Building more accurate decision trees with the additive tree.

Abstract:

:The expansion of machine learning to high-stakes application domains such as medicine, finance, and criminal justice, where making informed decisions requires clear understanding of the model, has increased the interest in interpretable machine learning. The widely used Classification and Regression Trees (CART) have played a major role in health sciences, due to their simple and intuitive explanation of predictions. Ensemble methods like gradient boosting can improve the accuracy of decision trees, but at the expense of the interpretability of the generated model. Additive models, such as those produced by gradient boosting, and full interaction models, such as CART, have been investigated largely in isolation. We show that these models exist along a spectrum, revealing previously unseen connections between these approaches. This paper introduces a rigorous formalization for the additive tree, an empirically validated learning technique for creating a single decision tree, and shows that this method can produce models equivalent to CART or gradient boosted stumps at the extremes by varying a single parameter. Although the additive tree is designed primarily to provide both the model interpretability and predictive performance needed for high-stakes applications like medicine, it also can produce decision trees represented by hybrid models between CART and boosted stumps that can outperform either of these approaches.

authors

Luna JM,Gennatas ED,Ungar LH,Eaton E,Diffenderfer ES,Jensen ST,Simone CB 2nd,Friedman JH,Solberg TD,Valdes G

doi

10.1073/pnas.1816748116

subject

Has Abstract

pub_date

2019-10-01 00:00:00

pages

19887-19893

issue

40

eissn

0027-8424

issn

1091-6490

pii

1816748116

journal_volume

116

pub_type

杂志文章
  • Daisy-chain gene drives for the alteration of local populations.

    abstract::If they are able to spread in wild populations, CRISPR-based gene-drive elements would provide new ways to address ecological problems by altering the traits of wild organisms, but the potential for uncontrolled spread tremendously complicates ethical development and use. Here, we detail a self-exhausting form of CRIS...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1716358116

    authors: Noble C,Min J,Olejarz J,Buchthal J,Chavez A,Smidler AL,DeBenedictis EA,Church GM,Nowak MA,Esvelt KM

    更新日期:2019-04-23 00:00:00

  • Interleukin 1 participates in the development of anti-Listeria responses in normal and SCID mice.

    abstract::Using T- and B-cell deficient C.B-17 mice with the scid mutation, we have previously documented the existence of a T-cell-independent but interferon gamma-dependent pathway of macrophage activation that confers upon the host partial resistance to the facultative intracellular bacterium Listeria monocytogenes. This pat...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.89.3.1011

    authors: Rogers HW,Sheehan KC,Brunt LM,Dower SK,Unanue ER,Schreiber RD

    更新日期:1992-02-01 00:00:00

  • Brain-wide structural and functional disruption in mice with oligodendrocyte-specific Nf1 deletion is rescued by inhibition of nitric oxide synthase.

    abstract::Neurofibromin gene (NF1) mutation causes neurofibromatosis type 1 (NF1), a disorder in which brain white matter deficits identified by neuroimaging are common, yet of unknown cellular etiology. In mice, Nf1 loss in adult oligodendrocytes causes myelin decompaction and increases oligodendrocyte nitric oxide (NO) levels...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.2008391117

    authors: Asleh J,Shofty B,Cohen N,Kavushansky A,López-Juárez A,Constantini S,Ratner N,Kahn I

    更新日期:2020-09-08 00:00:00

  • Functional coupling of Ca2+ channels and ryanodine receptors in cardiac myocytes.

    abstract::In skeletal muscle, dihydropyridine receptors are functionally coupled to ryanodine receptors of the sarcoplasmic reticulum in triadic or diadic junctional complexes. In cardiac muscle direct physical or functional couplings have not been demonstrated. We have tested the hypothesis of functional coupling of L-type Ca2...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.92.1.121

    authors: Sham JS,Cleemann L,Morad M

    更新日期:1995-01-03 00:00:00

  • Racemization as a stereochemical measure of dynamics and robustness in shape-shifting organic molecules.

    abstract::Bullvalene is a structurally unique dynamic molecule thought to interconvert among 1.2 million degenerate isomers. The incorporation of different chemical substituents onto the bullvalene core should lead to a "shape-shifting" molecule that can interconvert among thousands of discrete structural isomers. Previous NMR ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1108170108

    authors: He M,Bode JW

    更新日期:2011-09-06 00:00:00

  • KCNE1 and KCNE3 modulate KCNQ1 channels by affecting different gating transitions.

    abstract::KCNE β-subunits assemble with and modulate the properties of voltage-gated K+ channels. In the heart, KCNE1 associates with the α-subunit KCNQ1 to generate the slowly activating, voltage-dependent potassium current (IKs) in the heart that controls the repolarization phase of cardiac action potentials. By contrast, in ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1710335114

    authors: Barro-Soria R,Ramentol R,Liin SI,Perez ME,Kass RS,Larsson HP

    更新日期:2017-08-29 00:00:00

  • Intraprotomer masking of third variable loop (V3) epitopes by the first and second variable loops (V1V2) within the native HIV-1 envelope glycoprotein trimer.

    abstract::Within the trimeric HIV-1 envelope (Env) spike, the first and second variable loops (V1V2 region) and the third variable loop (V3) of the gp120 subunit play dual roles in antibody recognition, because they contain neutralization epitopes and also participate in epitope masking. The spatial relationships between V1V2 a...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1104840108

    authors: Liu L,Cimbro R,Lusso P,Berger EA

    更新日期:2011-12-13 00:00:00

  • The fatal fungal outbreak on Vancouver Island is characterized by enhanced intracellular parasitism driven by mitochondrial regulation.

    abstract::In 1999, the population of Vancouver Island, Canada, began to experience an outbreak of a fatal fungal disease caused by a highly virulent lineage of Cryptococcus gattii. This organism has recently spread to the Canadian mainland and Pacific Northwest, but the molecular cause of the outbreak remains unknown. Here we s...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0902963106

    authors: Ma H,Hagen F,Stekel DJ,Johnston SA,Sionov E,Falk R,Polacheck I,Boekhout T,May RC

    更新日期:2009-08-04 00:00:00

  • Paleogenomics of echinoids reveals an ancient origin for the double-negative specification of micromeres in sea urchins.

    abstract::Establishing a timeline for the evolution of novelties is a common, unifying goal at the intersection of evolutionary and developmental biology. Analyses of gene regulatory networks (GRNs) provide the ability to understand the underlying genetic and developmental mechanisms responsible for the origin of morphological ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1610603114

    authors: Thompson JR,Erkenbrack EM,Hinman VF,McCauley BS,Petsios E,Bottjer DJ

    更新日期:2017-06-06 00:00:00

  • Photoperiod and temperature separately regulate nymphal development through JH and insulin/TOR signaling pathways in an insect.

    abstract::Insects living in the temperate zone enter a physiological state of arrested or slowed development to overcome an adverse season, such as winter. Developmental arrest, called diapause, occurs at a species-specific developmental stage, and embryonic and pupal diapauses have been extensively studied in mostly holometabo...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1922747117

    authors: Miki T,Shinohara T,Chafino S,Noji S,Tomioka K

    更新日期:2020-03-10 00:00:00

  • 14-3-3 proteins associate with cdc25 phosphatases.

    abstract::The cdc25 phosphatases play key roles in cell cycle progression by activating cyclin-dependent kinases. Two members of the 14-3-3 protein family have been isolated in a yeast two-hybrid screen designed to identify proteins that interact with the human cdc25A and cdc25B phosphatases. Genes encoding the human homolog of...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.92.17.7892

    authors: Conklin DS,Galaktionov K,Beach D

    更新日期:1995-08-15 00:00:00

  • Murine leukemia virus morphogenesis: cleavage of P70 in vitro can be accompanied by a shift from a concentrically coiled internal strand ("immature") to a collapsed ("mature") form of the virus core.

    abstract::Disruption of Rauscher leukemia virus (RLV) with low levels of Nonidet P-40 yielded "immature" cores. These cores have a diameter of about 920 A, as opposed to the 1300-A diameter of RLV, possess knob-like protuberances, and contain a concentrically coiled internal strand apposed to the core shell. The two major polyp...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.74.8.3446

    authors: Yoshinaka Y,Luftig RB

    更新日期:1977-08-01 00:00:00

  • Epstein-Barr virus co-opts TFIIH component XPB to specifically activate essential viral lytic promoters.

    abstract::Epstein-Barr virus (EBV) is associated with epithelial and lymphoid malignancies, establishes latent infection in memory B cells, and intermittently produces infectious virions through lytic replication. Released virions play a key role in latent reservoir maintenance and transmission. Lytic EBV transcription differs ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.2000625117

    authors: Verma D,Church TM,Swaminathan S

    更新日期:2020-06-09 00:00:00

  • Maximum leaf conductance driven by CO2 effects on stomatal size and density over geologic time.

    abstract::Stomatal pores are microscopic structures on the epidermis of leaves formed by 2 specialized guard cells that control the exchange of water vapor and CO(2) between plants and the atmosphere. Stomatal size (S) and density (D) determine maximum leaf diffusive (stomatal) conductance of CO(2) (g(c(max))) to sites of assim...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0904209106

    authors: Franks PJ,Beerling DJ

    更新日期:2009-06-23 00:00:00

  • A mutation in the alpha 3 chain of type IX collagen causes autosomal dominant multiple epiphyseal dysplasia with mild myopathy.

    abstract::Multiple epiphyseal dysplasia (MED) is a degenerative cartilage condition shown in some cases to be caused by mutations in genes encoding cartilage oligomeric matrix protein or type IX collagen. We studied a family with autosomal dominant MED affecting predominantly the knee joints and a mild proximal myopathy. Geneti...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.97.3.1212

    authors: Bönnemann CG,Cox GF,Shapiro F,Wu JJ,Feener CA,Thompson TG,Anthony DC,Eyre DR,Darras BT,Kunkel LM

    更新日期:2000-02-01 00:00:00

  • Histone H3K27 methyltransferase Ezh2 represses Wnt genes to facilitate adipogenesis.

    abstract::Wnt/beta-catenin signaling inhibits adipogenesis. Genome-wide profiling studies have revealed the enrichment of histone H3K27 methyltransferase Ezh2 on Wnt genes. However, the functional significance of such a direct link between the two types of developmental regulators in mammalian cells, and the role of Ezh2 in adi...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1000031107

    authors: Wang L,Jin Q,Lee JE,Su IH,Ge K

    更新日期:2010-04-20 00:00:00

  • In vitro modulation of antigen-primed T cells by a glycosylation-inhibiting factor that regulates the formation of antigen-specific suppressive factors.

    abstract::BDF1 [(C57BL/6 X DBA/2)F1] mice were primed with alum-absorbed ovalbumin, and their spleen cells were cultured with ovalbumin to activate antigen-primed T cells. The activated T cells were then propagated in interleukin 2-containing medium in the presence or absence of affinity-purified glycosylation-inhibiting factor...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.84.8.2444

    authors: Iwata M,Ishizaka K

    更新日期:1987-04-01 00:00:00

  • Photosynthetic electron partitioning between [FeFe]-hydrogenase and ferredoxin:NADP+-oxidoreductase (FNR) enzymes in vitro.

    abstract::Photosynthetic water splitting, coupled to hydrogenase-catalyzed hydrogen production, is considered a promising clean, renewable source of energy. It is widely accepted that the oxygen sensitivity of hydrogen production, combined with competition between hydrogenases and NADPH-dependent carbon dioxide fixation are the...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1103659108

    authors: Yacoby I,Pochekailov S,Toporik H,Ghirardi ML,King PW,Zhang S

    更新日期:2011-06-07 00:00:00

  • Mesolimbic neuropeptide W coordinates stress responses under novel environments.

    abstract::Neuropeptide B (NPB) and neuropeptide W (NPW) are endogenous neuropeptide ligands for the G protein-coupled receptors NPBWR1 and NPBWR2. Here we report that the majority of NPW neurons in the mesolimbic region possess tyrosine hydroxylase immunoreactivity, indicating that a small subset of dopaminergic neurons coexpre...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1518658113

    authors: Motoike T,Long JM,Tanaka H,Sinton CM,Skach A,Williams SC,Hammer RE,Sakurai T,Yanagisawa M

    更新日期:2016-05-24 00:00:00

  • Ligand-directed retroviral targeting of human breast cancer cells.

    abstract::We explored the feasibility of designing retroviral vectors that can target human breast cancer cells with characteristic receptors via ligand-receptor interaction. The ecotropic Moloney murine leukemia virus envelope was modified by insertion of sequences encoding human heregulin. Ecotropic virus, which normally does...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.92.21.9747

    authors: Han X,Kasahara N,Kan YW

    更新日期:1995-10-10 00:00:00

  • HLA-C is the inhibitory ligand that determines dominant resistance to lysis by NK1- and NK2-specific natural killer cells.

    abstract::Natural killer (NK) cells recognize alloantigens on normal cells. One of these alloantigens correlates with homozygosity for a dimorphism of HLA-C at positions 77-80, which is shared by a number of HLA-C alleles. A second allelic alloantigen correlates with homozygosity for the alternative HLA-C dimorphism, which is s...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.90.24.12000

    authors: Colonna M,Borsellino G,Falco M,Ferrara GB,Strominger JL

    更新日期:1993-12-15 00:00:00

  • Controllability analysis of the directed human protein interaction network identifies disease genes and drug targets.

    abstract::The protein-protein interaction (PPI) network is crucial for cellular information processing and decision-making. With suitable inputs, PPI networks drive the cells to diverse functional outcomes such as cell proliferation or cell death. Here, we characterize the structural controllability of a large directed human PP...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1603992113

    authors: Vinayagam A,Gibson TE,Lee HJ,Yilmazel B,Roesel C,Hu Y,Kwon Y,Sharma A,Liu YY,Perrimon N,Barabási AL

    更新日期:2016-05-03 00:00:00

  • Recombinant human respiratory syncytial virus (RSV) monoclonal antibody Fab is effective therapeutically when introduced directly into the lungs of RSV-infected mice.

    abstract::Previously, recombinant human respiratory syncytial virus (RSV) monoclonal antibody Fabs were generated by antigen selection from random combinatorial libraries displayed at the tip of filamentous phage. Two such Fabs, which exhibited high binding affinity for RSV F glycoprotein (a major protective antigen), were eval...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.91.4.1386

    authors: Crowe JE Jr,Murphy BR,Chanock RM,Williamson RA,Barbas CF 3rd,Burton DR

    更新日期:1994-02-15 00:00:00

  • Molecular codes for cell type specification in Brn3 retinal ganglion cells.

    abstract::Visual information is conveyed from the eye to the brain by distinct types of retinal ganglion cells (RGCs). It is largely unknown how RGCs acquire their defining morphological and physiological features and connect to upstream and downstream synaptic partners. The three Brn3/Pou4f transcription factors (TFs) particip...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1618551114

    authors: Sajgo S,Ghinia MG,Brooks M,Kretschmer F,Chuang K,Hiriyanna S,Wu Z,Popescu O,Badea TC

    更新日期:2017-05-16 00:00:00

  • spoT-dependent accumulation of guanosine tetraphosphate in response to fatty acid starvation in Escherichia coli.

    abstract::We previously isolated a mutant of Escherichia coli that is preferentially affected in the synthesis of rRNA and has a mutation in the gene (accD) encoding a subunit of acetyl-CoA carboxylase. Using this mutant and other mutants of the pathway for fatty acid and phospholipid biosynthesis as well as cerulenin, a specif...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.90.23.11004

    authors: Seyfzadeh M,Keener J,Nomura M

    更新日期:1993-12-01 00:00:00

  • Impact and cost-effectiveness of new tuberculosis vaccines in low- and middle-income countries.

    abstract::To help reach the target of tuberculosis (TB) disease elimination by 2050, vaccine development needs to occur now. We estimated the impact and cost-effectiveness of potential TB vaccines in low- and middle-income countries using an age-structured transmission model. New vaccines were assumed to be available in 2024, t...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1404386111

    authors: Knight GM,Griffiths UK,Sumner T,Laurence YV,Gheorghe A,Vassall A,Glaziou P,White RG

    更新日期:2014-10-28 00:00:00

  • PD134308, a selective antagonist of cholecystokinin type B receptor, enhances the analgesic effect of morphine and synergistically interacts with intrathecal galanin to depress spinal nociceptive reflexes.

    abstract::The effects of systemic PD134308 [0.1-3 mg/kg; an antagonist of the cholecystokinin (CCK) type B receptor], morphine, and intrathecal (i.t.) galanin (GAL) on the excitability of the spinal nociceptive flexor reflex and in the hot plate test were examined in rats. PD134308 caused a weak naloxone-reversible depression o...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.87.18.7105

    authors: Wiesenfeld-Hallin Z,Xu XJ,Hughes J,Horwell DC,Hökfelt T

    更新日期:1990-09-01 00:00:00

  • Antagonistic gene transcripts regulate adaptation to new growth environments.

    abstract::Cells have evolved complex regulatory networks that reorganize gene expression patterns in response to changing environmental conditions. These changes often involve redundant mechanisms that affect various levels of gene expression. Here, we examine the consequences of enhanced mRNA degradation in the galactose utili...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1111408109

    authors: Baumgartner BL,Bennett MR,Ferry M,Johnson TL,Tsimring LS,Hasty J

    更新日期:2011-12-27 00:00:00

  • Conformational change and enhanced stabilization of the vitamin D receptor by the 1,25-dihydroxyvitamin D3 analog KH1060.

    abstract::The 1,25-dihydroxyvitamin D3 [1,25-(OH)2vitamin D3] analog KH1060 exerts very potent effects on cell proliferation and cell differentiation via the vitamin D receptor (VDR). However, the activities of KH1060 are not associated with an increased affinity for the VDR. We now show that increased stabilization of the VDR-...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.93.20.10685

    authors: van den Bemd GC,Pols HA,Birkenhäger JC,van Leeuwen JP

    更新日期:1996-10-01 00:00:00

  • Analogues of diadenosine 5',5'''-P1,P4-tetraphosphate (Ap4A) as potential anti-platelet-aggregation agents.

    abstract::Dense granules of platelets contain a high content of diadenosine 5',5'''-P1,P4-tetraphosphate (Ap4A). We have previously demonstrated an antithrombotic effect of this compound in a live rabbit model. In the present study we find that certain synthetic Ap4A analogues are superior to Ap4A in inhibiting ADP-induced aggr...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.89.6.2370

    authors: Zamecnik PC,Kim B,Gao MJ,Taylor G,Blackburn GM

    更新日期:1992-03-15 00:00:00