Professional Education


  • Bachelor of Science, Politecnico Di Milano (2009)
  • Master of Science, Universita Degli Studi Di Milano (2012)
  • Doctor of Philosophy, Universita Degli Studi Di Milano (2016)

Stanford Advisors


All Publications


  • Withholding or withdrawing invasive interventions may not accelerate time to death among dying ICU patients. PloS one Ramazzotti, D., Clardy, P., Celi, L. A., Stone, D. J., Rudin, R. S. 2019; 14 (2): e0212439

    Abstract

    BACKGROUND: Critically ill patients may die despite invasive intervention. In this study, we examine trends in the application of two such treatments over a decade, namely, endotracheal ventilation and vasopressors and inotropes administration, as well as the impact of these trends on survival durations in patients who die within a month of ICU admission.METHODS: We considered observational data available from the MIMIC-III open-access ICU database and collected within a study period between year 2002 up to 2011. If a patient had multiple admissions to the ICU during the 30 days before death, only the first stay was analyzed, leading to a final set of 6,436 unique ICU admissions during the study period. We tested two hypotheses: (i) administration of invasive intervention during the ICU stay immediately preceding end-of-life would decrease over the study time period and (ii) time-to-death from ICU admission would also decrease, due to the decrease in invasive intervention administration. To investigate the latter hypothesis, we performed a subgroups analysis by considering patients with lowest and highest severity. To do so, we stratified the patients based on their SAPS I scores, and we considered patients within the first and the third tertiles of the score. We then assessed differences in trends within these groups between years 2002-05 vs. 2008-11.RESULTS: Comparing the period 2002-2005 vs. 2008-2011, we found a reduction in endotracheal ventilation among patients who died within 30 days of ICU admission (120.8 vs. 68.5 hours for the lowest severity patients, p<0.001; 47.7 vs. 46.0 hours for the highest severity patients, p = 0.004). This is explained in part by an increase in the use of non-invasive ventilation. Comparing the period 2002-2005 vs. 2008-2011, we found a reduction in the use of vasopressors and inotropes among patients with the lowest severity who died within 30 days of ICU admission (41.8 vs. 36.2 hours, p<0.001) but not among those with the highest severity. Despite a reduction in the use of invasive interventions, we did not find a reduction in the time to death between 2002-2005 vs. 2008-2011 (7.8 days vs. 8.2 days for the lowest severity patients, p = 0.32; 2.1 days vs. 2.0 days for the highest severity patients, p = 0.74).CONCLUSION: We found that the reduction in the use of invasive treatments over time in patients with very poor prognosis did not shorten the time-to-death. These findings may be useful for goals of care discussions.

    View details for DOI 10.1371/journal.pone.0212439

    View details for PubMedID 30763372

  • Efficient computational strategies to learn the structure of probabilistic graphical models of cumulative phenomena Ramazzotti, D., Nobile, M. S., Antoniotti, M., Graudenzi, A. ELSEVIER SCIENCE BV. 2019: 1–10
  • Improved Survival of Cancer Patients Admitted to the Intensive Care Unit between 2002 and 2011 at a U.S. Teaching Hospital. Cancer research and treatment : official journal of Korean Cancer Association Sauer, C. M., Dong, J., Celi, L. A., Ramazzotti, D. 2018

    Abstract

    Purpose: Cancer patients are at increased risk of treatment- or disease-related admission to the intensive care unit [1]. Over the past decades, both critical care and cancer care have improved substantially. Due to increased cancer-specific survival [2], we hypothesized that the number of cancer patients admitted to the intensive care unit (ICU) and survival have increased.Materials and Methods: MIMIC-III [3] was used to study trends and outcomes of cancer patients admitted to the ICU between 2002 and 2011. Multiple logistic regression analysis was performed to adjust for confounders of mortality.Results: Among 41,468 patients analyzed, 1,083 were hemato-oncologic, 4,330 were oncologic and 66 patients had both a hematological and solid malignancy. Admission numbers more than doubled and the proportion of cancer patients in the ICU increased steadily from 2002 to 2011. In both the univariate and multivariate analyses, solid cancers and hematologic cancers were strongly associated with 28-day mortality. This association was even stronger for 1-year mortality, with odds ratios of 4.02 (95% confidence interval [CI], 3.69 to 4.38) and 2.25 (95% CI, 1.93 to 2.62), respectively. Over the 10-year study period, both 28-day and 1-year mortality decreased, with hematologic patients showing the strongest annual adjusted decrease in the odds of death. There was considerable heterogeneity among solid cancer types.Conclusion: Between 2002 and 2011, the number of cancer patients admitted to the ICU more than doubled, while clinical severity scores remained overall unchanged, suggesting improved treatment. Although cancer patients had higher mortality rates, both 28-day and 1-year mortality of hematologic patients decreased faster than that of non-cancer patients, while mortality rates of cancer patients strongly depended on cancer type.

    View details for DOI 10.4143/crt.2018.360

    View details for PubMedID 30309220

  • Detecting repeated cancer evolution from multiregion tumor sequencing data NATURE METHODS Caravagna, G., Giarratano, Y., Ramazzotti, D., Tomlinson, I., Graham, T. A., Sanguinetti, G., Sottoriva, A. 2018; 15 (9): 707-+

    Abstract

    Recurrent successions of genomic changes, both within and between patients, reflect repeated evolutionary processes that are valuable for the anticipation of cancer progression. Multi-region sequencing allows the temporal order of some genomic changes in a tumor to be inferred, but the robust identification of repeated evolution across patients remains a challenge. We developed a machine-learning method based on transfer learning that allowed us to overcome the stochastic effects of cancer evolution and noise in data and identified hidden evolutionary patterns in cancer cohorts. When applied to multi-region sequencing datasets from lung, breast, renal, and colorectal cancer (768 samples from 178 patients), our method detected repeated evolutionary trajectories in subgroups of patients, which were reproduced in single-sample cohorts (n = 2,935). Our method provides a means of classifying patients on the basis of how their tumor evolved, with implications for the anticipation of disease progression.

    View details for DOI 10.1038/s41592-018-0108-x

    View details for Web of Science ID 000443439700028

    View details for PubMedID 30171232

  • Modeling Cumulative Biological Phenomena with Suppes-Bayes Causal Networks EVOLUTIONARY BIOINFORMATICS Ramazzotti, D., Graudenzi, A., Caravagna, G., Antoniotti, M. 2018; 14
  • Causal data science for financial stress testing Gao, G., Mishra, B., Ramazzotti, D. ELSEVIER SCIENCE BV. 2018: 294–304
  • SIMLR: A Tool for Large-Scale Genomic Analyses by Multi-Kernel Learning. Proteomics Wang, B., Ramazzotti, D., De Sano, L., Zhu, J., Pierson, E., Batzoglou, S. 2018; 18 (2)

    Abstract

    SIMLR (Single-cell Interpretation via Multi-kernel LeaRning), an open-source tool that implements a novel framework to learn a sample-to-sample similarity measure from expression data observed for heterogenous samples, is presented here. SIMLR can be effectively used to perform tasks such as dimension reduction, clustering, and visualization of heterogeneous populations of samples. SIMLR was benchmarked against state-of-the-art methods for these three tasks on several public datasets, showing it to be scalable and capable of greatly improving clustering performance, as well as providing valuable insights by making the data more interpretable via better a visualization. SIMLR is available on https://github.com/BatzoglouLabSU/SIMLRGitHub in both R and MATLAB implementations. Furthermore, it is also available as an R package on http://bioconductor.org.

    View details for DOI 10.1002/pmic.201700232

    View details for PubMedID 29265724

  • Multi-omic tumor data reveal diversity of molecular mechanisms that correlate with survival. Nature communications Ramazzotti, D., Lal, A., Wang, B., Batzoglou, S., Sidow, A. 2018; 9 (1): 4453

    Abstract

    Outcomes for cancer patients vary greatly even within the same tumor type, and characterization of molecular subtypes of cancer holds important promise for improving prognosis and personalized treatment. This promise has motivated recent efforts to produce large amounts of multidimensional genomic (multi-omic) data, but current algorithms still face challenges in the integrated analysis of such data. Here we present Cancer Integration via Multikernel Learning (CIMLR), a new cancer subtyping method that integrates multi-omic data to reveal molecular subtypes of cancer. We apply CIMLR to multi-omic data from 36 cancer types and show significant improvements in both computational efficiency and ability to extract biologically meaningful cancer subtypes. The discovered subtypes exhibit significant differences in patient survival for 27 of 36 cancer types. Our analysis reveals integrated patterns of gene expression, methylation, point mutations, and copy number changes in multiple cancers and highlights patterns specifically associated with poor patient outcomes.

    View details for DOI 10.1038/s41467-018-06921-8

    View details for PubMedID 30367051

  • Learning the Structure of Bayesian Networks: A Quantitative Assessment of the Effect of Different Algorithmic Schemes COMPLEXITY Beretta, S., Castelli, M., Goncalves, I., Henriques, R., Ramazzotti, D. 2018
  • Probabilistic Causal Analysis of Social Influence Bonchi, F., Gullo, F., Mishra, B., Ramazzotti, D., Cuzzocrea, A., Allan, J., Paton, N., Srivastava, D., Agrawal, R., Broder, A., Zaki, M., Candan, S., Labrinidis, A., Schuster, A., Wang, H. ASSOC COMPUTING MACHINERY. 2018: 1003–12
  • OncoScore: a novel, Internetbased tool to assess the oncogenic potential of genes SCIENTIFIC REPORTS Rocco, P., Daniele, R., Roberta, S., Alessandra, P., Luca, D., Pierangelo, F., Vera, M., Nicoletta, C., Nitesh, S., Carlo, G. 2017; 7: 46290

    Abstract

    The complicated, evolving landscape of cancer mutations poses a formidable challenge to identify cancer genes among the large lists of mutations typically generated in NGS experiments. The ability to prioritize these variants is therefore of paramount importance. To address this issue we developed OncoScore, a text-mining tool that ranks genes according to their association with cancer, based on available biomedical literature. Receiver operating characteristic curve and the area under the curve (AUC) metrics on manually curated datasets confirmed the excellent discriminating capability of OncoScore (OncoScore cut-off threshold = 21.09; AUC = 90.3%, 95% CI: 88.1-92.5%), indicating that OncoScore provides useful results in cases where an efficient prioritization of cancer-associated genes is needed.

    View details for DOI 10.1038/srep46290

    View details for Web of Science ID 000398640800001

    View details for PubMedID 28387367

    View details for PubMedCentralID PMC5384236

  • Visualization and analysis of single-cell RNA-seq data by kernel-based similarity learning. Nature methods Wang, B., Zhu, J., Pierson, E., Ramazzotti, D., Batzoglou, S. 2017

    Abstract

    We present single-cell interpretation via multikernel learning (SIMLR), an analytic framework and software which learns a similarity measure from single-cell RNA-seq data in order to perform dimension reduction, clustering and visualization. On seven published data sets, we benchmark SIMLR against state-of-the-art methods. We show that SIMLR is scalable and greatly enhances clustering performance while improving the visualization and interpretability of single-cell sequencing data.

    View details for DOI 10.1038/nmeth.4207

    View details for PubMedID 28263960