arXiv subjects

David Burstein

Publications and source records attributed to David Burstein.

At least 19 recordsLinked to original sources

arXiv2025

Leveraging Natural Language Processing to Unravel the Mystery of Life: A Review of NLP Approaches in Genomics, Transcriptomics, and Proteomics

Natural Language Processing (NLP) has transformed various fields beyond linguistics by applying techniques originally developed for human language to the analysis of biological sequences. This review explores the application of NLP methods to biological sequence data, focusing on genomics, transcriptomics, and proteomics. We examine how various NLP methods, from classic approaches like word2vec to advanced models employing transformers and hyena operators, are being adapted to analyze DNA, RNA, protein sequences, and entire genomes. The review also examines tokenization strategies and model architectures, evaluating their strengths, limitations, and suitability for different biological tasks. We further cover recent advances in NLP applications for biological data, such as structure prediction, gene expression, and evolutionary analysis, highlighting the potential of these methods for extracting meaningful insights from large-scale genomic data. As language models continue to advance, their integration into bioinformatics holds immense promise for advancing our understanding of biological processes in all domains of life.

cs.CL↗

arXiv2018

Leveraging local network communities to predict academic performance

For more than 20 years, social network analysis of student collaboration networks has focused on a student's centrality to predict academic performance. And even though a growing amount of sociological literature has supported that academic success is contagious, identifying central students in the network alone does not capture how peer interactions facilitate the spread of academic success throughout the network. Consequently, we propose novel predictors that treat academic success as a contagion by identifying a student's learning community, consisting of the peers that are most likely to influence a student's performance in a course. We evaluate the importance of these learning communities by predicting academic outcomes in an introductory college statistics course with 103 students. In particular, we observe that by including these learning community predictors, the resulting model is 68 times more likely to be the correct model than the current state-of-the-art centrality network models in the literature.

cs.SI↗

arXiv2017

Asymptotics of the spectral radius for directed Chung-Lu random graphs with community structure

The spectral radius of the adjacency matrix can impact both algorithmic efficiency as well as the stability of solutions to an underlying dynamical process. Although much research has considered the distribution of the spectral radius for undirected random graph models, as symmetric adjacency matrices are amenable to spectral analysis, very little work has focused on directed graphs. Consequently, we provide novel concentration results for the spectral radius of the directed Chung-Lu random graph model. We emphasize that our concentration results are applicable both asymptotically and to networks of finite size. Subsequently, we extend our concentration results to a generalization of the directed Chung-Lu model that allows for community structure.

math.CO↗

arXiv2016

The K Shortest Paths Problem with Application to Routing

Due to the computational complexity of finding almost shortest simple paths, we propose that identifying a larger collection of (nonbacktracking) paths is more efficient than finding almost shortest simple paths on positively weighted real-world networks. First, we present an easy to implement $O(m\log m+kL)$ solution for finding all (nonbacktracking) paths with bounded length $D$ between two arbitrary nodes on a positively weighted graph, where $L$ is an upperbound for the number of nodes in any of the $k$ outputted paths. Subsequently, we illustrate that for undirected Chung-Lu random graphs, the ratio between the number of nonbacktracking and simple paths asymptotically approaches $1$ with high probability for a wide range of parameters. We then consider an application to the almost shortest paths algorithm to measure path diversity for internet routing in a snapshot of the Autonomous System graph subject to an edge deletion process.

cs.DS↗

arXiv2015

Degree switching and partitioning for enumerating graphs to arbitrary orders of accuracy

We provide a novel method for constructing asymptotics (to arbitrary accuracy) for the number of directed graphs that realize a fixed bidegree sequence $d = a \times b$ with maximum degree $d_{max}=O(S^{\frac{1}{2}-\tau})$ for an arbitrarily small positive number $\tau$, where $S$ is the number edges specified by $d$. Our approach is based on two key steps, graph partitioning and degree preserving switches. The former idea allows us to relate enumeration results for given sequences to those for sequences that are especially easy to handle, while the latter facilitates expansions based on numbers of shared neighbors of pairs of nodes. While we focus primarily on directed graphs allowing loops, our results can be extended to other cases, including bipartite graphs, as well as directed and undirected graphs without loops. In addition, we can relax the constraint that $d_{max} = O(S^{\frac{1}{2}-\tau})$ and replace it with $a_{max} b_{max} = O(S^{1-\tau})$. where $a_{max}$ and $b_{max}$ are the maximum values for $a$ and $b$ respectively. The previous best results, from Greenhill et al., only allow for $d_{max} = o(S^{\frac{1}{3}})$ or alternatively $a_{max} b_{max} = o(S^{\frac{2}{3}})$. Since in many real world networks, $d_{max}$ scales larger than $o(S^{\frac{1}{3}})$, we expect that this work will be helpful for various applications.

math.CO↗

arXiv2015

Sufficient Conditions for Graphicality of Bidegree Sequences

There are a variety of existing conditions for a degree sequence to be graphic. When a degree sequence satisfies any of these conditions, there exists a graph that realizes the sequence. We formulate several novel sufficient graphicality criteria that depend on the number of elements in the sequence, corresponding to the number of nodes in an associated graph, and the mean degree of the sequence. These conditions, which are stated in terms of bidegree sequences for directed graphs, are easier to apply than classic necessary and sufficient graphicality conditions involving multiple inequalities. They are also more flexible than more recent graphicality conditions, in that they imply graphicality of some degree sequences not covered by those conditions. The form of our results will allow them to be easily used for the generation of graphs with particular degree sequences for applications.

math.CO↗

arXiv2015

Interception in Distance-Vector Routing Networks

Despite the large effort devoted to cybersecurity research over the last decades, cyber intrusions and attacks are still increasing. With respect to routing networks, route hijacking has highlighted the need to reexamine the existing protocols that govern traffic routing. In particular, our pri- mary question is how the topology of a network affects the susceptibility of a routing protocol to endogenous route misdirection. In this paper we define and analyze an abstract model of traffic interception (i.e. eavesdropping) in distance-vector routing networks. Specifically, we study al- gorithms that measure the potential of groups of dishonest agents to divert traffic through their infrastructure under the constraint that messages must reach their intended destinations. We relate two variants of our model based on the allowed kinds of lies, define strategies for colluding agents, and prove optimality in special cases. In our main theorem we derive a provably optimal monitoring strategy for subsets of agents in which no two are adjacent, and we extend this strategy to the general case. Finally, we use our results to analyze the susceptibility of real and synthetic networks to endogenous traffic interception. In the Autonomous Systems (AS) graph of the United States, we show that compromising only 18 random nodes in the AS graph surprisingly captures 10% of all traffic paths in the network in expectation when a distance-vector routing protocol is in use.

cs.CR↗

arXiv2007

Metal Abundance Properties of M81 Globular Cluster System

This paper is the third in the series of papers on M81 globular clusters. In this paper, we present spatial and metal abundance properties of 95 M81 globular clusters, which comprise nearly half of all the M81 globular cluster system. These globular clusters are divided into two M81 metallicity groups by a KMM test. Our results show that, the metal-rich clusters did not demonstrate a centrally concentrated spatial distribution as ones in M31, and metal-poor clusters tend to be less spatially concentrated. In other words, the distribution of the metal-rich clusters in M81 is not very similar to that of M31. Most of the metal-rich clusters distribute at projected radii of 4-8 kpc. It is also noted that the metal-rich clusters distribute within the inner 20 kpc, and the metal-poor ones do out to radii of ~40 kpc. Like our Galaxy and M31, the metallicity distribution of globular clusters in M81 along galactocentric radius suggests that some dissipation occurred during the formation of the globular cluster system, i.e. smooth, pressure-supported collapse models of galaxies are unlikely to produce such radial distribution of metallicity presented in this paper. There is not evident correlation between globular cluster luminosity and metallicity in M81 globular clusters. The overwhelming conclusion of this paper seems to be that a more complete and thorough cluster search is needed in M81.

astro-ph↗

arXiv2006

Age constraints for an M31 globular cluster from SEDs-fit

We have constrained the age of the globular cluster S312 in the Andromeda galaxy (M31) by comparing its multicolor photometry with theoretical stellar population synthesis models. This is both a check on the age of this globular cluster, as well a check on our methodology. Main-sequence photometry has been the most direct method for determining the age of a star cluster. S312 was observed as part of the Beijing-Arizona-Taiwan-Connecticut (BATC) Multicolor Sky Survey from 1995 February to 2003 December. The photometry of BATC images for S312 was taken with 9 intermediate-band filters covering 5000-10000Å. Combined with photometry in the near-ultraviolet (NUV) of {\sl GALEX}, broad-band $UBVR$ and infrared $JHK_s$ of 2MASS, we obtained the accurate spectral energy distributions (SEDs) of S312 from 2267-20000Å. A quantitative comparison to simple stellar population models yields an age of $9.5_{-0.99}^{+1.15}$ Gyr, which is in very good agreement with the previous determination by main-sequence photometry. S312 has a mass of $9.8\pm{1.85}\times 10^5 \rm M_\odot$, and is a medium-mass globular cluster in M31. By analysis of errors of ages determined based on the SED fitting method of this paper, secure age constraints are derived with errors of $< 3$ Gyr for ages younger than 9 Gyr. In fact, the theoretical SEDs are not sensitive to the variation of age for ages greater than $\sim 10$ Gyr. Therefore, for globular clusters as old as the majority of the Galactic GCs, our method do not distinguish them accurately. We emphasize that our results show that even with multiband photometry spanning NUV to $K_s$, our age constraints from SED fitting are distressingly uncertain, which has implications for age derivations in extragalactic globular cluster systems.

astro-ph↗

arXiv2005

Age Estimations of M31 Globular Clusters from Their Spectral Energy Distributions

This paper presents accurate spectral energy distributions (SEDs) of 16 M31 globular clusters (GCs) confirmed by spectroscopy and/or high spatial-resolution imaging, as well as 30 M31 globular cluster candidates detected by Mochejska et al. Most of these candidates have m_V > 18, deeper than previous searches, and these candidates have not yet been confirmed to be globular clusters. The SEDs of these clusters and candidates are obtained as part of the BATC Multicolor Survey of the Sky, in which the spectrophotometrically-calibrated CCD images of M31 in 13 intermediate-band filters from 4000 to 10000 A were observed. These filters are specifically designed to exclude most of the bright and variable night-sky emission lines including the OH forest. In comparison to the SEDs of true GCs, we find that some of the candidate objects are not GCs in M31. SED fits show that theoretical simple stellar population (SSP) models can fit the true GCs very well. We estimate the ages of these GCs by comparing with SSP models. We find that, the M31 clusters range in age from a few ten Myr to a few Gyr old, as well as old GCs, confirming the conclusion that has been found by Barmby et a, Williams & Hodge, Beasley et al., Burstein et al. and Puzia et al. in their investigations of the SEDs of M31 globular clusters.

astro-ph↗

arXiv2005

Spectral Energy Distributions of M81 Globular Clusters in BATC Multicolor Survey

In this paper, we give the spectral energy distributions of 42 M81 globular clusters in 13 intermediate-band filters from 4000 to 10000 A, using the CCD images of M81 observed as part of the BATC multicolor survey of the Sky. The BATC multicolor filter system is specifically designed to exclude most of the bright and variable night-sky emission lines including the OH forest. Hence, it can present accurate SEDs of the observed objects. These spectral energy distributions are low-resolution spectra, and can reflect the stellar populations of the globular clusters. This paper confirms the conclusions of Schroder et al. that, M81 contains clusters as young as a few Gyrs, which also were observed in both M31 and M33

astro-ph↗

arXiv2004

Structural properties of discs and bulges of early-type galaxies

We have used the EFAR sample of galaxies to study the light distributions of early-type galaxies. We decompose the 2D light distribution of the galaxies in a flattened spheroidal component with a Sersic radial light profile and an inclined disc component with an exponential light profile. We show that the brightest, bulge dominated elliptical galaxies have a fairly broad distribution in the Sersic profile shape parameter n_B, with a median of about 3.7 and a sigma of ~0.9. Other galaxies have smaller n_B values, meaning that spheroids are in general less concentrated than the n_B=4 de Vaucouleurs-law profile. The results of our light decompositions are robust, even though without kinematic information we cannot prove that the spheroids and discs are really pressure- and rotation-supported stellar systems. If we assume that the detected spheroids and discs are indeed separate components, we can draw the following conclusions: 1) the spheroid and disc scale sizes are correlated; 2) bulge-to-total luminosity ratios, bulge effective radii, and bulge n_B values are all positively correlated; 3) the bivariate space density distribution of elliptical galaxies in the (luminosity, scale size)-plane is well described by a Schechter luminosity function in and a log-normal scale-size distribution at a given luminosity; 4) at the brightest luminosities, the scale size distribution of elliptical galaxies is similar to those of bright spiral galaxies; at fainter luminosities the elliptical scale size distribution peaks at distinctly smaller sizes than the spiral galaxy distribution; and 5) bulge components of early-type galaxies are typically a factor 1.5 to 2.5 smaller than the disks of spiral galaxies, while disc components of early-type galaxies are typically twice as large as the discs of spiral galaxies. [abridged]

astro-ph↗

arXiv2004

Multicolor Photometric Observations of Optical Candidates to Faint ROSAT X-ray Sources in a 1 deg$^2$ field of the BATC Survey

We present optical candidates for 75 X-ray sources in a $\sim 1$ deg$^2$ overlapping region with the medium deep ROSAT survey. These candidates are selected using the multi-color CCD imaging observations made for the T329 field of the Beijing-Arizona-Taipei-Connecticut (BATC) Sky Survey. These X-ray sources are relatively faint (CR $<< 0.2 s^{-1}$) and thus mostly are not included in the RBS catalog, they also remain as X-ray sources without optical candidates in a previous identification program carried out by the Hamburg Quasar Survey. Within their position-error circles, almost all the X-ray sources are observed to have one or more spatially associated optical candidates within them down to the magnitude $m_V \sim 23.1$. We have classified 149 of 156 detected optical candidates with 73 of the 75 X-ray sources with a SED-based Object Classification Approach (SOCA). These optical candidates include: 31 QSOs, 39 stars, 37 starburst galaxies, 42 galaxies, and 7 "just" visible objects. We have also cross-correlated the positions of these optical objects with NED, the FIRST radio source catalog and the 2MASS catalog. Separately, we have also SED-classified the remaining 6011 objects in our field of view. Optical objects are found at the $6.5σ$ level above what one would expect from a random distribution, only QSOs are over-represented in these error circles at greater than 4$σ$ frequency. We estimate redshifts for all extragalactic objects, and find a good correspondence of our predicted redshift with the measured redshift (a mean error of 0.04 in $Δz$. There appears to be a supercluster at z $\sim$ 0.3-0.35 in this direction, including many of the galaxies in the X-ray error circles are found in this redshift range.

astro-ph↗

arXiv2003

Nitrogen Overabundance: Globular Cluster and Halo Formation

Halo globular clusters pose four succinct issues that must be solved in any scenario of their formation: single-age, single metallicity stellar populations; a lower limit ([Fe/H] ~ -2.3) to their average metallicity; comprising only 1% of the stellar halo mass, and being among the oldest stars in our Galaxy. New spectra are presented of Galactic stars and integrated spectra of Galactic globular clusters which extend to 3250 angstroms. These spectra show show that the most metal-poor and among the best-studied Galactic globular clusters show strong NH3360 absorption, even though their spectral energy distributions in the near-UV are dominated by blue horizontal branch, AF-type stars. These strong NH features must be coming from the main sequence stars in these clusters. These new data are combined with existing data on the wide range of carbon and nitrogen abundance in very metal-poor ([Fe/H] < -3.5) halo giant and dwarf stars, together with recent models of zero-metal star formation, to make a strawman scenario for globular cluster formation that can reproduce three of the above four issues, and well as related two of the three issues pertaining to nitrogen overabundance. This strawman proposal makes observational and theoretical predictions that are testable, needing specific help from the modelers to understand all of the elemental constraints on globular cluster and halo formation.

astro-ph↗

arXiv2003

Line-of-Sight Reddening Predictions: Zero Points, Accuracies, the Interstellar Medium, and the Stellar Populations of Elliptical Galaxies

Revised (B-V)_0-Mg_2 data for 402 elliptical galaxies are given to test reddening predictions which can also tell us both what the intrinsic errors are in this relationship among gE galaxy stellar populations, as well as details of nearby structure in the interstellar medium (ISM) of our Galaxy and of the intrinsic errors in reddening predictions. Using least-squares fits, the explicit 1-sigma errors in the Burstein-Heiles (BH) and the Schlegel et al. (IR) predicted reddenings are calculated, as well as the 1-sigma observational error in the (B-V)_0-Mg_2 for gE galaxies. It is found that, in directions with E(B-V)<0.100 mag (where most of these galaxies lie), 1-sigma errors in the IR reddening predictions are 0.006 to 0.009 in E(B-V) mag, those for BH reddening prediction are 0.011 mag, and the 1-sigma agreement between the two reddening predictions is 0.007 mag. IR predictions have an accuracy of 0.010-0.011 mag in directions with E(B-V)>= 0.100 mag, significantly better than those of the BH predictions (0.024-0.025). Gas-to-dust variations that vary by a factor of 3, both high and low, exist along many lines-of-sight in our Galaxy. The approx 0.02 higher reddening zero point in E(B-V) previously determined by Schlegel et al. is confirmed, primarily at the Galactic poles. Despite this, both methods also predict many directions with E(B-V)<0.015 mag. Independent evidence of reddening at the North Galactic pole is reviewed, with the conclusion that there still exists directions at the NGP that have E(B-V)<<0.01. Two lines of evidence suggest that IR reddenings are overpredicted in directions with high gas-to-dust ratios. As high gas-to-dust directions in the ISM also include the Galactic poles, this overprediction is the likely cause of the E(B-V) = 0.02 mag larger IR reddening zero point.

astro-ph↗

arXiv2003

The Multiphase Intracluster Medium in Galaxy Groups Probed by the Lyman Alpha Forest

The case is made that the intracluster medium (ICM) in spiral-rich galaxy groups today probably has undergone much slower evolution than that in elliptical-rich groups and clusters. The environments of proto-clusters and proto-groups at z > 2 are likely similar to spiral-rich group environments at lower redshift. Therefore, like the ICM in spiral-rich groups today, the ICM in proto-groups and proto-clusters at z > 2 is predicted to be significantly multiphased. The QSO Lyman alpha forest in the vicinity of galaxies is an effective probe of the ICM at a wide range of redshift. Two recent observations of Lyman alpha absorption around galaxies by Adelberger et al. and by Pascarelle et al are reconciled, and it is shown that observations support the multiphase ICM scenario. Galaxy redshifts must be very accurate for such studies to succeed. This scenario can also explain the lower metallicity and lower hot gas fraction in groups.

astro-ph↗

arXiv2003

An X-ray Atlas of Groups of Galaxies

A search was conducted for a hot intragroup medium in 109 low-redshift galaxy groups observed with the ROSAT PSPC. Evidence for diffuse, extended X-ray emission is found in at least 61 groups. Approximately one-third of these detections have not been previously reported in the literature. Most of the groups are detected out to less than half of the virial radius with ROSAT. Although some spiral-rich groups do contain an intragroup medium, diffuse emission is restricted to groups that contain at least one early-type galaxy.

astro-ph↗

arXiv2002

The Role of a Hot Gas Environment on the Evolution of Galaxies

Most spiral galaxies are found in galaxy groups with low velocity dispersions; most E/S0 galaxies are found in galaxy groups with relatively high velocity dispersions. The mass of the hot gas we can observe in the E/S0 groups via their thermal X-ray emission is, on average, as much as the baryonic mass of the galaxies in these groups. By comparison, galaxy clusters have as much or more hot gas than stellar mass. Hot gas in S-rich groups, however, is of low enough temperature for its X-ray emission to suffer heavy absorption due to Galactic HI and related observational effects, and hence is hard to detect. We postulate that such lower temperature hot gas does exist in low velocity dispersion, S-rich groups, and explore the consequences of this assumption. For a wide range of metallicity and density, hot gas in S-rich groups can cool in far less than a Hubble time. If such gas exists and can cool, especially when interacting with HI in existing galaxies, then it can help link together a number of disparate observations, both Galactic and extragalactic, that are otherwise difficult to understand.

astro-ph↗