80 research outputs found
Foreword
No full textPublished: Sudha Setty, Foreword, 41 W. NEW ENG. L. REV. 1 (2019).
In this Article, the Author reflects on legal education and the role of law reviews. Law reviews not only serve as an educational opportunity, but offer potential legal reforms to help legal scholars, practitioners, and the public understand possible shortcomings of the current state of the law and help law and policy makers contemplate potential improvements
Cell metadata for "The emergent landscape of the mouse gut endoderm at single-cell resolution"
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Neoliberal National Security: Wielding Counterterrorism Powers to Protect Economic Growth, in Liberalization and Globalization: Changing Legal Paradigm
No full textForthcoming: Sudha Setty, Neoliberal National Security: Wielding Counterterrorism Powers to Protect Economic Growth, in LIBERALIZATION AND GLOBALIZATION: CHANGING LEGAL PARADIGM (National Law School of India University Book Series 2017), edited by Sairam Bhat.
The Indian government’s crackdown on anti-nationalist protest and its secret implementation of broad data collection and surveillance regime illustrates the dangers of empowering the government’s use of its vast powers to prevent, curtail or punish those who pose or are perceived to pose a threat to the economic security of India. This Book Chapter describes three strands to view with each other to understand the concern surrounding the use of counterterrorism powers to preserve neo-liberal goals in the face of criticism and protest.
These strands are the political imperative of the Indian government to protect and grow the economy while dealing with the fear that terrorism may derail India’s economic development; second, the inclusion of economic insecurity in the legal definition of a national security threat; and third, the vast powers granted to and used by intelligence and law enforcement agencies dealing with perceived national security threats with little judicial or other external constraint. The characterization of anti-nationalist protest as a form of sedition that led to the harsh treatment of the Jawaharlal Nehru University protesters and the largely secret but extremely broad Central Monitoring System data gathering and surveillance system are exemplars of concerns that arise with the granting of broad national security and counterterrorism powers and without strong oversight or constraint.
The Author proposes that Parliament reconsider its current authorization of the use of counterterrorism powers to deal with potential economic threats, and the courts be willing to look closely at cases that curtail the rights to expression, due process, and privacy in the name of economic security. If India is to ensure adherence to the rule of law while fulfilling the national priority of growing its economy, the Parliament courts and the public must insist on better transparency and accountability
Computational modeling of gene regulatory programs in differentiation and disease
No full textCell state transitions are tightly controlled by numerous regulatory mechanisms to achieve cellular differentiation. Dysregulation of these regulatory mechanisms through the acquisition of somatic mutations and/or copy number changes can lead to oncogenic transformation. Binding of transcription factors (TFs) to regulatory elements is a primary mechanism controlling gene expression. TFs work in conjunction with chromatin to either activate or repress specific genes. miRNA-mediated degradation is another key regulatory mechanism involved in post transcriptional repression of genes. Genomics projects like ENCODE, Roadmap Epigenomics, TCGA and others are generating rich datasets across cell lines, primary tissues and cancers. These datasets enable computational modeling of transcriptional and miRNA mediated regulation. In this thesis, I will present our work on integrating multimodal datasets along with DNA sequence information to decipher novel regulatory programs in human disease and differentiation. First, we use the TCGA generated GBM dataset as a case study to infer gene regulatory programs in disease. We model the gene expression change in GBM relative to normal brain as a function of copy number of the gene, and TF and miRNA binding sites in the promoter and 3'UTR respectively. We use regularized least squares regression to fit the expression change of all genes for each sample. This framework achieves significant accuracy compared to randomized gene expression values and clustering of regression models recapitulates expression subtypes. We then employ a multi-task learning framework to learn regression models of all samples simultaneously and define a feature-scoring scheme to identify subtype-specific and common regulators. Using these experiments and literature search, we were able to identify a core regulatory network centered at the REST repression complex in the proneural subtype of GBM. I will then present our work on characterizing regulatory changes in hematopoietic differentiation primarily using DNase-seq enhancer maps from the Roadmap Epigenomics project. We first developed a tool, SeqGL, which demonstrates significantly greater sensitivity to binding signals underlying enhancer maps compared to traditional motif discovery algorithms. We then characterize the locus complexity, defined as number of DNase peaks assigned to a gene, in the hematopoietic system and observe that high complexity genes tend to be cell-type specific in expression and are enriched for functionally relevant ontologies. Furthermore, we observe extensive poising of enhancers in progenitor cells for function in differentiated cell types. We then use SeqGL scores to predict gene expression change in a transition from stem and progenitor cells to differentiated cell types with high accuracy and identify a potentially novel mechanistic role for PU.1 in B cell and monocyte specification
Neoliberal National Security: Wielding Counterterrorism Powers to Protect Economic Growth, in Liberalization and Globalization: Changing Legal Paradigm
No full textForthcoming: Sudha Setty, Neoliberal National Security: Wielding Counterterrorism Powers to Protect Economic Growth, in LIBERALIZATION AND GLOBALIZATION: CHANGING LEGAL PARADIGM (National Law School of India University Book Series 2017), edited by Sairam Bhat.
The Indian government’s crackdown on anti-nationalist protest and its secret implementation of broad data collection and surveillance regime illustrates the dangers of empowering the government’s use of its vast powers to prevent, curtail or punish those who pose or are perceived to pose a threat to the economic security of India. This Book Chapter describes three strands to view with each other to understand the concern surrounding the use of counterterrorism powers to preserve neo-liberal goals in the face of criticism and protest.
These strands are the political imperative of the Indian government to protect and grow the economy while dealing with the fear that terrorism may derail India’s economic development; second, the inclusion of economic insecurity in the legal definition of a national security threat; and third, the vast powers granted to and used by intelligence and law enforcement agencies dealing with perceived national security threats with little judicial or other external constraint. The characterization of anti-nationalist protest as a form of sedition that led to the harsh treatment of the Jawaharlal Nehru University protesters and the largely secret but extremely broad Central Monitoring System data gathering and surveillance system are exemplars of concerns that arise with the granting of broad national security and counterterrorism powers and without strong oversight or constraint.
The Author proposes that Parliament reconsider its current authorization of the use of counterterrorism powers to deal with potential economic threats, and the courts be willing to look closely at cases that curtail the rights to expression, due process, and privacy in the name of economic security. If India is to ensure adherence to the rule of law while fulfilling the national priority of growing its economy, the Parliament courts and the public must insist on better transparency and accountability
Neoliberal National Security: Wielding Counterterrorism Powers to Protect Economic Growth, in Liberalization and Globalization: Changing Legal Paradigm
No full textForthcoming: Sudha Setty, Neoliberal National Security: Wielding Counterterrorism Powers to Protect Economic Growth, in LIBERALIZATION AND GLOBALIZATION: CHANGING LEGAL PARADIGM (National Law School of India University Book Series 2017), edited by Sairam Bhat.
The Indian government’s crackdown on anti-nationalist protest and its secret implementation of broad data collection and surveillance regime illustrates the dangers of empowering the government’s use of its vast powers to prevent, curtail or punish those who pose or are perceived to pose a threat to the economic security of India. This Book Chapter describes three strands to view with each other to understand the concern surrounding the use of counterterrorism powers to preserve neo-liberal goals in the face of criticism and protest.
These strands are the political imperative of the Indian government to protect and grow the economy while dealing with the fear that terrorism may derail India’s economic development; second, the inclusion of economic insecurity in the legal definition of a national security threat; and third, the vast powers granted to and used by intelligence and law enforcement agencies dealing with perceived national security threats with little judicial or other external constraint. The characterization of anti-nationalist protest as a form of sedition that led to the harsh treatment of the Jawaharlal Nehru University protesters and the largely secret but extremely broad Central Monitoring System data gathering and surveillance system are exemplars of concerns that arise with the granting of broad national security and counterterrorism powers and without strong oversight or constraint.
The Author proposes that Parliament reconsider its current authorization of the use of counterterrorism powers to deal with potential economic threats, and the courts be willing to look closely at cases that curtail the rights to expression, due process, and privacy in the name of economic security. If India is to ensure adherence to the rule of law while fulfilling the national priority of growing its economy, the Parliament courts and the public must insist on better transparency and accountability
SparCAssist: A Model Risk Assessment Assistant Based on Sparse Generated Counterfactuals
No full textWe introduce SparCAssist, a general-purpose risk assessment tool for the machine learning models trained for language tasks. It evaluates models' risk by inspecting their behavior on counterfactuals, namely out-of-distribution instances generated based on the given data instance. The counterfactuals are generated by replacing tokens in rational subsequences identified by ExPred, while the replacements are retrieved using HotFlip or the Masked-Language-Model-based algorithms. The main purpose of our system is to help the human annotators to assess the model's risk on deployment. The counterfactual instances generated during the assessment are the by-product and can be used to train more robust NLP models in the future.Green Open Access added to TU Delft Institutional Repository 'You share, we take care!' - Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.Web Information System
SeqGL Identifies Context-Dependent Binding Signals in Genome-Wide Regulatory Element Maps.
No full textGenome-wide maps of transcription factor (TF) occupancy and regions of open chromatin implicitly contain DNA sequence signals for multiple factors. We present SeqGL, a novel de novo motif discovery algorithm to identify multiple TF sequence signals from ChIP-, DNase-, and ATAC-seq profiles. SeqGL trains a discriminative model using a k-mer feature representation together with group lasso regularization to extract a collection of sequence signals that distinguish peak sequences from flanking regions. Benchmarked on over 100 ChIP-seq experiments, SeqGL outperformed traditional motif discovery tools in discriminative accuracy. Furthermore, SeqGL can be naturally used with multitask learning to identify genomic and cell-type context determinants of TF binding. SeqGL successfully scales to the large multiplicity of sequence signals in DNase- or ATAC-seq maps. In particular, SeqGL was able to identify a number of ChIP-seq validated sequence signals that were not found by traditional motif discovery algorithms. Thus compared to widely used motif discovery algorithms, SeqGL demonstrates both greater discriminative accuracy and higher sensitivity for detecting the DNA sequence signals underlying regulatory element maps. SeqGL is available at http://cbio.mskcc.org/public/Leslie/SeqGL/
Searching, Learning, and Subtopic Ordering: A Simulation-Based Analysis
No full textComplex search tasks—such as those from the Search as Learning (SAL) domain—often result in users developing an information need composed of several aspects. However, current models of searcher behaviour assume that individuals have an atomic need, regardless of the task. While these models generally work well for simpler informational needs, we argue that searcher models need to be developed further to allow for the decomposition of a complex search task into multiple aspects. As no searcher model yet exists that considers both aspects and the SAL domain, we propose, by augmenting the Complex Searcher Model (CSM), the Subtopic Aware Complex Searcher Model (SACSM)—modelling aspects as subtopics to the user’s need. We then instantiate several agents (i.e., simulated users), with different subtopic selection strategies, which can be considered as different prototypical learning strategies (e.g., should I deeply examine one subtopic at a time, or shallowly cover several subtopics?). Finally, we report on the first large-scale simulated analysis of user behaviours in the SAL domain. Results demonstrate that the SACSM, under certain conditions, simulates user behaviours accurately.Green Open Access added to TU Delft Institutional Repository 'You share, we take care!' - Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.Web Information System
Evaluating the Robustness of Retrieval Pipelines with Query Variation Generators
No full textHeavily pre-trained transformers for language modeling, such as BERT, have shown to be remarkably effective for Information Retrieval (IR) tasks, typically applied to re-rank the results of a first-stage retrieval model. IR benchmarks evaluate the effectiveness of retrieval pipelines based on the premise that a single query is used to instantiate the underlying information need. However, previous research has shown that (I) queries generated by users for a fixed information need are extremely variable and, in particular, (II) neural models are brittle and often make mistakes when tested with modified inputs. Motivated by those observations we aim to answer the following question: how robust are retrieval pipelines with respect to different variations in queries that do not change the queries’ semantics? In order to obtain queries that are representative of users’ querying variability, we first created a taxonomy based on the manual annotation of transformations occurring in a dataset (UQV100) of user-created query variations. For each syntax-changing category of our taxonomy, we employed different automatic methods that when applied to a query generate a query variation. Our experimental results across two datasets for two IR tasks reveal that retrieval pipelines are not robust to these query variations, with effectiveness drops of ≈ 20 % on average. The code and datasets are available at https://github.com/Guzpenha/query_variation_generators.Green Open Access added to TU Delft Institutional Repository 'You share, we take care!' - Taverne project https://www.openaccess.nl/en/you-share-we-take-care Otherwise as indicated in the copyright section: the publisher is the copyright holder of this work and the author uses the Dutch legislation to make this work public.Web Information System
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