\begin{algorithm}
\caption{The Queue Shuffle }  \label{algo:qs}
\begin{algorithmic}[1]
\Require $\mathcal{T}$ \Comment{Current Tree}
\Require $\mathcal{N} = \{\nu_0,\nu_1,...\}$ \Comment{set of all non-root nodes}
\State $Q = [\nu_0,\nu_1]$ \Comment{"queue" of nodes to process}
\State $L = \{\nu_0 : 0, \nu_1 : 1\}$ \Comment{node:label mapping}
\State $l_{\text{next}} = 2$\Comment{next available label}
\State $P = []$ \Comment{processed nodes}
\While{$Q \neq []$}
\State $\nu = Q[0]$ \Comment{node to process}
\State Q = Q[1:] \Comment{$\nu$ will be processed}
\State $\text{append}(P,\nu)$ \Comment{$\nu$ will be processed}
\If{$\text{isLeaf}(\nu)$}
\State \textbf{continue} \Comment{move to next node}
\EndIf
\State $a,b = \text{randChildren}(\nu)$ \Comment{get \textbf{randomly ordered} children of $\nu$}
\State $L[a] = L[\nu]$ \Comment{label $a$ with $\nu$'s label}
\State $L[b] =  l_{\text{next}}$ \Comment{give $b$ next available label}
\State  $l_{\text{next}} =  l_{\text{next}} +1$
\State append($Q,a$) \Comment{add $a$ to the queue}
\State append$(Q,b)$ \Comment{add $b$ to the queue}
\EndWhile
\State \text{{Return }} $L$ \Comment{Ordering determined by values of $L$ for leaf nodes}
\end{algorithmic}
\end{algorithm}

\begin{algorithm}
\caption{The Queue Shuffle } \begin{algorithmic}
[1]
\Require $\mathcal{T}$ \Comment{Current Tree}
\Require $\mathcal{N} = \{\nu_0,\nu_1,...\}$ \Comment{set of all non-root nodes}
\State $Q = [\nu_0,\nu_1]$ \Comment{"queue" of nodes to process}
\State $L = \{\nu_0 : 0, \nu_1 : 1\}$ \Comment{node:label mapping}
\State $l_{\text{next}} = 2$\Comment{next available label}
\State $P = []$ \Comment{processed nodes}
\While{$Q \neq []$}
\State $\nu = Q[0]$ \Comment{node to process}
\State Q = Q[1:] \Comment{$\nu$ will be processed}
\State $\text{append}(P,\nu)$ \Comment{$\nu$ will be processed}
\If{$\text{isLeaf}(\nu)$}
\State \textbf{continue} \Comment{move to next node}
\EndIf
\State $a,b = \text{randChildren}(\nu)$ \Comment{get \textbf{randomly ordered} children of $\nu$}
\State $L[a] = L[\nu]$ \Comment{label $a$ with $\nu$'s label}
\State $L[b] = l_{\text{next}}$ \Comment{give $b$ next available label}
\State $l_{\text{next}} = l_{\text{next}} +1$
\State append($Q,a$) \Comment{add $a$ to the queue}
\State append$(Q,b)$ \Comment{add $b$ to the queue}
\EndWhile
\State \text{{Return }} $L$ \Comment{Ordering determined by values of $L$ for leaf nodes}
\end{algorithmic}
\end{algorithm}
{
    "title": "leaping through tree space: continuous phylogenetic inference for rooted   and unrooted trees",
    "id": "2306.05739",
    "abstract": "phylogenetics is now fundamental in life sciences, providing insights into the earliest branches of life and the origins and spread of epidemics. however, finding suitable phylogenies from the vast space of possible trees remains challenging. to address this problem, for the first time, we perform both tree exploration and inference in a continuous space where the computation of gradients is possible. this continuous relaxation allows for major leaps across tree space in both rooted and unrooted trees, and is less susceptible to convergence to local minima. our approach outperforms the current best methods for inference on unrooted trees and, in simulation, accurately infers the tree and root in ultrametric cases. the approach is effective in cases of empirical data with negligible amounts of data, which we demonstrate on the phylogeny of jawed vertebrates. indeed, only a few genes with an ultrametric signal were generally sufficient for resolving the major lineages of vertebrates. optimisation is possible via automatic differentiation and our method presents an effective way forwards for exploring the most difficult, data-deficient phylogenetic questions.",
    "categories": "q-bio.pe cs.lg",
    "doi": "10.1093/gbe/evad213",
    "created": "2023-06-09",
    "updated": "2024-01-23",
    "authors": [
        "matthew j penn",
        "neil scheidwasser",
        "joseph penn",
        "christl a donnelly",
        "david a duch\u00eane",
        "samir bhatt"
    ],
    "affiliation": [],
    "url": "https://arxiv.org/abs/2306.05739"
}
{
    "ToxicityFilter": {
        "text_to_toxicity_attributes": {
            "tab/table1_new.tex": {
                "toxicity_score": 0.011058134,
                "severe_toxicity_score": 0.0014781952,
                "identity_attack_score": 0.0034408006,
                "insult_score": 0.0073798755,
                "profanity_score": 0.016957775,
                "threat_score": 0.0074306927,
                "sexually_explicit_score": 0.014744292,
                "flirtation_score": 0.30222267
            },
            "05_new.tex": {
                "toxicity_score": 0.016712861,
                "severe_toxicity_score": 0.0011348724,
                "identity_attack_score": 0.0036627878,
                "insult_score": 0.00819688,
                "profanity_score": 0.017231047,
                "threat_score": 0.007637825,
                "sexually_explicit_score": 0.013859635,
                "flirtation_score": 0.4380761
            },
            "00_merge.bbl": {
                "toxicity_score": 0.017843807,
                "severe_toxicity_score": 0.0013160706,
                "identity_attack_score": 0.00362579,
                "insult_score": 0.009374888,
                "profanity_score": 0.017299367,
                "threat_score": 0.00746953,
                "sexually_explicit_score": 0.013800657,
                "flirtation_score": 0.47433925
            },
            "old/06_Discussion.tex": {
                "toxicity_score": 0.021432023,
                "severe_toxicity_score": 0.0012159348,
                "identity_attack_score": 0.0039957687,
                "insult_score": 0.009450888,
                "profanity_score": 0.014293353,
                "threat_score": 0.008375733,
                "sexually_explicit_score": 0.01102873,
                "flirtation_score": 0.23011881
            },
            "diff/04_diff.tex": {
                "toxicity_score": 0.019226074,
                "severe_toxicity_score": 0.0012969971,
                "identity_attack_score": 0.007288578,
                "insult_score": 0.008576883,
                "profanity_score": 0.017231047,
                "threat_score": 0.008349842,
                "sexually_explicit_score": 0.016159745,
                "flirtation_score": 0.32601726
            },
            "References.bib": {
                "toxicity_score": 0.012880214,
                "severe_toxicity_score": 0.002822876,
                "identity_attack_score": 0.0018313939,
                "insult_score": 0.007892879,
                "profanity_score": 0.017709278,
                "threat_score": 0.0062137907,
                "sexually_explicit_score": 0.021703599,
                "flirtation_score": 0.2261802
            },
            "diff/05_diff.tex": {
                "toxicity_score": 0.016712861,
                "severe_toxicity_score": 0.0011348724,
                "identity_attack_score": 0.0036627878,
                "insult_score": 0.00819688,
                "profanity_score": 0.017231047,
                "threat_score": 0.007637825,
                "sexually_explicit_score": 0.013859635,
                "flirtation_score": 0.4380761
            },
            "fig/figS1_new.tex": {
                "toxicity_score": 0.012063419,
                "severe_toxicity_score": 0.00166893,
                "identity_attack_score": 0.0032003147,
                "insult_score": 0.0075888764,
                "profanity_score": 0.019758832,
                "threat_score": 0.0069905366,
                "sexually_explicit_score": 0.018282922,
                "flirtation_score": 0.26782113
            },
            "fig/fig3_new.tex": {
                "toxicity_score": 0.012063419,
                "severe_toxicity_score": 0.00166893,
                "identity_attack_score": 0.0032003147,
                "insult_score": 0.0075888764,
                "profanity_score": 0.019758832,
                "threat_score": 0.0069905366,
                "sexually_explicit_score": 0.018282922,
                "flirtation_score": 0.26782113
            },
            "fig/figS2_new.tex": {
                "toxicity_score": 0.018849092,
                "severe_toxicity_score": 0.0020503998,
                "identity_attack_score": 0.0039772694,
                "insult_score": 0.009165886,
                "profanity_score": 0.021876704,
                "threat_score": 0.007870848,
                "sexually_explicit_score": 0.018518832,
                "flirtation_score": 0.26668414
            },
            "old/04_Methods.tex": {
                "toxicity_score": 0.012566062,
                "severe_toxicity_score": 0.0009727478,
                "identity_attack_score": 0.0046987277,
                "insult_score": 0.0074368757,
                "profanity_score": 0.014839902,
                "threat_score": 0.00789674,
                "sexually_explicit_score": 0.012149297,
                "flirtation_score": 0.3866249
            },
            "old/05_Results.tex": {
                "toxicity_score": 0.016712861,
                "severe_toxicity_score": 0.0011348724,
                "identity_attack_score": 0.0036627878,
                "insult_score": 0.00819688,
                "profanity_score": 0.017231047,
                "threat_score": 0.007637825,
                "sexually_explicit_score": 0.013859635,
                "flirtation_score": 0.4380761
            },
            "fig/fig2_new.tex": {
                "toxicity_score": 0.012063419,
                "severe_toxicity_score": 0.00166893,
                "identity_attack_score": 0.0032003147,
                "insult_score": 0.0075888764,
                "profanity_score": 0.019758832,
                "threat_score": 0.0069905366,
                "sexually_explicit_score": 0.018282922,
                "flirtation_score": 0.26782113
            },
            "orcidlink.sty": {
                "toxicity_score": 0.02249265,
                "severe_toxicity_score": 0.0015640259,
                "identity_attack_score": 0.0035147965,
                "insult_score": 0.010096892,
                "profanity_score": 0.018734055,
                "threat_score": 0.007974415,
                "sexually_explicit_score": 0.014508383,
                "flirtation_score": 0.5118947
            },
            "02bis_Significance.tex": {
                "toxicity_score": 0.015267765,
                "severe_toxicity_score": 0.0009822845,
                "identity_attack_score": 0.004587734,
                "insult_score": 0.0074368757,
                "profanity_score": 0.01265371,
                "threat_score": 0.0071199946,
                "sexually_explicit_score": 0.008669644,
                "flirtation_score": 0.21362288
            },
            "old/table2.tex": {
                "toxicity_score": 0.011058134,
                "severe_toxicity_score": 0.0014781952,
                "identity_attack_score": 0.0034408006,
                "insult_score": 0.0073798755,
                "profanity_score": 0.016957775,
                "threat_score": 0.0074306927,
                "sexually_explicit_score": 0.014744292,
                "flirtation_score": 0.30222267
            },
            "diff/03_diff.tex": {
                "toxicity_score": 0.044388983,
                "severe_toxicity_score": 0.005760193,
                "identity_attack_score": 0.011173353,
                "insult_score": 0.015416925,
                "profanity_score": 0.04065997,
                "threat_score": 0.0103175985,
                "sexually_explicit_score": 0.04804322,
                "flirtation_score": 0.3224956
            },
            "04_new.tex": {
                "toxicity_score": 0.013508516,
                "severe_toxicity_score": 0.00093460083,
                "identity_attack_score": 0.0052166977,
                "insult_score": 0.007968879,
                "profanity_score": 0.013234417,
                "threat_score": 0.0073789097,
                "sexually_explicit_score": 0.011795434,
                "flirtation_score": 0.26738107
            },
            "tab/table2_new.tex": {
                "toxicity_score": 0.011058134,
                "severe_toxicity_score": 0.0014781952,
                "identity_attack_score": 0.0034408006,
                "insult_score": 0.0073798755,
                "profanity_score": 0.016957775,
                "threat_score": 0.0074306927,
                "sexually_explicit_score": 0.014744292,
                "flirtation_score": 0.30222267
            },
            "diff/Appendix_diff.tex": {
                "toxicity_score": 0.008859074,
                "severe_toxicity_score": 0.001077652,
                "identity_attack_score": 0.002626848,
                "insult_score": 0.0067433715,
                "profanity_score": 0.014669105,
                "threat_score": 0.0071070488,
                "sexually_explicit_score": 0.012680092,
                "flirtation_score": 0.21909615
            },
            "old/03_Introduction.tex": {
                "toxicity_score": 0.014765122,
                "severe_toxicity_score": 0.0013160706,
                "identity_attack_score": 0.0058456613,
                "insult_score": 0.007911879,
                "profanity_score": 0.015557245,
                "threat_score": 0.007922632,
                "sexually_explicit_score": 0.013977589,
                "flirtation_score": 0.24788079
            },
            "fig/fig1_new.tex": {
                "toxicity_score": 0.012063419,
                "severe_toxicity_score": 0.00166893,
                "identity_attack_score": 0.0032003147,
                "insult_score": 0.0075888764,
                "profanity_score": 0.019758832,
                "threat_score": 0.0069905366,
                "sexually_explicit_score": 0.018282922,
                "flirtation_score": 0.26782113
            },
            "02_Abstract.tex": {
                "toxicity_score": 0.013320025,
                "severe_toxicity_score": 0.00081062317,
                "identity_attack_score": 0.004088263,
                "insult_score": 0.0070948736,
                "profanity_score": 0.011782649,
                "threat_score": 0.007094103,
                "sexually_explicit_score": 0.007961918,
                "flirtation_score": 0.26731902
            },
            "03_new.tex": {
                "toxicity_score": 0.013822667,
                "severe_toxicity_score": 0.0011587143,
                "identity_attack_score": 0.0050317086,
                "insult_score": 0.007645877,
                "profanity_score": 0.014498309,
                "threat_score": 0.0076119336,
                "sexually_explicit_score": 0.013859635,
                "flirtation_score": 0.25467622
            },
            "minted-cache/default.pygstyle": {
                "toxicity_score": 0.032391842,
                "severe_toxicity_score": 0.002708435,
                "identity_attack_score": 0.006622616,
                "insult_score": 0.013440913,
                "profanity_score": 0.027000591,
                "threat_score": 0.010369381,
                "sexually_explicit_score": 0.028898813,
                "flirtation_score": 0.3184096
            },
            "minted-cache/listing1.pygtex": {
                "toxicity_score": 0.0076338826,
                "severe_toxicity_score": 0.0013542175,
                "identity_attack_score": 0.001655654,
                "insult_score": 0.00654387,
                "profanity_score": 0.016616182,
                "threat_score": 0.0062849927,
                "sexually_explicit_score": 0.0136827035,
                "flirtation_score": 0.31068373
            },
            "diff/06_diff.tex": {
                "toxicity_score": 0.021432023,
                "severe_toxicity_score": 0.0012159348,
                "identity_attack_score": 0.0039957687,
                "insult_score": 0.009450888,
                "profanity_score": 0.014293353,
                "threat_score": 0.008375733,
                "sexually_explicit_score": 0.01102873,
                "flirtation_score": 0.23011881
            },
            "01_main.tex": {
                "toxicity_score": 0.008733413,
                "severe_toxicity_score": 0.0008916855,
                "identity_attack_score": 0.0023678627,
                "insult_score": 0.007493876,
                "profanity_score": 0.013234417,
                "threat_score": 0.006835188,
                "sexually_explicit_score": 0.009908165,
                "flirtation_score": 0.2653076
            },
            "06_new.tex": {
                "toxicity_score": 0.021432023,
                "severe_toxicity_score": 0.0012159348,
                "identity_attack_score": 0.0039957687,
                "insult_score": 0.009450888,
                "profanity_score": 0.014293353,
                "threat_score": 0.008375733,
                "sexually_explicit_score": 0.01102873,
                "flirtation_score": 0.23011881
            },
            "mbe.bst": {
                "toxicity_score": 0.10609736,
                "severe_toxicity_score": 0.005569458,
                "identity_attack_score": 0.030433474,
                "insult_score": 0.02618698,
                "profanity_score": 0.07223598,
                "threat_score": 0.02613456,
                "sexually_explicit_score": 0.057760242,
                "flirtation_score": 0.30470067
            },
            "old/Appendix.tex": {
                "toxicity_score": 0.008859074,
                "severe_toxicity_score": 0.001077652,
                "identity_attack_score": 0.002626848,
                "insult_score": 0.0067433715,
                "profanity_score": 0.014669105,
                "threat_score": 0.0071070488,
                "sexually_explicit_score": 0.012680092,
                "flirtation_score": 0.21909615
            },
            "00_merge.tex": {
                "toxicity_score": 0.028620722,
                "severe_toxicity_score": 0.0015830994,
                "identity_attack_score": 0.004384246,
                "insult_score": 0.012034904,
                "profanity_score": 0.017367685,
                "threat_score": 0.008349842,
                "sexually_explicit_score": 0.016513607,
                "flirtation_score": 0.40547138
            },
            "fig/figS3_new.tex": {
                "toxicity_score": 0.012063419,
                "severe_toxicity_score": 0.00166893,
                "identity_attack_score": 0.0032003147,
                "insult_score": 0.0075888764,
                "profanity_score": 0.019758832,
                "threat_score": 0.0069905366,
                "sexually_explicit_score": 0.018282922,
                "flirtation_score": 0.26782113
            },
            "Appendix_new.tex": {
                "toxicity_score": 0.008859074,
                "severe_toxicity_score": 0.001077652,
                "identity_attack_score": 0.002626848,
                "insult_score": 0.0067433715,
                "profanity_score": 0.014669105,
                "threat_score": 0.0071070488,
                "sexually_explicit_score": 0.012680092,
                "flirtation_score": 0.21909615
            },
            "bioRxiv.cls": {
                "toxicity_score": 0.015833238,
                "severe_toxicity_score": 0.0014019012,
                "identity_attack_score": 0.0039587705,
                "insult_score": 0.008044879,
                "profanity_score": 0.01535229,
                "threat_score": 0.007754337,
                "sexually_explicit_score": 0.01209032,
                "flirtation_score": 0.3940294
            }
        },
        "reason": null
    }
}
{
    "num_done": {
        "figure": 0,
        "algorithm": 2,
        "plot": 0
    }
}
{
    "NonTrivialRenderingFilter": {
        "white_pixels_ratio": 92.10342417889588,
        "hash": "387c3c3c3f383c3c",
        "most_frequent_color_ratio": 92.10342417889588
    }
}