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Book ; Online: Transformers for Green Semantic Communication

Mukherjee, Shubhabrata / Beard, Cory / Song, Sejun

Less Energy, More Semantics

2023

Abstract: Semantic communication aims to transmit meaningful and effective information rather than focusing on individual symbols or bits, resulting in benefits like reduced latency, bandwidth usage, and higher throughput compared to traditional communication. ... ...

Abstract	Semantic communication aims to transmit meaningful and effective information rather than focusing on individual symbols or bits, resulting in benefits like reduced latency, bandwidth usage, and higher throughput compared to traditional communication. However, semantic communication poses significant challenges due to the need for universal metrics for benchmarking the joint effects of semantic information loss and practical energy consumption. This research presents a novel multi-objective loss function named "Energy-Optimized Semantic Loss" (EOSL), addressing the challenge of balancing semantic information loss and energy consumption. Through comprehensive experiments on transformer models, including CPU and GPU energy usage, it is demonstrated that EOSL-based encoder model selection can save up to 90\% of energy while achieving a 44\% improvement in semantic similarity performance during inference in this experiment. This work paves the way for energy-efficient neural network selection and the development of greener semantic communication architectures.
Keywords	Computer Science - Machine Learning ; Computer Science - Networking and Internet Architecture
Publishing date	2023-10-11
Publishing country	us
Document type	Book ; Online
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Article: Pervasive biases in proxy GWAS based on parental history of Alzheimer's disease.

Wu, Yuchang / Sun, Zhongxuan / Zheng, Qinwen / Miao, Jiacheng / Dorn, Stephen / Mukherjee, Shubhabrata / Fletcher, Jason M / Lu, Qiongshi

bioRxiv : the preprint server for biology

2023

Abstract: Almost every recent Alzheimer's disease (AD) genome-wide association study (GWAS) has performed meta-analysis to combine studies with clinical diagnosis of AD with studies that use proxy phenotypes based on parental disease history. Here, we report major ...

Abstract	Almost every recent Alzheimer's disease (AD) genome-wide association study (GWAS) has performed meta-analysis to combine studies with clinical diagnosis of AD with studies that use proxy phenotypes based on parental disease history. Here, we report major limitations in current GWAS-by-proxy (GWAX) practices due to uncorrected survival bias and non-random participation of parental illness survey, which cause substantial discrepancies between AD GWAS and GWAX results. We demonstrate that current AD GWAX provide highly misleading genetic correlations between AD risk and higher education which subsequently affects a variety of genetic epidemiologic applications involving AD and cognition. Our study sheds important light on the design and analysis of mid-aged biobank cohorts and underscores the need for caution when interpreting genetic association results based on proxy-reported parental disease history.
Language	English
Publishing date	2023-10-17
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.10.13.562272
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Article ; Online: Local ancestry at APOE modifies Alzheimer's disease risk in Caribbean Hispanics.

Blue, Elizabeth E / Horimoto, Andréa R V R / Mukherjee, Shubhabrata / Wijsman, Ellen M / Thornton, Timothy A

Alzheimer's & dementia : the journal of the Alzheimer's Association

2019 Volume 15, Issue 12, Page(s) 1524–1532

Abstract: Introduction: Although the relationship between APOE and Alzheimer's disease (AD) is well established in populations of European descent, the effects of APOE and ancestry on AD risk in diverse populations is not well understood.: Methods: Logistic ... ...

Abstract	Introduction: Although the relationship between APOE and Alzheimer's disease (AD) is well established in populations of European descent, the effects of APOE and ancestry on AD risk in diverse populations is not well understood. Methods: Logistic mixed model regression and survival analyses were performed in a sample of 3067 Caribbean Hispanics and 3028 individuals of European descent to assess the effects of APOE genotype, local ancestry, and genome-wide ancestry on AD risk and age at onset. Results: Among the Caribbean Hispanics, individuals with African-derived ancestry at APOE had 39% lower odds of AD than individuals with European-derived APOE, after adjusting for APOE genotype, age, and genome-wide ancestry. While APOE E2 and E4 effects on AD risk and age at onset were significant in the Caribbean Hispanics, they were substantially attenuated compared with those in European ancestry individuals. Discussion: These results suggest that additional genetic variation in the APOE region influences AD risk beyond APOE E2/E3/E4.
MeSH term(s)	Age of Onset ; Aged ; Alzheimer Disease/epidemiology ; Alzheimer Disease/genetics ; Apolipoproteins E/genetics ; Black People/genetics ; Caribbean Region/ethnology ; Ethnicity/statistics & numerical data ; Female ; Genotype ; Hispanic or Latino/genetics ; Humans ; Male ; Middle Aged ; White People/genetics
Chemical Substances	Apolipoproteins E
Language	English
Publishing date	2019-10-09
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2211627-8
ISSN	1552-5279 ; 1552-5260
ISSN (online)	1552-5279
ISSN	1552-5260
DOI	10.1016/j.jalz.2019.07.016
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Article ; Online: Cognitively defined Alzheimer's dementia subgroups have distinct atrophy patterns.

Crane, Paul K / Groot, Colin / Ossenkoppele, Rik / Mukherjee, Shubhabrata / Choi, Seo-Eun / Lee, Michael / Scollard, Phoebe / Gibbons, Laura E / Sanders, R Elizabeth / Trittschuh, Emily / Saykin, Andrew J / Mez, Jesse / Nakano, Connie / Donald, Christine Mac / Sohi, Harkirat / Risacher, Shannon

Alzheimer's & dementia : the journal of the Alzheimer's Association

2023 Volume 20, Issue 3, Page(s) 1739–1752

Abstract: Introduction: We sought to determine structural magnetic resonance imaging (MRI) characteristics across subgroups defined based on relative cognitive domain impairments using data from the Alzheimer's Disease Neuroimaging Initiative (ADNI) and to ... ...

Abstract	Introduction: We sought to determine structural magnetic resonance imaging (MRI) characteristics across subgroups defined based on relative cognitive domain impairments using data from the Alzheimer's Disease Neuroimaging Initiative (ADNI) and to compare cognitively defined to imaging-defined subgroups. Methods: We used data from 584 people with Alzheimer's disease (AD) (461 amyloid positive, 123 unknown amyloid status) and 118 amyloid-negative controls. We used voxel-based morphometry to compare gray matter volume (GMV) for each group compared to controls and to AD-Memory. Results: There was pronounced bilateral lower medial temporal lobe atrophy with relative cortical sparing for AD-Memory, lower left hemisphere GMV for AD-Language, anterior lower GMV for AD-Executive, and posterior lower GMV for AD-Visuospatial. Formal asymmetry comparisons showed substantially more asymmetry in the AD-Language group than any other group (p = 1.15 × 10 Discussion: MRI findings differ across cognitively defined AD subgroups.
MeSH term(s)	Humans ; Alzheimer Disease/pathology ; Brain/diagnostic imaging ; Brain/pathology ; Cognitive Dysfunction/diagnostic imaging ; Cognitive Dysfunction/pathology ; Neuroimaging/methods ; Magnetic Resonance Imaging ; Atrophy/pathology
Language	English
Publishing date	2023-12-13
Publishing country	United States
Document type	Journal Article
ZDB-ID	2211627-8
ISSN	1552-5279 ; 1552-5260
ISSN (online)	1552-5279
ISSN	1552-5260
DOI	10.1002/alz.13567
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Article ; Online: A guide for researchers seeking training in retrospective data harmonization for population neuroscience studies of Alzheimer's disease and related dementias.

Shaaban, C Elizabeth / Tudorascu, Dana L / Glymour, M Maria / Cohen, Ann D / Thurston, Rebecca C / Snyder, Heather M / Hohman, Timothy J / Mukherjee, Shubhabrata / Yu, Lan / Snitz, Beth E

Frontiers in neuroimaging

2022 Volume 1

Abstract: Due to needs surrounding rigor and reproducibility, subgroup specific disease knowledge, and questions of external validity, data harmonization is an essential tool in population neuroscience of Alzheimer's disease and related dementias (ADRD). ... ...

Abstract	Due to needs surrounding rigor and reproducibility, subgroup specific disease knowledge, and questions of external validity, data harmonization is an essential tool in population neuroscience of Alzheimer's disease and related dementias (ADRD). Systematic harmonization of data elements is necessary to pool information from heterogeneous samples, and such pooling allows more expansive evaluations of health disparities, more precise effect estimates, and more opportunities to discover effective prevention or treatment strategies. The key goal of this Tutorial in Population Neuroimaging Curriculum, Instruction, and Pedagogy article is to guide researchers in creating a customized population neuroscience of ADRD harmonization training plan to fit their needs or those of their mentees. We provide brief guidance for retrospective data harmonization of multiple data types in this area, including: (1) clinical and demographic, (2) neuropsychological, and (3) neuroimaging data. Core competencies and skills are reviewed, and resources are provided to fill gaps in training as well as data needs. We close with an example study in which harmonization is a critical tool. While several aspects of this tutorial focus specifically on ADRD, the concepts and resources are likely to benefit population neuroscientists working in a range of research areas.
Language	English
Publishing date	2022-09-26
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	3123824-5
ISSN	2813-1193 ; 2813-1193
ISSN (online)	2813-1193
ISSN	2813-1193
DOI	10.3389/fnimg.2022.978350
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Article ; Online: Functional excitatory to inhibitory synaptic imbalance and loss of cognitive performance in people with Alzheimer's disease neuropathologic change.

Scaduto, Pietro / Lauterborn, Julie C / Cox, Conor D / Fracassi, Anna / Zeppillo, Tommaso / Gutierrez, Berenice A / Keene, C Dirk / Crane, Paul K / Mukherjee, Shubhabrata / Russell, William K / Taglialatela, Giulio / Limon, Agenor

Acta neuropathologica

2022 Volume 145, Issue 3, Page(s) 303–324

Abstract: Individuals at distinct stages of Alzheimer's disease (AD) show abnormal electroencephalographic activity, which has been linked to network hyperexcitability and cognitive decline. However, whether pro-excitatory changes at the synaptic level are ... ...

Abstract	Individuals at distinct stages of Alzheimer's disease (AD) show abnormal electroencephalographic activity, which has been linked to network hyperexcitability and cognitive decline. However, whether pro-excitatory changes at the synaptic level are observed in brain areas affected early in AD, and if they are emergent in MCI, is not clearly known. Equally important, it is not known whether global synaptic E/I imbalances correlate with the severity of cognitive impairment in the continuum of AD. Measuring the amplitude of ion currents of human excitatory and inhibitory synaptic receptors microtransplanted from the hippocampus and temporal cortex of cognitively normal, mildly cognitively impaired and AD individuals into surrogate cells, we found regional differences in pro-excitatory shifts of the excitatory to inhibitory (E/I) current ratio that correlates positively with toxic proteins and degree of pathology, and impinges negatively on cognitive performance scores. Using these data with electrophysiologically anchored analysis of the synapto-proteome in the same individuals, we identified a group of proteins sustaining synaptic function and those related to synaptic toxicity. We also found an uncoupling between the function and expression of proteins for GABAergic signaling in the temporal cortex underlying larger E/I and worse cognitive performance. Further analysis of transcriptomic and in situ hybridization datasets from an independent cohort across the continuum of AD confirm regional differences in pro-excitatory shifts of the E/I balance that correlate negatively with the most recent calibrated composite scores for memory, executive function, language and visuospatial abilities, as well as overall cognitive performance. These findings indicate that early shifts of E/I balance may contribute to loss of cognitive capabilities in the continuum of AD clinical syndrome.
MeSH term(s)	Humans ; Alzheimer Disease/pathology ; Cognitive Dysfunction/pathology ; Brain/pathology ; Hippocampus/pathology ; Cognition
Language	English
Publishing date	2022-12-20
Publishing country	Germany
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1079-0
ISSN	1432-0533 ; 0001-6322
ISSN (online)	1432-0533
ISSN	0001-6322
DOI	10.1007/s00401-022-02526-0
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Article ; Online: Failure to detect synergy between variants in transferrin and hemochromatosis and Alzheimer's disease in large cohort.

Vance, Elizabeth / Gonzalez Murcia, Josue D / Miller, Justin B / Staley, Lyndsay / Crane, Paul K / Mukherjee, Shubhabrata / Kauwe, John S K

Neurobiology of aging

2020 Volume 89, Page(s) 142.e9–142.e12

Abstract: Alzheimer's disease (AD) is the most common cause of dementia and, despite decades of effort, there is no effective treatment. In the last decade, many association studies have identified genetic markers that are associated with AD status. Two of these ... ...

Abstract	Alzheimer's disease (AD) is the most common cause of dementia and, despite decades of effort, there is no effective treatment. In the last decade, many association studies have identified genetic markers that are associated with AD status. Two of these studies suggest that an epistatic interaction between variants rs1049296 in the transferrin (TF) gene and rs1800562 in the homeostatic iron regulator (HFE) gene, commonly known as hemochromatosis, is in genetic association with AD. TF and HFE are involved in the transport and regulation of iron in the brain, and disrupting these processes exacerbates AD pathology through increased neurodegeneration and oxidative stress. However, by using a significantly larger data set from the Alzheimer's Disease Genetics Consortium, we fail to detect an association between TF rs1049296 or HFE rs1800562 with AD risk (TF rs1049296 p = 0.38 and HFE rs1800562 p = 0.40). In addition, logistic regression with an interaction term and a synergy factor analysis both failed to detect epistasis between TF rs1049296 and HFE rs1800562 (SF = 0.94; p = 0.48) in AD cases. Each of these analyses had sufficient statistical power (power > 0.99), suggesting that previously reported associations may be the result of more complex epistatic interactions, genetic heterogeneity, or false-positive associations because of limited sample sizes.
MeSH term(s)	Alzheimer Disease/genetics ; Cohort Studies ; Epistasis, Genetic/genetics ; Genetic Association Studies ; Genetic Predisposition to Disease/genetics ; Genetic Variation ; Hemochromatosis/genetics ; Hemochromatosis Protein/genetics ; Humans ; Negative Results ; Oxidative Stress/genetics ; Risk ; Transferrin/genetics
Chemical Substances	HFE protein, human ; Hemochromatosis Protein ; Transferrin
Language	English
Publishing date	2020-02-12
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	604505-4
ISSN	1558-1497 ; 0197-4580
ISSN (online)	1558-1497
ISSN	0197-4580
DOI	10.1016/j.neurobiolaging.2020.01.013
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Article ; Online: Assessing the associations between known genetic variants and substance use in people with HIV in the United States.

PloS one

2023 Volume 18, Issue 10, Page(s) e0292068

Abstract: Background: The prevalence of substance use in people with HIV (PWH) in the United States is higher than in the general population and is an important driver of HIV-related outcomes. We sought to assess if previously identified genetic associations that ...

Abstract	Background: The prevalence of substance use in people with HIV (PWH) in the United States is higher than in the general population and is an important driver of HIV-related outcomes. We sought to assess if previously identified genetic associations that contribute to substance use are also observed in a population of PWH. Methods: We performed genome-wide association studies (GWAS) of alcohol, smoking, and cannabis use phenotypes in a multi-ancestry population of 7,542 PWH from the Center for AIDS Research Network of Integrated Clinical Systems (CNICS). We conducted multi-ancestry GWAS for individuals of African (n = 3,748), Admixed American (n = 1,334), and European (n = 2,460) ancestry. Phenotype data were self-reported and collected using patient reported outcomes (PROs) and three questions from AUDIT-C, an alcohol screening tool. We analyzed nine phenotypes: 1) frequency of alcohol consumption, 2) typical number of drinks on a day when drinking alcohol, 3) frequency of five or more alcoholic drinks in a 30-day period, 4) smoking initiation, 5) smoking cessation, 6) cigarettes per day, 7) cannabis use initiation, 8) cannabis use cessation, 9) frequency of cannabis use during the previous 30 days. For each phenotype we considered a) variants previously identified as associated with a substance use trait and b) novel associations. Results: We observed evidence for effects of previously reported single nucleotide polymorphisms (SNPs) related to alcohol (rs1229984, p = 0.001), tobacco (rs11783093, p = 2.22E-4), and cannabis use (rs2875907, p = 0.005). We also report two novel loci (19p13.2, p = 1.3E-8; and 20p11.21, p = 2.1E-8) associated with cannabis use cessation. Conclusions: Our analyses contribute to understanding the genetic bases of substance use in a population with relatively higher rates of use compared to the general population.
MeSH term(s)	Humans ; United States/epidemiology ; Genome-Wide Association Study ; Smoking/genetics ; Smoking/epidemiology ; Alcohol Drinking/genetics ; Alcohol Drinking/epidemiology ; Substance-Related Disorders/epidemiology ; Substance-Related Disorders/genetics ; Cannabis/genetics ; Ethanol ; HIV Infections/epidemiology ; HIV Infections/genetics
Chemical Substances	Ethanol (3K9958V90M)
Language	English
Publishing date	2023-10-05
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2267670-3
ISSN	1932-6203 ; 1932-6203
ISSN (online)	1932-6203
ISSN	1932-6203
DOI	10.1371/journal.pone.0292068
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Article ; Online: Analysis of genes (TMEM106B, GRN, ABCC9, KCNMB2, and APOE) implicated in risk for LATE-NC and hippocampal sclerosis provides pathogenetic insights: a retrospective genetic association study.

Dugan, Adam J / Nelson, Peter T / Katsumata, Yuriko / Shade, Lincoln M P / Boehme, Kevin L / Teylan, Merilee A / Cykowski, Matthew D / Mukherjee, Shubhabrata / Kauwe, John S K / Hohman, Timothy J / Schneider, Julie A / Fardo, David W

Acta neuropathologica communications

2021 Volume 9, Issue 1, Page(s) 152

Abstract: Limbic-predominant age-related TDP-43 encephalopathy neuropathologic change (LATE-NC) is the most prevalent subtype of TDP-43 proteinopathy, affecting up to 1/3rd of aged persons. LATE-NC often co-occurs with hippocampal sclerosis (HS) pathology. It is ... ...

Abstract	Limbic-predominant age-related TDP-43 encephalopathy neuropathologic change (LATE-NC) is the most prevalent subtype of TDP-43 proteinopathy, affecting up to 1/3rd of aged persons. LATE-NC often co-occurs with hippocampal sclerosis (HS) pathology. It is currently unknown why some individuals with LATE-NC develop HS while others do not, but genetics may play a role. Previous studies found associations between LATE-NC phenotypes and specific genes: TMEM106B, GRN, ABCC9, KCNMB2, and APOE. Data from research participants with genomic and autopsy measures from the National Alzheimer's Coordinating Center (NACC; n = 631 subjects included) and the Religious Orders Study and Memory and the Rush Aging Project (ROSMAP; n = 780 included) were analyzed in the current study. Our goals were to reevaluate disease-associated genetic variants using newly collected data and to query whether the specific genotype/phenotype associations could provide new insights into disease-driving pathways. Research subjects included in prior LATE/HS genome-wide association studies (GWAS) were excluded. Single nucleotide variants (SNVs) within 10 kb of TMEM106B, GRN, ABCC9, KCNMB2, and APOE were tested for association with HS and LATE-NC, and separately for Alzheimer's pathologies, i.e. amyloid plaques and neurofibrillary tangles. Significantly associated SNVs were identified. When results were meta-analyzed, TMEM106B, GRN, and APOE had significant gene-based associations with both LATE and HS, whereas ABCC9 had significant associations with HS only. In a sensitivity analysis limited to LATE-NC + cases, ABCC9 variants were again associated with HS. By contrast, the associations of TMEM106B, GRN, and APOE with HS were attenuated when adjusting for TDP-43 proteinopathy, indicating that these genes may be associated primarily with TDP-43 proteinopathy. None of these genes except APOE appeared to be associated with Alzheimer's-type pathology. In summary, using data not included in prior studies of LATE or HS genomics, we replicated several previously reported gene-based associations and found novel evidence that specific risk alleles can differentially affect LATE-NC and HS.
MeSH term(s)	Aged, 80 and over ; Apolipoproteins E/genetics ; Cohort Studies ; Female ; Follow-Up Studies ; Genetic Predisposition to Disease/epidemiology ; Genetic Predisposition to Disease/genetics ; Genome-Wide Association Study/methods ; Hippocampus/pathology ; Humans ; Large-Conductance Calcium-Activated Potassium Channel beta Subunits/genetics ; Male ; Membrane Proteins/genetics ; Nerve Tissue Proteins/genetics ; Progranulins/genetics ; Retrospective Studies ; Sclerosis ; Sulfonylurea Receptors/genetics
Chemical Substances	ABCC9 protein, human ; ApoE protein, human ; Apolipoproteins E ; GRN protein, human ; KCNMB2 protein, human ; Large-Conductance Calcium-Activated Potassium Channel beta Subunits ; Membrane Proteins ; Nerve Tissue Proteins ; Progranulins ; Sulfonylurea Receptors ; TMEM106B protein, human
Language	English
Publishing date	2021-09-15
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S.
ZDB-ID	2715589-4
ISSN	2051-5960 ; 2051-5960
ISSN (online)	2051-5960
ISSN	2051-5960
DOI	10.1186/s40478-021-01250-2
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Article ; Online: Association between WWOX/MAF variants and dementia-related neuropathologic endophenotypes.

Dugan, Adam J / Nelson, Peter T / Katsumata, Yuriko / Shade, Lincoln M P / Teylan, Merilee A / Boehme, Kevin L / Mukherjee, Shubhabrata / Kauwe, John S K / Hohman, Timothy J / Schneider, Julie A / Fardo, David W

Neurobiology of aging

2021 Volume 111, Page(s) 95–106

Abstract: The genetic locus containing the WWOX and MAF genes was implicated as a clinical Alzheimer's disease (AD) risk locus in two recent large meta-analytic genome wide association studies (GWAS). In a prior GWAS, we identified a variant in WWOX as a ... ...

Abstract	The genetic locus containing the WWOX and MAF genes was implicated as a clinical Alzheimer's disease (AD) risk locus in two recent large meta-analytic genome wide association studies (GWAS). In a prior GWAS, we identified a variant in WWOX as a suggestive risk allele for hippocampal sclerosis. We hypothesized that the WWOX/MAF locus may be preferentially associated with non-plaque- and non-tau-related neuropathological changes (NC). Data from research participants with GWAS and autopsy measures from the National Alzheimer's Coordinating Center and the Religious Orders Study and the Rush Memory and Aging Project were meta-analyzed. Notably, no variants in the locus were significantly associated with ADNC. However, several WWOX/MAF variants had significant adjusted associations with limbic-predominant age-related TDP-43 encephalopathy NC (LATE-NC), HS, and brain arteriolosclerosis. These associations remained largely unchanged after adjustment for ADNC (operationalized with standard semiquantitative staging), suggesting that these associations are independent of ADNC. Thus, WWOX genetic variants were associated pathologically with LATE-NC, not ADNC.
MeSH term(s)	Aged ; Aged, 80 and over ; Alzheimer Disease/genetics ; Dementia/genetics ; Female ; Genetic Variation/genetics ; Genome-Wide Association Study/methods ; Humans ; Male ; Phenotype ; Proto-Oncogene Proteins c-maf/genetics ; TDP-43 Proteinopathies/genetics ; Tumor Suppressor Proteins/genetics ; WW Domain-Containing Oxidoreductase/genetics
Chemical Substances	MAF protein, human ; Proto-Oncogene Proteins c-maf ; Tumor Suppressor Proteins ; WW Domain-Containing Oxidoreductase (EC 1.1.1.-) ; WWOX protein, human (EC 1.1.1.-)
Language	English
Publishing date	2021-10-29
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	604505-4
ISSN	1558-1497 ; 0197-4580
ISSN (online)	1558-1497
ISSN	0197-4580
DOI	10.1016/j.neurobiolaging.2021.10.011
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