment of mRNA to\u0000ribosomes. Regulation of translation initiation factors, such as eIF4E, eIF4E2,\u0000and eIF2, through phosphorylation and interactions with binding proteins,\u0000modulates translation efficiency under stress conditions. This review also\u0000highlights the control of translation initiation through factors like the eIF4F\u0000complex and the ternary complex and also underscores the importance of\u0000eIF2{alpha} phosphorylation in stress granule formation and cellular stress\u0000responses. Additionally, the impact of amino acid deprivation, mTOR signaling,\u0000and ribosome biogenesis on translation regulation and cellular adaptation to\u0000stress is also discussed. Understanding the intricate mechanisms of\u0000translational regulation during stress provides insights into cellular\u0000adaptation mechanisms and potential therapeutic targets for various diseases,\u0000offering valuable avenues for addressing conditions associated with\u0000dysregulated protein synthesis.","PeriodicalId":501325,"journal":{"name":"arXiv - QuanBio - Molecular Networks","volume":"62 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140885469","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Interplay between Contractivity and Monotonicity for Reaction Networks 反应网络的契约性与单调性之间的相互作用

arXiv - QuanBio - Molecular Networks Pub Date : 2024-04-29 DOI: arxiv-2404.18734

Alon Duvall, M. Ali Al-Radhawi, Dhruv D. Jatkar, Eduardo Sontag

引用次数: 0

P53 Orchestrates Cancer Metabolism: Unveiling Strategies to Reverse the Warburg Effect P53 协调癌症代谢：揭示逆转沃伯格效应的策略

arXiv - QuanBio - Molecular Networks Pub Date : 2024-04-29 DOI: arxiv-2404.18613

Roba Abukwaik, Elias Vera-Siguenza, Daniel Tennant, Fabian Spill

{"title":"P53 Orchestrates Cancer Metabolism: Unveiling Strategies to Reverse the Warburg Effect","authors":"Roba Abukwaik, Elias Vera-Siguenza, Daniel Tennant, Fabian Spill","doi":"arxiv-2404.18613","DOIUrl":"https://doi.org/arxiv-2404.18613","url":null,"abstract":"Cancer cells exhibit significant alterations in their metabolism,\u0000characterised by a reduction in oxidative phosphorylation (OXPHOS) and an\u0000increased reliance on glycolysis, even in the presence of oxygen. This\u0000metabolic shift, known as the Warburg effect, is pivotal in fuelling cancer's\u0000uncontrolled growth, invasion, and therapeutic resistance. While dysregulation\u0000of many genes contributes to this metabolic shift, the tumour suppressor gene\u0000p53 emerges as a master player. Yet, the molecular mechanisms remain elusive.\u0000This study introduces a comprehensive mathematical model, integrating essential\u0000p53 targets, offering insights into how p53 orchestrates its targets to\u0000redirect cancer metabolism towards an OXPHOS-dominant state. Simulation\u0000outcomes align closely with experimental data comparing glucose metabolism in\u0000colon cancer cells with wild-type and mutated p53. Additionally, our findings\u0000reveal the dynamic capability of elevated p53 activation to fully reverse the\u0000Warburg effect, highlighting the significance of its activity levels not just\u0000in triggering apoptosis (programmed cell death) post-chemotherapy but also in\u0000modifying the metabolic pathways implicated in treatment resistance. In\u0000scenarios of p53 mutations, our analysis suggests targeting\u0000glycolysis-instigating signalling pathways as an alternative strategy, whereas\u0000targeting solely synthesis of cytochrome c oxidase 2 (SCO2) does support\u0000mitochondrial respiration but may not effectively suppress the glycolysis\u0000pathway, potentially boosting the energy production and cancer cell viability.","PeriodicalId":501325,"journal":{"name":"arXiv - QuanBio - Molecular Networks","volume":"22 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140840549","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

On Hybrid Gene Regulatory Networks 论混合基因调控网络

arXiv - QuanBio - Molecular Networks Pub Date : 2024-04-24 DOI: arxiv-2404.16197

Adrian Wurm, Honglu Sun

引用次数: 0

Transitions and Thermodynamics on Species Graphs of Chemical Reaction Networks 化学反应网络物种图上的转变和热力学

arXiv - QuanBio - Molecular Networks Pub Date : 2024-04-22 DOI: arxiv-2404.14336

Keisuke Sugie, Dimitri Loutchko, Tetsuya J. Tobayashi

{"title":"Transitions and Thermodynamics on Species Graphs of Chemical Reaction Networks","authors":"Keisuke Sugie, Dimitri Loutchko, Tetsuya J. Tobayashi","doi":"arxiv-2404.14336","DOIUrl":"https://doi.org/arxiv-2404.14336","url":null,"abstract":"Chemical reaction networks (CRNs) exhibit complex dynamics governed by their\u0000underlying network structure. In this paper, we propose a novel approach to\u0000study the dynamics of CRNs by representing them on species graphs (S-graphs).\u0000By scaling concentrations by conservation laws, we obtain a graph\u0000representation of transitions compatible with the S-graph, which allows us to\u0000treat the dynamics in CRNs as transitions between chemicals. We also define\u0000thermodynamic-like quantities on the S-graph from the introduced transitions\u0000and investigate their properties, including the relationship between\u0000specieswise forces, activities, and conventional thermodynamic quantities.\u0000Remarkably, we demonstrate that this formulation can be developed for a class\u0000of irreversible CRNs, while for reversible CRNs, it is related to conventional\u0000thermodynamic quantities associated with reactions. The behavior of these\u0000specieswise quantities is numerically validated using an oscillating system\u0000(Brusselator). Our work provides a novel methodology for studying dynamics on\u0000S-graphs, paving the way for a deeper understanding of the intricate interplay\u0000between the structure and dynamics of chemical reaction networks.","PeriodicalId":501325,"journal":{"name":"arXiv - QuanBio - Molecular Networks","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140798784","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A computational scheme connecting gene regulatory network dynamics with heterogeneous stem cell regeneration 连接基因调控网络动力学与异质干细胞再生的计算方案

arXiv - QuanBio - Molecular Networks Pub Date : 2024-04-17 DOI: arxiv-2404.11761

Yakun Li, Xiyin Liang, Jinzhi Lei

{"title":"A computational scheme connecting gene regulatory network dynamics with heterogeneous stem cell regeneration","authors":"Yakun Li, Xiyin Liang, Jinzhi Lei","doi":"arxiv-2404.11761","DOIUrl":"https://doi.org/arxiv-2404.11761","url":null,"abstract":"Stem cell regeneration is a vital biological process in self-renewing\u0000tissues, governing development and tissue homeostasis. Gene regulatory network\u0000dynamics are pivotal in controlling stem cell regeneration and cell type\u0000transitions. However, integrating the quantitative dynamics of gene regulatory\u0000networks at the single-cell level with stem cell regeneration at the population\u0000level poses significant challenges. This study presents a computational\u0000framework connecting gene regulatory network dynamics with stem cell\u0000regeneration through a data-driven formulation of the inheritance function. The\u0000inheritance function captures epigenetic state transitions during cell division\u0000in heterogeneous stem cell populations. Our scheme allows the derivation of the\u0000inheritance function based on a hybrid model of cross-cell-cycle gene\u0000regulation network dynamics. The proposed scheme enables us to derive the\u0000inheritance function based on the hybrid model of cross-cell-cycle gene\u0000regulation network dynamics. By explicitly incorporating gene regulatory\u0000network structure, it replicates cross-cell-cycling gene regulation dynamics\u0000through individual-cell-based modeling. The numerical scheme holds the\u0000potential for extension to diverse gene regulatory networks, facilitating a\u0000deeper understanding of the connection between gene regulation dynamics and\u0000stem cell regeneration.","PeriodicalId":501325,"journal":{"name":"arXiv - QuanBio - Molecular Networks","volume":"10 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140626215","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Logic-dependent emergence of multistability, hysteresis, and biphasic dynamics in a minimal positive feedback network with an autoloop 带有自动回路的最小正反馈网络中出现的多稳定性、滞后和双相动态的逻辑依赖性

arXiv - QuanBio - Molecular Networks Pub Date : 2024-04-08 DOI: arxiv-2404.05379

Akriti Srivastava, Mubasher Rashid

{"title":"Logic-dependent emergence of multistability, hysteresis, and biphasic dynamics in a minimal positive feedback network with an autoloop","authors":"Akriti Srivastava, Mubasher Rashid","doi":"arxiv-2404.05379","DOIUrl":"https://doi.org/arxiv-2404.05379","url":null,"abstract":"Cellular decision-making (CDM) is a dynamic phenomenon often controlled by\u0000regulatory networks defining interactions between genes and transcription\u0000factor proteins. Traditional studies have focussed on molecular switches such\u0000as positive feedback circuits that exhibit at most bistability. However,\u0000higher-order dynamics such as tristability is also prominent in many biological\u0000processes. It is thus imperative to identify a minimal circuit that can alone\u0000explain mono, bi, and tristable dynamics. In this work, we consider a\u0000two-component positive feedback network with an autoloop and explore these\u0000regimes of stability for different degrees of multimerization and the choice of\u0000Boolean logic functions. We report that this network can exhibit numerous\u0000dynamical scenarios such as bi-and tristability, hysteresis, and biphasic\u0000kinetics, explaining the possibilities of abrupt cell state transitions and the\u0000smooth state swap without a step-like switch. Specifically, while with\u0000monomeric regulation and competitive OR logic, the circuit exhibits mono-and\u0000bistability and biphasic dynamics, with non-competitive AND and OR logics only\u0000monostability can be achieved. To obtain bistability in the latter cases, we\u0000show that the autoloop must have (at least) dimeric regulation. In pursuit of\u0000higher-order stability, we show that tristability occurs with higher degrees of\u0000multimerization and with non-competitive OR logic only. Our results, backed by\u0000rigorous analytical calculations and numerical examples, thus explain the\u0000association between multistability, multimerization, and logic in this minimal\u0000circuit. Since this circuit underlies various biological processes, including\u0000epithelial-mesenchymal transition which often drives carcinoma metastasis,\u0000these results can thus offer crucial inputs to control cell state transition by\u0000manipulating multimerization and the logic of regulation in cells.","PeriodicalId":501325,"journal":{"name":"arXiv - QuanBio - Molecular Networks","volume":"50 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140569138","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Chemical mass-action systems as analog computers: implementing arithmetic computations at specified speed 作为模拟计算机的化学质量作用系统：以特定速度进行算术计算

arXiv - QuanBio - Molecular Networks Pub Date : 2024-04-05 DOI: arxiv-2404.04396

David F. Anderson, Badal Joshi

{"title":"Chemical mass-action systems as analog computers: implementing arithmetic computations at specified speed","authors":"David F. Anderson, Badal Joshi","doi":"arxiv-2404.04396","DOIUrl":"https://doi.org/arxiv-2404.04396","url":null,"abstract":"Recent technological advances allow us to view chemical mass-action systems\u0000as analog computers. In this context, the inputs to a computation are encoded\u0000as initial values of certain chemical species while the outputs are the\u0000limiting values of other chemical species. In this paper, we design chemical\u0000systems that carry out the elementary arithmetic computations of:\u0000identification, inversion, $m$th roots (for $m ge 2$), addition,\u0000multiplication, absolute difference, rectified subtraction over non-negative\u0000real numbers, and partial real inversion over real numbers. We prove that these\u0000``elementary modules'' have a speed of computation that is independent of the\u0000inputs to the computation. Moreover, we prove that finite sequences of such\u0000elementary modules, running in parallel, can carry out composite arithmetic\u0000over real numbers, also at a rate that is independent of inputs. Furthermore,\u0000we show that the speed of a composite computation is precisely the speed of the\u0000slowest elementary step. Specifically, the scale of the composite computation,\u0000i.e. the number of elementary steps involved in the composite, does not affect\u0000the overall asymptotic speed -- a feature of the parallel computing nature of\u0000our algorithm. Our proofs require the careful mathematical analysis of certain\u0000non-autonomous systems, and we believe this analysis will be useful in\u0000different areas of applied mathematics, dynamical systems, and the theory of\u0000computation. We close with a discussion on future research directions,\u0000including numerous important open theoretical questions pertaining to the field\u0000of computation with reaction networks.","PeriodicalId":501325,"journal":{"name":"arXiv - QuanBio - Molecular Networks","volume":"56 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140569409","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Automated Inference of Graph Transformation Rules 图转换规则的自动推理

arXiv - QuanBio - Molecular Networks Pub Date : 2024-04-03 DOI: arxiv-2404.02692

Jakob L. Andersen, Akbar Davoodi, Rolf Fagerberg, Christoph Flamm, Walter Fontana, Juri Kolčák, Christophe V. F. P. Laurent, Daniel Merkle, Nikolai Nøjgaard

{"title":"Automated Inference of Graph Transformation Rules","authors":"Jakob L. Andersen, Akbar Davoodi, Rolf Fagerberg, Christoph Flamm, Walter Fontana, Juri Kolčák, Christophe V. F. P. Laurent, Daniel Merkle, Nikolai Nøjgaard","doi":"arxiv-2404.02692","DOIUrl":"https://doi.org/arxiv-2404.02692","url":null,"abstract":"The explosion of data available in life sciences is fueling an increasing\u0000demand for expressive models and computational methods. Graph transformation is\u0000a model for dynamic systems with a large variety of applications. We introduce\u0000a novel method of the graph transformation model construction, combining\u0000generative and dynamical viewpoints to give a fully automated data-driven model\u0000inference method. The method takes the input dynamical properties, given as a \"snapshot\" of the\u0000dynamics encoded by explicit transitions, and constructs a compatible model.\u0000The obtained model is guaranteed to be minimal, thus framing the approach as\u0000model compression (from a set of transitions into a set of rules). The\u0000compression is permissive to a lossy case, where the constructed model is\u0000allowed to exhibit behavior outside of the input transitions, thus suggesting a\u0000completion of the input dynamics. The task of graph transformation model inference is naturally highly\u0000challenging due to the combinatorics involved. We tackle the exponential\u0000explosion by proposing a heuristically minimal translation of the task into a\u0000well-established problem, set cover, for which highly optimized solutions\u0000exist. We further showcase how our results relate to Kolmogorov complexity\u0000expressed in terms of graph transformation.","PeriodicalId":501325,"journal":{"name":"arXiv - QuanBio - Molecular Networks","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140594500","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0