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Ankur P. Parikh

dblp:80/8411 · DBLP profile ↗
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27ranked-venue papers
9as first author
7since 2021 · last 2023
—ORCID · none

Domains — the database's venue-derived domains; a paper can count in several

Artificial intelligence and machine learning · 23 · 7 first-author · 6 since 2021Applied, interdisciplinary, general and emerging computing · 3 · 2 first-authorGraphics, computer vision, multimedia, augmented reality and games · 1 · 1 since 2021

Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.

Artificial intelligence
16 papers
Language models and text generation · 48% Reinforcement learning · 11% Question answering and dialogue systems · 8%
Network and information security
1 paper
Security and privacy of machine learning · 50% Web and mobile security · 50%
Databases, data mining, and information retrieval
2 papers
Information retrieval · 100%
Theoretical computer science
3 papers
Algorithms and data structures · 72% Automata and formal languages · 28%

Topics — the 30 heaviest of 39, each with the papers that count most for it

TopicWeightPapersLastEvidence papers
Natural language and speech › Language models and text generation
text generation
1.122023
Extrapolative Controlled Sequence Generation via Iterative Refinement · ICML 2023
ToTTo: A Controlled Table-To-Text Generation Dataset · EMNLP (1) 2020
Natural language and speech › Language models and text generation › large language model evaluation › automatic evaluation
learned evaluation metric
0.922021
Learning Compact Metrics for MT · EMNLP (1) 2021
BLEURT: Learning Robust Metrics for Text Generation · ACL 2020
Natural language and speech › Language models and text generation › text generation › data-to-text generation
table-to-text generation
0.822020
ToTTo: A Controlled Table-To-Text Generation Dataset · EMNLP (1) 2020
Handling Divergent Reference Texts when Evaluating Table-to-Text Generation · ACL (1) 2019
Information retrieval
retrieval models
0.722019
Real-Time Open-Domain Question Answering with Dense-Sparse Phrase Index · ACL (1) 2019
Phrase-Indexed Question Answering: A New Challenge for Scalable Document Comprehension · EMNLP 2018
Natural language and speech › Language models and text generation › text generation
conditional text generation
0.712023
Reward Gaming in Conditional Text Generation · ACL (1) 2023
Machine learning › Generative modeling
iterative refinement
0.712023
Extrapolative Controlled Sequence Generation via Iterative Refinement · ICML 2023
Natural language and speech › Question answering and dialogue systems
machine reading comprehension
0.722018
Multi-Mention Learning for Reading Comprehension with Neural Cascades · ICLR (Poster) 2018
Phrase-Indexed Question Answering: A New Challenge for Scalable Document Comprehension · EMNLP 2018
Machine learning › Reinforcement learning
reward learning
0.712023
Reward Gaming in Conditional Text Generation · ACL (1) 2023
Machine learning › Reinforcement learning › reward design
reward misspecification
0.712023
Reward Gaming in Conditional Text Generation · ACL (1) 2023
Natural language and speech › Language models and text generation › text summarization
summarization evaluation
0.712023
SEAHORSE: A Multilingual, Multifaceted Dataset for Summarization Evaluation · EMNLP 2023
Machine learning › Efficient and distributed learning › distillation
cross-lingual distillation
0.512021
Learning Compact Metrics for MT · EMNLP (1) 2021
Machine learning › Efficient and distributed learning › model compression
knowledge distillation
0.512021
Learning Compact Metrics for MT · EMNLP (1) 2021
Natural language and speech › Machine translation
machine translation evaluation
0.512021
Learning Compact Metrics for MT · EMNLP (1) 2021
Natural language and speech › Language models and text generation › text generation
data-to-text generation
0.412020
ToTTo: A Controlled Table-To-Text Generation Dataset · EMNLP (1) 2020
Web and mobile security › web security
API security
0.412020
Thieves on Sesame Street! Model Extraction of BERT-based APIs · ICLR 2020
Security and privacy of machine learning
model stealing
0.412020
Thieves on Sesame Street! Model Extraction of BERT-based APIs · ICLR 2020
Machine learning › Probabilistic and Bayesian machine learning › structured models
graphical models
0.432013
Hierarchical Tensor Decomposition of Latent Tree Graphical Models · ICML (3) 2013
Kernel Embeddings of Latent Tree Graphical Models · NIPS 2011
A Spectral Algorithm for Latent Tree Graphical Models · ICML 2011
Machine learning › Probabilistic and Bayesian machine learning › structured models › graphical models › latent variable graphical model
latent tree models
0.432013
Hierarchical Tensor Decomposition of Latent Tree Graphical Models · ICML (3) 2013
Kernel Embeddings of Latent Tree Graphical Models · NIPS 2011
A Spectral Algorithm for Latent Tree Graphical Models · ICML 2011
Natural language and speech › Language models and text generation › evaluation of language models
faithfulness evaluation
0.412019
Handling Divergent Reference Texts when Evaluating Table-to-Text Generation · ACL (1) 2019
Natural language and speech › Question answering and dialogue systems
open-domain question answering
0.412019
Real-Time Open-Domain Question Answering with Dense-Sparse Phrase Index · ACL (1) 2019
Algorithms and data structures
spectral methods
0.322014
Spectral Unsupervised Parsing with Additive Tree Metrics · ACL (1) 2014
A Spectral Algorithm for Latent Tree Graphical Models · ICML 2011
Natural language and speech › Language models and text generation › natural language understanding › sentence pair modeling
natural language inference
0.212016
A Decomposable Attention Model for Natural Language Inference · EMNLP 2016
Machine learning › Trustworthy machine learning
robustness
0.212023
Reward Gaming in Conditional Text Generation · ACL (1) 2023
Machine learning › Trustworthy machine learning › robustness
spurious correlation
0.212023
Reward Gaming in Conditional Text Generation · ACL (1) 2023
Natural language and speech › Language models and text generation › text summarization
summarization datasets
0.212023
SEAHORSE: A Multilingual, Multifaceted Dataset for Summarization Evaluation · EMNLP 2023
Bioinformatics and computational biology
protein engineering
0.212023
Extrapolative Controlled Sequence Generation via Iterative Refinement · ICML 2023
Natural language and speech › Language models and text generation › language modeling
n-gram language model
0.212014
Language Modeling with Power Low Rank Ensembles · EMNLP 2014
Natural language and speech › Language models and text generation › language modeling
statistical language modeling
0.212014
Language Modeling with Power Low Rank Ensembles · EMNLP 2014
Automata and formal languages
parsing
0.212014
Spectral Unsupervised Parsing with Additive Tree Metrics · ACL (1) 2014
Algorithms and data structures › numerical linear algebra › matrix and tensor decomposition
tensor decomposition
0.212013
Hierarchical Tensor Decomposition of Latent Tree Graphical Models · ICML (3) 2013

Methods — techniques the papers use, named apart from their topics

sequence editing · 1.3iterative refinement · 1.3reward modeling · 0.7reinforcement learning from human feedback · 0.7synthetic data generation · 0.5knowledge distillation · 0.5spectral methods · 0.5crowdsourcing · 0.4BERT · 0.4query-agnostic indexing · 0.4n-gram alignment · 0.4human evaluation · 0.4dense-sparse phrase encoding · 0.4phrase indexing · 0.3dual encoder · 0.3bilexical parsing · 0.2recursive decomposition · 0.2total variation regularization · 0.1
YearPublicationVenuePosition
2023 Reward Gaming in Conditional Text Generation
abstract
To align conditional text generation model outputs with desired behaviors, there has been an increasing focus on training the model using reinforcement learning (RL) with reward functions learned from human annotations.Under this framework, we identify three common cases where high rewards are incorrectly assigned to undesirable patterns: noise-induced spurious correlation, naturally occurring spurious correlation, and covariate shift.We show that even though learned metrics achieve high performance on the distribution of the data used to train the reward function, the undesirable patterns may be amplified during RL training of the text generation model.While there has been discussion about reward gaming in the RL or safety community, in this discussion piece, we would like to highlight reward gaming in the natural language generation (NLG) community using concrete conditional text generation examples and discuss potential fixes and areas for future work.
Richard Yuanzhe Pang, Vishakh Padmakumar, Thibault Sellam, Ankur P. Parikh, He He 0001
ACL (1)4
2023 SEAHORSE: A Multilingual, Multifaceted Dataset for Summarization Evaluation
abstract
Elizabeth Clark, Shruti Rijhwani, Sebastian Gehrmann, Joshua Maynez, Roee Aharoni, Vitaly Nikolaev, Thibault Sellam, Aditya Siddhant, Dipanjan Das, Ankur Parikh. Proceedings of the 2023 Conference on Empirical Methods in Natural Language Processing. 2023.
Elizabeth Clark, Shruti Rijhwani, Sebastian Gehrmann, Joshua Maynez, Roee Aharoni, Vitaly Nikolaev, Thibault Sellam, Aditya Siddhant, Dipanjan Das 0001, Ankur P. Parikh
EMNLP10
2023 SQuId: Measuring Speech Naturalness in Many Languages
abstract
Much of text-to-speech research relies on human evaluation. This incurs heavy costs and slows down the development process, especially in heavily multilingual applications where recruiting and polling annotators can take weeks. We introduce SQuId (Speech Quality Identification), a multilingual naturalness prediction model trained on over a million ratings and tested in 65 locales—the largest effort of this type to date. The main insight is that training one model on many locales consistently surpasses mono-locale baselines. We show that the model outperforms a competitive baseline based on w2v-BERT and VoiceMOS by 50.0%. We then demonstrate the effectiveness of cross-locale transfer during fine-tuning and highlight its effect on zero-shot locales, for which there is no fine-tuning data. We highlight the role of non-linguistic effects such as sound artifacts in cross-locale transfer. Finally, we present the effect of model size and pre-training diversity with ablation experiments.
Thibault Sellam, Ankur Bapna, Joshua Camp, Diana Mackinnon, Ankur P. Parikh, Jason Riesa
ICASSP5
2023 Extrapolative Controlled Sequence Generation via Iterative Refinement
abstract
We study the problem of extrapolative controlled generation, i.e., generating sequences with attribute values beyond the range seen in training. This task is of significant importance in automated design, especially drug discovery, where the goal is to design novel proteins that are better (e.g., more stable) than existing sequences. Thus, by definition the target sequences and their attribute values are out of the training distribution, posing challenges to existing methods that aim to directly generate the target sequence. Instead, in this work, we propose Iterative Controlled Extrapolation (ICE) which iteratively makes local edits to a sequence to enable extrapolation. We train the model on synthetically generated sequence pairs that demonstrate small improvement in the attribute value. Results on one natural language task (sentiment analysis) and two protein engineering tasks (ACE2 stability and AAV fitness) show that ICE outperforms state-of-the-art approaches despite its simplicity.
Vishakh Padmakumar, Richard Yuanzhe Pang, He He 0001, Ankur P. Parikh
ICML4
2021 Learning Compact Metrics for MT
abstract
Recent developments in machine translation and multilingual text generation have led researchers to adopt trained metrics such as COMET or BLEURT, which treat evaluation as a regression problem and use representations from multilingual pre-trained models such as XLM-RoBERTa or mBERT.Yet studies on related tasks suggest that these models are most efficient when they are large, which is costly and impractical for evaluation.We investigate the trade-off between multilinguality and model capacity with RemBERT, a stateof-the-art multilingual language model, using data from the WMT Metrics Shared Task.We present a series of experiments which show that model size is indeed a bottleneck for cross-lingual transfer, then demonstrate how distillation can help addressing this bottleneck, by leveraging synthetic data generation and transferring knowledge from one teacher to multiple students trained on related languages.Our method yields up to 10.5% improvement over vanilla fine-tuning and reaches 92.6% of RemBERT's performance using only a third of its parameters. * Work done during an internship at Google.
Amy Pu, Hyung Won Chung, Ankur P. Parikh, Sebastian Gehrmann, Thibault Sellam
EMNLP (1)3
2021 Towards Continual Learning for Multilingual Machine Translation via Vocabulary Substitution
abstract
Xavier Garcia, Noah Constant, Ankur Parikh, Orhan Firat. Proceedings of the 2021 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies. 2021.
Xavier Garcia, Noah Constant, Ankur P. Parikh, Orhan Firat
NAACL-HLT3
2021 Harnessing Multilinguality in Unsupervised Machine Translation for Rare Languages
abstract
Xavier Garcia, Aditya Siddhant, Orhan Firat, Ankur Parikh. Proceedings of the 2021 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies. 2021.
Xavier Garcia, Aditya Siddhant, Orhan Firat, Ankur P. Parikh
NAACL-HLT4
2020 BLEURT: Learning Robust Metrics for Text Generation
abstract
Text generation has made significant advances in the last few years.Yet, evaluation metrics have lagged behind, as the most popular choices (e.g., BLEU and ROUGE) may correlate poorly with human judgments.We propose BLEURT, a learned evaluation metric based on BERT that can model human judgments with a few thousand possibly biased training examples.A key aspect of our approach is a novel pre-training scheme that uses millions of synthetic examples to help the model generalize.BLEURT provides state-ofthe-art results on the last three years of the WMT Metrics shared task and the WebNLG Competition dataset.In contrast to a vanilla BERT-based approach, it yields superior results even when the training data is scarce and out-of-distribution.
Thibault Sellam, Dipanjan Das 0001, Ankur P. Parikh
ACL3
2020 ToTTo: A Controlled Table-To-Text Generation Dataset
abstract
Ankur Parikh, Xuezhi Wang, Sebastian Gehrmann, Manaal Faruqui, Bhuwan Dhingra, Diyi Yang, Dipanjan Das. Proceedings of the 2020 Conference on Empirical Methods in Natural Language Processing (EMNLP). 2020.
Ankur P. Parikh, Xuezhi Wang 0002, Sebastian Gehrmann, Manaal Faruqui, Bhuwan Dhingra, Diyi Yang, Dipanjan Das 0001
EMNLP (1)1
2020 Thieves on Sesame Street! Model Extraction of BERT-based APIs
Kalpesh Krishna, Gaurav Tomar, Ankur P. Parikh, Nicolas Papernot, Mohit Iyyer
ICLR3
2019 Handling Divergent Reference Texts when Evaluating Table-to-Text Generation
abstract
Automatically constructed datasets for generating text from semi-structured data (tables), such as WikiBio (Lebret et al., 2016), often contain reference texts that diverge from the information in the corresponding semistructured data.We show that metrics which rely solely on the reference texts, such as BLEU and ROUGE, show poor correlation with human judgments when those references diverge.We propose a new metric, PAR-ENT, which aligns n-grams from the reference and generated texts to the semi-structured data before computing their precision and recall.Through a large scale human evaluation study of table-to-text models for WikiBio, we show that PARENT correlates with human judgments better than existing text generation metrics.We also adapt and evaluate the information extraction based evaluation proposed in Wiseman et al. (2017), and show that PAR-ENT has comparable correlation to it, while being easier to use.We show that PARENT is also applicable when the reference texts are elicited from humans using the data from the WebNLG challenge.1 * Work done during an internship at Google.
Bhuwan Dhingra, Manaal Faruqui, Ankur P. Parikh, Ming-Wei Chang, Dipanjan Das 0001, William W. Cohen
ACL (1)3
2019 Real-Time Open-Domain Question Answering with Dense-Sparse Phrase Index
abstract
Existing open-domain question answering (QA) models are not suitable for real-time usage because they need to process several long documents on-demand for every input query, which is computationally prohibitive. In this paper, we introduce query-agnostic indexable representations of document phrases that can drastically speed up open-domain QA. In particular, our dense-sparse phrase encoding effectively captures syntactic, semantic, and lexical information of the phrases and eliminates the pipeline filtering of context documents. Leveraging strategies for optimizing training and inference time, our model can be trained and deployed even in a single 4-GPU server. Moreover, by representing phrases as pointers to their start and end tokens, our model indexes phrases in the entire English Wikipedia (up to 60 billion phrases) using under 2TB. Our experiments on SQuAD-Open show that our model is on par with or more accurate than previous models with 6000x reduced computational cost, which translates into at least 68x faster end-to-end inference benchmark on CPUs. Code and demo are available at nlp.cs.washington.edu/denspi
Minjoon Seo, Jinhyuk Lee, Tom Kwiatkowski, Ankur P. Parikh, Ali Farhadi, Hannaneh Hajishirzi
ACL (1)4
2019 Natural Questions: a Benchmark for Question Answering Research
abstract
We present the Natural Questions corpus, a question answering data set. Questions consist of real anonymized, aggregated queries issued to the Google search engine. An annotator is presented with a question along with a Wikipedia page from the top 5 search results, and annotates a long answer (typically a paragraph) and a short answer (one or more entities) if present on the page, or marks null if no long/short answer is present. The public release consists of 307,373 training examples with single annotations; 7,830 examples with 5-way annotations for development data; and a further 7,842 examples with 5-way annotated sequestered as test data. We present experiments validating quality of the data. We also describe analysis of 25-way annotations on 302 examples, giving insights into human variability on the annotation task. We introduce robust metrics for the purposes of evaluating question answering systems; demonstrate high human upper bounds on these metrics; and establish baseline results using competitive methods drawn from related literature.
Tom Kwiatkowski, Jennimaria Palomaki, Olivia Redfield, Michael Collins 0001, Ankur P. Parikh, Christopher Alberti, Danielle Epstein, Illia Polosukhin, Jacob Devlin, Kenton Lee, Kristina Toutanova, Llion Jones, Matthew Kelcey, Ming-Wei Chang, Andrew M. Dai, Jakob Uszkoreit, Quoc V. Le, Slav Petrov
Trans. Assoc. Comput. Linguistics5
2018 Phrase-Indexed Question Answering: A New Challenge for Scalable Document Comprehension
abstract
We formalize a new modular variant of current question answering tasks by enforcing complete independence of the document encoder from the question encoder.This formulation addresses a key challenge in machine comprehension by requiring a standalone representation of the document discourse.It additionally leads to a significant scalability advantage since the encoding of the answer candidate phrases in the document can be pre-computed and indexed offline for efficient retrieval.We experiment with baseline models for the new task, which achieve a reasonable accuracy but significantly underperform unconstrained QA models.We invite the QA research community to engage in Phrase-Indexed Question Answering (PIQA, pika) for closing the gap.The leaderboard is at: nlp.
Minjoon Seo, Tom Kwiatkowski, Ankur P. Parikh, Ali Farhadi, Hannaneh Hajishirzi
EMNLP3
2018 Multi-Mention Learning for Reading Comprehension with Neural Cascades
Swabha Swayamdipta, Ankur P. Parikh, Tom Kwiatkowski
ICLR (Poster)2
2016 A Decomposable Attention Model for Natural Language Inference
abstract
We propose a simple neural architecture for natural language inference.Our approach uses attention to decompose the problem into subproblems that can be solved separately, thus making it trivially parallelizable.On the Stanford Natural Language Inference (SNLI) dataset, we obtain state-of-the-art results with almost an order of magnitude fewer parameters than previous work and without relying on any word-order information.Adding intra-sentence attention that takes a minimum amount of order into account yields further improvements.
Ankur P. Parikh, Oscar Täckström, Dipanjan Das 0001, Jakob Uszkoreit
EMNLP1
2015 Grounded Semantic Parsing for Complex Knowledge Extraction
abstract
Recently, there has been increasing interest in learning semantic parsers with indirect supervision, but existing work focuses almost exclusively on question answering.Separately, there have been active pursuits in leveraging databases for distant supervision in information extraction, yet such methods are often limited to binary relations and none can handle nested events.In this paper, we generalize distant supervision to complex knowledge extraction, by proposing the first approach to learn a semantic parser for extracting nested event structures without annotated examples, using only a database of such complex events and unannotated text.The key idea is to model the annotations as latent variables, and incorporate a prior that favors semantic parses containing known events.Experiments on the GENIA event extraction dataset show that our approach can learn from and extract complex biological pathway events.Moreover, when supplied with just five example words per event type, it becomes competitive even among supervised systems, outperforming 19 out of 24 teams that participated in the original shared task.
Ankur P. Parikh, Hoifung Poon, Kristina Toutanova
HLT-NAACL1
2014 Spectral Unsupervised Parsing with Additive Tree Metrics
abstract
We propose a spectral approach for unsupervised constituent parsing that comes with theoretical guarantees on latent structure recovery.Our approach is grammarless -we directly learn the bracketing structure of a given sentence without using a grammar model.The main algorithm is based on lifting the concept of additive tree metrics for structure learning of latent trees in the phylogenetic and machine learning communities to the case where the tree structure varies across examples.Although finding the "minimal" latent tree is NP-hard in general, for the case of projective trees we find that it can be found using bilexical parsing algorithms.Empirically, our algorithm performs favorably compared to the constituent context model of Klein and Manning (2002) without the need for careful initialization.
Ankur P. Parikh, Shay B. Cohen, Eric P. Xing
ACL (1)1
2014 Language Modeling with Power Low Rank Ensembles
abstract
We present power low rank ensembles (PLRE), a flexible framework for n-gram language modeling where ensembles of low rank matrices and tensors are used to obtain smoothed probability estimates of words in context.Our method can be understood as a generalization of ngram modeling to non-integer n, and includes standard techniques such as absolute discounting and Kneser-Ney smoothing as special cases.PLRE training is efficient and our approach outperforms stateof-the-art modified Kneser Ney baselines in terms of perplexity on large corpora as well as on BLEU score in a downstream machine translation task.
Ankur P. Parikh, Avneesh Saluja, Chris Dyer, Eric P. Xing
EMNLP1
2014 Network Analysis of Breast Cancer Progression and Reversal Using a Tree-Evolving Network Algorithm
abstract
The HMT3522 progression series of human breast cells have been used to discover how tissue architecture, microenvironment and signaling molecules affect breast cell growth and behaviors. However, much remains to be elucidated about malignant and phenotypic reversion behaviors of the HMT3522-T4-2 cells of this series. We employed a "pan-cell-state" strategy, and analyzed jointly microarray profiles obtained from different state-specific cell populations from this progression and reversion model of the breast cells using a tree-lineage multi-network inference algorithm, Treegl. We found that different breast cell states contain distinct gene networks. The network specific to non-malignant HMT3522-S1 cells is dominated by genes involved in normal processes, whereas the T4-2-specific network is enriched with cancer-related genes. The networks specific to various conditions of the reverted T4-2 cells are enriched with pathways suggestive of compensatory effects, consistent with clinical data showing patient resistance to anticancer drugs. We validated the findings using an external dataset, and showed that aberrant expression values of certain hubs in the identified networks are associated with poor clinical outcomes. Thus, analysis of various reversion conditions (including non-reverted) of HMT3522 cells using Treegl can be a good model system to study drug effects on breast cancer.
Ankur P. Parikh, Ross E. Curtis, Irene Kuhn, Sabine Becker-Weimann, Mina J. Bissell, Eric P. Xing, Wei Wu 0023
PLoS Comput. Biol.1
2013 Hierarchical Tensor Decomposition of Latent Tree Graphical Models
abstract
We approach the problem of estimating the parameters of a latent tree graphical model from a hierarchical tensor decomposition point of view. In this new view, the marginal probability table of the observed variables in a latent tree is treated as a tensor, and we show that: (i) the latent variables induce low rank structures in various matricizations of the tensor; (ii) this collection of low rank matricizations induce a hierarchical low rank decomposition of the tensor. Exploiting these properties, we derive an optimization problem for estimating the parameters of a latent tree graphical model, i.e., hierarchical decomposion of a tensor which minimizes the Frobenius norm of the difference between the original tensor and its decomposition. When the latent tree graphical models are correctly specified, we show that a global optimum of the optimization problem can be obtained via a recursive decomposition algorithm. This algorithm recovers previous spectral algorithms for hidden Markov models (Hsu et al., 2009; Foster et al., 2012) and latent tree graphical models (Parikh et al., 2011; Song et al., 2011) as special cases, elucidating the global objective these algorithms are optimizing for. When the latent tree graphical models are misspecified, we derive a better decomposition based on our framework, and provide approximation guarantee for this new estimator. In both synthetic and real world data, this new estimator significantly improves over the-state-of-the-art.
Mariya Ishteva, Ankur P. Parikh, Eric P. Xing, Haesun Park
ICML (3)3
2012 A Spectral Algorithm for Latent Junction Trees
Ankur P. Parikh, Mariya Ishteva, Gabi Teodoru, Eric P. Xing
UAI1
2012 Enabling dynamic network analysis through visualization in TVNViewer
abstract
BACKGROUND: Many biological processes are context-dependent or temporally specific. As a result, relationships between molecular constituents evolve across time and environments. While cutting-edge machine learning techniques can recover these networks, exploring and interpreting the rewiring behavior is challenging. Information visualization shines in this type of exploratory analysis, motivating the development ofTVNViewer (http://sailing.cs.cmu.edu/tvnviewer), a visualization tool for dynamic network analysis. RESULTS: In this paper, we demonstrate visualization techniques for dynamic network analysis by using TVNViewer to analyze yeast cell cycle and breast cancer progression datasets. CONCLUSIONS: TVNViewer is a powerful new visualization tool for the analysis of biological networks that change across time or space.
Ross E. Curtis, Jing Xiang, Ankur P. Parikh, Peter Kinnaird, Eric P. Xing
BMC Bioinform.3
2011 A Spectral Algorithm for Latent Tree Graphical Models
Ankur P. Parikh, Eric P. Xing
ICML1
2011 Kernel Embeddings of Latent Tree Graphical Models
abstract
Latent tree graphical models are natural tools for expressing long range and hierarchical dependencies among many variables which are common in computer vision, bioinformatics and natural language processing problems. However, existing models are largely restricted to discrete and Gaussian variables due to computational constraints; furthermore, algorithms for estimating the latent tree structure and learning the model parameters are largely restricted to heuristic local search. We present a method based on kernel embeddings of distributions for latent tree graphical models with continuous and non-Gaussian variables. Our method can recover the latent tree structures with provable guarantees and perform local-minimum free parameter learning and efficient inference. Experiments on simulated and real data show the advantage of our proposed approach.
Ankur P. Parikh, Eric P. Xing
NIPS2
2011 TREEGL: reverse engineering tree-evolving gene networks underlying developing biological lineages
abstract
MOTIVATION: Estimating gene regulatory networks over biological lineages is central to a deeper understanding of how cells evolve during development and differentiation. However, one challenge in estimating such evolving networks is that their host cells not only contiguously evolve, but also branch over time. For example, a stem cell evolves into two more specialized daughter cells at each division, forming a tree of networks. Another example is in a laboratory setting: a biologist may apply several different drugs individually to malignant cancer cells to analyze the effects of each drug on the cells; the cells treated by one drug may not be intrinsically similar to those treated by another, but rather to the malignant cancer cells they were derived from. RESULTS: We propose a novel algorithm, Treegl, an ℓ(1) plus total variation penalized linear regression method, to effectively estimate multiple gene networks corresponding to cell types related by a tree-genealogy, based on only a few samples from each cell type. Treegl takes advantage of the similarity between related networks along the biological lineage, while at the same time exposing sharp differences between the networks. We demonstrate that our algorithm performs significantly better than existing methods via simulation. Furthermore we explore an application to a breast cancer dataset, and show that our algorithm is able to produce biologically valid results that provide insight into the progression and reversion of breast cancer cells. AVAILABILITY: Software will be available at http://www.sailing.cs.cmu.edu/. CONTACT: [email protected].
Ankur P. Parikh, Wei Wu 0023, Ross E. Curtis, Eric P. Xing
Bioinform.1
2010 On Sparse Nonparametric Conditional Covariance Selection
Mladen Kolar, Ankur P. Parikh, Eric P. Xing
ICML2