Hu Fu 0001

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31ranked-venue papers
13as first author
10since 2021 · last 2026
0009-0005-4217-4329ORCID · conflict

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Theory of computation · 19 · 11 first-author · 3 since 2021Artificial intelligence and machine learning · 16 · 7 first-author · 6 since 2021Applied, interdisciplinary, general and emerging computing · 4 · 2 first-author · 2 since 2021Graphics, computer vision, multimedia, augmented reality and games · 3 · 2 since 2021Databases, data management, data science and information retrieval · 2 · 1 since 2021Computer networks · 1
YearPublicationVenuePosition
2026 Incentives for early arrival in online cooperative games
Dengji Zhao, Yaoxin Ge, Yao Zhang 0011, Zhihao Gavin Tang, Hu Fu 0001, Pinyan Lu
Artif. Intell.5
2025 Incentives for Early Arrival in Cost Sharing
Junyu Zhang 0005, Yao Zhang 0011, Yaoxin Ge, Dengji Zhao, Hu Fu 0001, Zhihao Gavin Tang, Pinyan Lu
AAMAS5
2025 Incentives for Early Arrival in Cooperative Games (Extended Abstract)
abstract
We study cooperative games where players join sequentially, and the value generated by those who have joined at any point must be irrevocably divided among these players. We introduce two desiderata for the value division mechanism: that the players should have incentives to join as early as possible, and that the division should be considered fair. For the latter, we require that each player's expected share in the mechanism should equal her Shapley value if the players' arrival order is uniformly at random. When the value generation function is submodular, allocating the marginal value to the player satisfies these properties. This is no longer true for more general functions. Our main technical contribution is a complete characterization of 0-1 value games for which desired mechanisms exist. We show that a natural mechanism, Rewarding First Critical Player (RFC), is complete, in that a 0-1 value function admits a mechanism with the properties above if and only if RFC satisfies them; we analytically characterize all such value functions. Moreover, we give an algorithm that decomposes, in an online fashion, any value function into 0-1 value functions, on each of which RFC can be run. In this way, we design an extension of RFC for general monotone games, and the properties are proved to be maintained.
Yaoxin Ge, Yao Zhang 0011, Dengji Zhao, Zhihao Gavin Tang, Hu Fu 0001, Pinyan Lu
IJCAI5
2025 Price Stability and Improved Buyer Utility with Presentation Design: A Theoretical Study of the Amazon Buy Box
abstract
Platforms design the form of presentation by which sellers are shown to the buyers. This design not only shapes the buyers' experience but also leads to different market equilibria or dynamics. One component in this design is through the platform's mediation of the search frictions experienced by the buyers for different sellers. We take a model of monopolistic competition and show that, on one hand, when all sellers have the same inspection costs, the market sees no stable price since the sellers always have incentives to undercut each other, and, on the other hand, the platform may stabilize the price by giving prominence to one seller chosen by a carefully designed mechanism. This calls to mind Amazon's Buy Box. We study natural mechanisms for choosing the prominent seller, characterize the range of equilibrium prices implementable by them, and find that in certain scenarios the buyers' surplus improves as the search friction increases.
Ophir Friedler, Hu Fu 0001, Anna R. Karlin, Ariana Tang
WWW2
2024 Pay to (Not) Play: Monetizing Impatience in Mobile Games
abstract
Mobile gaming is a rapidly growing and incredibly profitable sector; having grown seven-fold over the past 10 years, it now grosses over $100 billion annually. This growth was due in large part to a shift in monetization strategies: rather than charging players an upfront cost ("pay-to-play"), games often request optional microtransactions throughout gameplay ("free-to-play"). We focus on a common scenario in which games include wait times---gating either items or game progression---that players can pay to skip. Game designers typically say that they optimize for player happiness rather than revenue; however, prices for skips are typically set at levels that few players are willing to pay, leading to low purchase rates. Under a traditional analysis, it would seem that game designers fail at their stated goal if few players buy what they are selling. We argue that an alternate model can better explain this dynamic: players value tasks more highly as they are perceived to be more difficult. While skips can increase players' utilities by providing instant gratification, pricing skips too cheaply can lower players' utilities by decreasing the perceived amount of work needed to complete a task. We show that high revenue, high player utility, and low purchase rates can all coexist under this model, particularly under a realistic distribution of players having few buyers but a few big-spending "whales." We also investigate how a game designer should optimize prices under our model. An appendix of the paper with proofs, more comprehensive results and visualizations can be found at https://arxiv.org/abs/2312.10205.
Taylor Lundy, Narun K. Raman, Hu Fu 0001, Kevin Leyton-Brown
AAAI3
2024 Sample-Based Matroid Prophet Inequalities
abstract
The classical prophet inequalities problem introduced by Krengel and Sucheston [1977, 1978] assumed complete knowledge of distributions. However, such an assumption may be unrealistic both in practice and for some applications.
Hu Fu 0001, Pinyan Lu, Zhihao Gavin Tang, Hongxun Wu, Qianfan Zhang 0002
EC1
2023 On the Last-iterate Convergence in Time-varying Zero-sum Games: Extra Gradient Succeeds where Optimism Fails
abstract
Last-iterate convergence has received extensive study in two player zero-sum games starting from bilinear, convex-concave up to settings that satisfy the MVI condition. Typical methods that exhibit last-iterate convergence for the aforementioned games include extra-gradient (EG) and optimistic gradient descent ascent (OGDA). However, all the established last-iterate convergence results hold for the restrictive setting where the underlying repeated game does not change over time. Recently, a line of research has focused on regret analysis of OGDA in time-varying games, i.e., games where payoffs evolve with time; the last-iterate behavior of OGDA and EG in time-varying environments remains unclear though. In this paper, we study the last-iterate behavior of various algorithms in two types of unconstrained, time-varying, bilinear zero-sum games: periodic and convergent perturbed games. These models expand upon the usual repeated game formulation and incorporate external environmental factors, such as the seasonal effects on species competition and vanishing external noise. In periodic games, we prove that EG will converge while OGDA and momentum method will diverge. This is quite surprising, as to the best of our knowledge, it is the first result that indicates EG and OGDA have qualitatively different last-iterate behaviors and do not exhibit similar behavior. In convergent perturbed games, we prove all these algorithms converge as long as the game itself stabilizes with a faster rate than $1/t$.
Hu Fu 0001, Qun Hu, Ioannis Panageas, Xiao Wang 0036
NeurIPS2
2023 Pandora Box Problem with Nonobligatory Inspection: Hardness and Approximation Scheme
abstract
Weitzman (1979) introduced the Pandora Box problem as a model for sequential search with inspection costs, and gave an elegant index-based policy that attains provably optimal expected payoff. In various scenarios, the searching agent may select an option without making a costly inspection. The variant of the Pandora box problem with non-obligatory inspection has attracted interest from both economics and algorithms researchers. Various simple algorithms have proved suboptimal, with the best known 0.8-approximation algorithm due to Guha et al. (2008). No hardness result for the problem was known.
Hu Fu 0001, Jiawei Li 0014, Daogao Liu
STOC1
2022 Stability of Decentralized Queueing Networks Beyond Complete Bipartite Cases
Hu Fu 0001, Qun Hu, Jia'nan Lin
WINE1
2021 Random Order Vertex Arrival Contention Resolution Schemes for Matching, with Applications
abstract
With a wide range of applications, stochastic matching problems have been studied in different models, including prophet inequality, Query-Commit, and Price-of-Information. While there have been recent breakthroughs in all these settings for bipartite graphs, few non-trivial results are known for general graphs. In this paper, we study the random order vertex arrival contention resolution scheme for matching in general graphs, which is inspired by the recent work of Ezra et al. (EC 2020). We design an 8/15-selectable batched RCRS for matching and apply it to achieve 8/15-competitive/approximate algorithms for all the three models. Our results are the first non-trivial results for random order prophet matching and Price-of-Information matching in general graphs. For the Query-Commit model, our result substantially improves upon the 0.501 approximation ratio by Tang et al. (STOC 2020). We also show that no batched RCRS for matching can be better than 1/2+1/(2e²) ≈ 0.567-selectable.
Hu Fu 0001, Zhihao Gavin Tang, Hongxun Wu, Qianfan Zhang 0002
ICALP1
2020 Limitations of Incentive Compatibility on Discrete Type Spaces
Taylor Lundy, Hu Fu 0001
AAAI2
2020 Learning Utilities and Equilibria in Non-Truthful Auctions
abstract
In non-truthful auctions, agents' utility for a strategy depends on the strategies of the opponents and also the prior distribution over their private types; the set of Bayes Nash equilibria generally has an intricate dependence on the prior. Using the First Price Auction as our main demonstrating example, we show that $\tilde O(n / \epsilon^2)$ samples from the prior with $n$ agents suffice for an algorithm to learn the interim utilities for all monotone bidding strategies. As a consequence, this number of samples suffice for learning all approximate equilibria. We give almost matching (up to polylog factors) lower bound on the sample complexity for learning utilities. We also consider a setting where agents must pay a search cost to discover their own types. Drawing on a connection between this setting and the first price auction, discovered recently by Kleinberg et al. (2016), we show that $\tilde O(n / \epsilon^2)$ samples suffice for utilities and equilibria to be estimated in a near welfare-optimal descending auction in this setting. En route, we improve the sample complexity bound, recently obtained by Guo et al. (2019), for the Pandora's Box problem, which is a classical model for sequential consumer search.
Hu Fu 0001, Tao Lin 0013
NeurIPS1
2020 Exponential Convergence of Gradient Methods in Concave Network Zero-Sum Games
Amit Kadan, Hu Fu 0001
ECML/PKDD (2)2
2018 The Value of Information Concealment
abstract
We consider a revenue optimizing seller selling a single item to a buyer, on whose private value the seller has a noisy signal. We show that, when the signal is kept private, arbitrarily more revenue could potentially be extracted than if the signal is leaked or revealed. We then show that, if the seller is not allowed to make payments to the buyer and if the value distribution conditioning on each signal is regular, the gap between the two is bounded by a multiplicative factor of 3. We give examples showing that both conditions are necessary for a constant bound on the gap to hold. We connect this scenario to multi-bidder single-item auctions where bidders’ values are correlated. Similarly to the setting above, we show that the revenue of a Bayesian incentive compatible, ex post individually rational auction can be arbitrarily larger than that of a dominant strategy incentive compatible auction, whereas the two are no more than a factor of 5 apart if the auctioneer never pays the bidders and if the distribution is jointly regular. The upper bounds in both settings degrade gracefully when the distribution is a mixture of a small number of regular distributions.
Hu Fu 0001, Christopher Liaw, Pinyan Lu, Zhihao Gavin Tang
SODA1
2017 The efficiency of open access in platforms for networked cournot markets
abstract
This paper studies how the efficiency of an online platform is impacted by the degree to which access of platform participants is open or controlled. The study is motivated by an emerging trend within platforms to impose increasingly fine-grained control over the options available to platform participants. While early online platforms allowed open access, e.g., Ebay allows any seller to interact with any buyer; modern platforms often impose matches directly, e.g., Uber directly matches drivers to riders. This control is performed with the goal of achieving more efficient market outcomes. However, the results in this paper highlight that imposing matches may create new strategic incentives that lead to increased inefficiency. In particular, in the context of networked Cournot competition, we prove that open access platforms guarantee social welfare within 7/16 of the optimal; whereas controlled allocation platforms can have social welfare unboundedly worse than optimal.
John Z. F. Pang, Hu Fu 0001, Won I. Lee, Adam Wierman
INFOCOM2
2015 Randomization Beats Second Price as a Prior-Independent Auction
abstract
Designing revenue optimal auctions for selling an item to $n$ symmetric bidders is a fundamental problem in mechanism design. Myerson (1981) shows that the second price auction with an appropriate reserve price is optimal when bidders' values are drawn i.i.d. from a known regular distribution. A cornerstone in the prior-independent revenue maximization literature is a result by Bulow and Klemperer (1996) showing that the second price auction without a reserve achieves (n-1)/n of the optimal revenue in the worst case. We construct a randomized mechanism that strictly outperforms the second price auction in this setting. Our mechanism inflates the second highest bid with a probability that varies with $n$. For two bidders we improve the performance guarantee from 0.5 to 0.512 of the optimal revenue. We also resolve a question in the design of revenue optimal mechanisms that have access to a single sample from an unknown distribution. We show that a randomized mechanism strictly outperforms all deterministic mechanisms in terms of worst case guarantee.
Hu Fu 0001, Nicole Immorlica, Brendan Lucier, Philipp Strack
EC1
2015 On the Complexity of Computing an Equilibrium in Combinatorial Auctions
abstract
We study combinatorial auctions where each item is sold separately but simultaneously via a second price auction. We ask whether it is possible to efficiently compute in this game a pure Nash equilibrium with social welfare close to the optimal one. We show that when the valuations of the bidders are submodular, in many interesting settings (e.g., constant number of bidders, budget additive bidders) computing an equilibrium with good welfare is essentially as easy as computing, completely ignoring incentives issues, an allocation with good welfare. On the other hand, for subadditive valuations, we show that computing an equilibrium requires exponential communication. Finally, for XOS (a.k.a. fractionally subadditive) valuations, we show that if there exists an efficient algorithm that finds an equilibrium, it must use techniques that are very different from the ones currently known.
Shahar Dobzinski, Hu Fu 0001, Robert D. Kleinberg
SODA2
2014 Improved Lower Bounds for Testing Triangle-freeness in Boolean Functions via Fast Matrix Multiplication
abstract
Understanding the query complexity for testing linear-invariant properties has been a central open problem in the study of algebraic property testing. Triangle-freeness in Boolean functions is a simple property whose testing complexity is unknown. Three Boolean functions f1, f2 and f3, mapping {0,1}^k to {0,1}, are said to be triangle free if there is no x, y in {0,1}^k such that f1(x) = f2(y) = f3(x + y) = 1. This property is known to be strongly testable (Green 2005), but the number of queries needed is upper-bounded only by a tower of twos whose height is polynomial in 1 / epsislon, where epsislon is the distance between the tested function triple and triangle-freeness, i.e., the minimum fraction of function values that need to be modified to make the triple triangle free. A lower bound of (1 / epsilon)^2.423 for any one-sided tester was given by Bhattacharyya and Xie (2010). In this work we improve this bound to (1 / epsilon)^6.619. Interestingly, we prove this by way of a combinatorial construction called uniquely solvable puzzles that was at the heart of Coppersmith and Winograd's renowned matrix multiplication algorithm.
Hu Fu 0001, Robert D. Kleinberg
APPROX-RANDOM1
2014 Approximate revenue maximization in interdependent value settings
abstract
We study revenue maximization in settings where agents' values are interdependent: each agent receives a signal drawn from a correlated distribution and agents' values are functions of all of the signals. We introduce a variant of the generalized VCG auction with reserve prices and random admission, and show that this auction gives a constant approximation to the optimal expected revenue in matroid environments. Our results do not require any assumptions on the signal distributions, however, they require the value functions to satisfy a standard single-crossing property and a concavity-type condition.
Shuchi Chawla 0001, Hu Fu 0001, Anna R. Karlin
EC2
2014 Optimal auctions for correlated buyers with sampling
abstract
Crémer and McLean [1985] showed that, when buyers' valuations are drawn from a correlated distribution, an auction with full knowledge on the distribution can extract the full social surplus. We study whether this phenomenon persists when the auctioneer has only incomplete knowledge of the distribution, represented by a finite family of candidate distributions, and has sample access to the real distribution. We show that the naive approach which uses samples to distinguish candidate distributions may fail, whereas an extended version of the Crémer-McLean auction simultaneously extracts full social surplus under each candidate distribution. With an algebraic argument, we give a tight bound on the number of samples needed by this auction, which is the difference between the number of candidate distributions and the dimension of the linear space they span.
Hu Fu 0001, Nima Haghpanah, Jason D. Hartline, Robert D. Kleinberg
EC1
2013 The Simple Economics of Approximately Optimal Auctions
abstract
The intuition that profit is optimized by maximizing marginal revenue is a guiding principle in microeconomics. In the classical auction theory for agents with quasi-linear utility and single-dimensional preferences, BR89 show that the optimal auction of M81 is in fact optimizing marginal revenue. In particular Myerson's virtual values are exactly the derivative of an appropriate revenue curve. This paper considers mechanism design in environments where the agents have multi-dimensional and non-linear preferences. Understanding good auctions for these environments is considered to be the main challenge in Bayesian optimal mechanism design. In these environments maximizing marginal revenue may not be optimal, and furthermore, there is sometimes no direct way to implement the marginal revenue maximization mechanism. Our contributions are three fold: we characterize the settings for which marginal revenue maximization is optimal (by identifying an important condition that we call revenue linearity), we give simple procedures for implementing marginal revenue maximization in general, and we show that marginal revenue maximization is approximately optimal. Our approximation factor smoothly degrades in a term that quantifies how far the environment is from an ideal one (i.e., where marginal revenue maximization is optimal). Because the marginal revenue mechanism is optimal for well-studied single-dimensional agents, our generalization immediately extends many approximation results for single-dimensional agents to more general preferences. Finally, one of the biggest open questions in Bayesian algorithmic mechanism design is in developing methodologies that are not brute-force in size of the agent type space (usually exponential in the dimension for multi-dimensional agents). Our methods identify a sub problem that, e.g., for unit-demand agents with values drawn from product distributions, enables approximation mechanisms that are polynomial in the dimension.
Saeed Alaei, Hu Fu 0001, Nima Haghpanah, Jason D. Hartline
FOCS2
2013 Prior-independent auctions for risk-averse agents
abstract
We study simple and approximately optimal auctions for agents with a particular form of risk-averse preferences. We show that, for symmetric agents, the optimal revenue (given a prior distribution over the agent preferences) can be approximated by the first-price auction (which is prior independent), and, for asymmetric agents, the optimal revenue can be approximated by an auction with simple form. These results are based on two technical methods. The first is for upper-bounding the revenue from a risk-averse agent. The second gives a payment identity for mechanisms with pay-your-bid semantics.
Hu Fu 0001, Jason D. Hartline, Darrell Hoy
EC1
2013 Cost-recovering bayesian algorithmic mechanism design
abstract
We study the design of Bayesian incentive compatible mechanisms in single parameter domains, for the objective of optimizing social efficiency as measured by social cost. In the problems we consider, a group of participants compete to receive service from a mechanism that can provide such services at a cost. The mechanism wishes to choose which agents to serve in order to maximize social efficiency, but is not willing to suffer an expected loss: the agents' payments should cover the cost of service in expectation.
Hu Fu 0001, Brendan Lucier, Balasubramanian Sivan, Vasilis Syrgkanis
EC1
2013 Simultaneous auctions are (almost) efficient
abstract
Simultaneous item auctions are simple and practical procedures for allocating items to bidders with potentially complex preferences. In a simultaneous auction, every bidder submits independent bids on all items simultaneously. The allocation and prices are then resolved for each item separately, based solely on the bids submitted on that item. We study the efficiency of Bayes-Nash equilibrium (BNE) outcomes of simultaneous first- and second-price auctions when bidders have complement-free (a.k.a. subadditive) valuations. While it is known that the social welfare of every pure Nash equilibrium (NE) constitutes a constant fraction of the optimal social welfare, a pure NE rarely exists, and moreover, the full information assumption is often unrealistic. Therefore, quantifying the welfare loss in Bayes-Nash equilibria is of particular interest. Previous work established a logarithmic bound on the ratio between the social welfare of a BNE and the expected optimal social welfare in both first-price auctions (Hassidim et al., 2011) and second-price auctions (Bhawalkar and Roughgarden, 2011), leaving a large gap between a constant and a logarithmic ratio. We introduce a new proof technique and use it to resolve both of these gaps in a unified way. Specifically, we show that the expected social welfare of any BNE is at least 1/2 of the optimal social welfare in the case of first-price auctions, and at least 1/4 in the case of second-price auctions.
Michal Feldman, Hu Fu 0001, Nick Gravin, Brendan Lucier
STOC2
2012 Ad Auctions with Data
Hu Fu 0001, Patrick R. Jordan, Mohammad Mahdian, Uri Nadav, Inbal Talgam-Cohen, Sergei Vassilvitskii
SAGT1
2012 Bayesian optimal auctions via multi- to single-agent reduction
abstract
We study an abstract optimal auction problem for selecting a subset of self-interested agents to whom to provide a service. A feasibility constraint governs which subsets can be simultaneously served; however, the mechanism may additionally choose to bundle unconstrained attributes such as payments or add-ons with the service. An agent's preference over service and attributes is given by her private type and may be multi-dimensional and non-linear. A single-agent problem is to optimizes a menu to offer an agent subject to constraints on the probabilities with which each of the agent's types is served. We give computationally tractable reductions from multi-agent auction problems to these single-agent problems. Our discussion focuses on maximizing revenue, but our results can be applied to other objectives (e.g., welfare).
Saeed Alaei, Hu Fu 0001, Nima Haghpanah, Jason D. Hartline, Azarakhsh Malekian
EC2
2012 Conditional equilibrium outcomes via ascending price processes with applications to combinatorial auctions with item bidding
abstract
A Walrasian equilibrium in an economy with non-identical indivisible items exists only for small classes of players' valuations (mostly "gross substitutes" valuations), and may not generally exist even with decreasing marginal values. This paper studies a relaxed notion, "conditional equilibrium", that requires individual rationality and "outward stability", i.e., a player will not want to add items to her allocation, at given prices. While a Walrasian equilibrium outcome is unconditionally stable, a conditional equilibrium outcome is stable if players cannot choose to drop only some of their allocated items.
Hu Fu 0001, Robert D. Kleinberg, Ron Lavi
EC1
2012 Sketching valuation functions
abstract
Motivated by the problem of querying and communicating bidders' valuations in combinatorial auctions, we study how well different classes of set functions can be sketched. More formally let f be a function mapping subsets of some ground set [n] to the non-negative real numbers. We say that f′ is an α-sketch of f if for every set S, the value f′(S) lies between f(S)/α and f(S), and f′ can be specified by poly(n) bits. We show that for every subadditive function f there exists an α-sketch where α = n1/2 · O(polylog(n)). Furthermore, we provide an algorithm that finds these sketches with a polynomial number of demand queries. This is essentially the best we can hope for since: 1. We show that there exist subadditive functions (in fact, XOS functions) that do not admit an o(n1/2) sketch. (Balcan and Harvey [3] previously showed that there exist functions belonging to the class of substitutes valuations that do not admit an O(n1/3) sketch.) 2. We prove that every deterministic algorithm that accesses the function via value queries only cannot guarantee a sketching ratio better than n1−ε. We also show that coverage functions, an interesting subclass of submodular functions, admit arbitrarily good sketches. Finally, we show an interesting connection between sketching and learning. We show that for every class of valuations, if the class admits an α-sketch, then it can be α-approximately learned in the PMAC model of Balcan and Harvey. The bounds we prove are only information-theoretic and do not imply the existence of computationally efficient learning algorithms in general.
Ashwinkumar Badanidiyuru, Shahar Dobzinski, Hu Fu 0001, Robert D. Kleinberg, Noam Nisan, Timothy Roughgarden
SODA3
2011 Optimal auctions with correlated bidders are easy
abstract
We consider the problem of designing a revenue-maximizing auction for a single item, when the values of the bidders are drawn from a correlated distribution. We observe that there exists an algorithm that finds the optimal randomized mechanism that runs in time polynomial in the size of the support. We leverage this result to show that in the oracle model introduced by Ronen and Saberi [FOCS'02], there exists a polynomial time truthful in expectation mechanism that provides a (1.5+ε)-approximation to the revenue achievable by an optimal truthful-in-expectation mechanism, and a polynomial time deterministic truthful mechanism that guarantees 5/3 approximation to the revenue achievable by an optimal deterministic truthful mechanism.
Shahar Dobzinski, Hu Fu 0001, Robert D. Kleinberg
STOC2
2010 Inapproximability for VCG-Based Combinatorial Auctions
abstract
The existence of incentive-compatible, computationally-efficient mechanisms for combinatorial auctions with good approximation ratios is the paradigmatic problem in algorithmic mechanism design. It is believed that, in many cases, good approximations for combinatorial auctions may be unattainable due to an inherent clash between truthfulness and computational efficiency. In this paper, we prove the first computational-complexity inapproximability results for incentive-compatible mechanisms for combinatorial auctions. Our results are tight, hold for the important class of VCG-based mechanisms, and are based on the complexity assumption that NP has no polynomial-size circuits. We show two different techniques to obtain such lower bounds: one for deterministic mechanisms that attains optimal dependence on the number of players and number of items, and one that also applies to a class of randomized mechanisms and attains optimal dependence on the number of players. Both techniques are based on novel VC dimension machinery.
David Buchfuhrer, Shaddin Dughmi, Hu Fu 0001, Robert D. Kleinberg, Elchanan Mossel, Christos H. Papadimitriou, Michael Schapira, Yaron Singer, Christopher Umans
SODA3
2007 Identifications of conserved 7-mers in 3'-UTRs and microRNAs in Drosophila
abstract
BACKGROUND: MicroRNAs (miRNAs) are a class of endogenous regulatory small RNAs which play an important role in posttranscriptional regulations by targeting mRNAs for cleavage or translational repression. The base-pairing between the 5'-end of miRNA and the target mRNA 3'-UTRs is essential for the miRNA:mRNA recognition. Recent studies show that many seed matches in 3'-UTRs, which are fully complementary to miRNA 5'-ends, are highly conserved. Based on these features, a two-stage strategy can be implemented to achieve the de novo identification of miRNAs by requiring the complete base-pairing between the 5'-end of miRNA candidates and the potential seed matches in 3'-UTRs. RESULTS: We presented a new method, which combined multiple pairwise conservation information, to identify the frequently-occurred and conserved 7-mers in 3'-UTRs. A pairwise conservation score (PCS) was introduced to describe the conservation of all 7-mers in 3'-UTRs between any two Drosophila species. Using PCSs computed from 6 pairs of flies, we developed a support vector machine (SVM) classifier ensemble, named Cons-SVM and identified 689 conserved 7-mers including 63 seed matches covering 32 out of 38 known miRNA families in the reference dataset. In the second stage, we searched for 90 nt conserved stem-loop regions containing the complementary sequences to the identified 7-mers and used the previously published miRNA prediction software to analyze these stem-loops. We predicted 47 miRNA candidates in the genome-wide screen. CONCLUSION: Cons-SVM takes advantage of the independent evolutionary information from the 6 pairs of flies and shows high sensitivity in identifying seed matches in 3'-UTRs. Combining the multiple pairwise conservation information by the machine learning approach, we finally identified 47 miRNA candidates in D. melanogaster.
Jin Gu, Hu Fu 0001, Xuegong Zhang, Yanda Li
BMC Bioinform.2