Tissues, organs, and entire organisms are composed of diverse cell populations, which are characterized by cell-type-specific gene activities. Bulk RNA-seq represents a robust, cost-effective, scalable method to measure gene activity at the bulk tissue level. However, pathomolecular processes lead to divergent changes in tissue composition and cell-type-specific gene deregulations, which cannot be resolved at the tissue bulk level without information on either change in cell-type proportion or expression at the single-cell level. Accordingly, methods have been developed that constrain bulk deconvolution by information from single-cell expression or cell-type proportion. In parallel, convolution methods have been developed to project single-cell expression to bulk tissue level (pseudobulk simulation). In the present review, we provide an overview of existing convolution and deconvolution methods, their interconnectivity, and benchmarking. Our unique approach lies in the joint consideration of both directions in a "holistic transcriptome model." Through analysis of published (de)convolution studies and benchmarks, we identified the reduced availability of suitable datasets and the use of inaccurate convolution-like methods for (de)convolution model assessment and training as key bottlenecks in the field. On that basis, we conclude with a holistic transcriptome model envisioning that a more integral approach to convolution and deconvolution is needed. With our suggestions for a unified framework we aim to spark collaborative efforts to enable major leaps forward in the field of (de)convolution.

The Compact Ocean Wind Vector Radiometer (COWVR) is the first space-based radiometer to utilize electronic polarization basis rotation (EPBR) to measure a swath of polarimetric brightness temperatures without the need to scan the receiver electronics. The COWVR instrument also utilizes internal calibration with noise diode standards to facilitate implementation of the simplified conical-scanning radiometer design. Following successful Calibration of the instrument on-orbit by the multi-agency COWVR Cal/Val team, data provided by the mission Ground Data Processing System (GDPS) was assessed. An analysis of COWVR Wind Speed and Direction performance was performed by Aerospace utilizing matchups with wind retrievals from the Advanced Scatterometer (ASCAT) on Metop-B and -C. This analysis found that COWVR meets its Ocean Surface Vector Wind requirements established for the COWVR mission.

Recommender systems play a key role in helping users find their favorite music to play among an often extremely large catalog of items on online streaming services. To correctly identify users' interests, recommendation algorithms rely on past user behavior and feedback to aim at learning users' preferences through the logged interactions. User modeling is a fundamental part of this large-scale system as it enables the model to learn an optimal representation for each user. For instance, in music recommendation, the focus of this paper, users' interests at any time is shaped by their general preferences for music as well as their recent or momentary interests in a particular type of music. In this paper, we present a novel approach for learning user representation based on general and slow-changing user interests as well as fast-moving current preferences. We propose a variational autoencoder-based model that takes fast and slow-moving features and learns an optimal user representation. Our model, which we call FS-VAE, consists of sequential and non-sequential encoders to capture patterns in user-item interactions and learn users' representations. We evaluate FS-VAE on a real-world music streaming dataset. Our experimental results show a clear improvement in learning optimal representations compared to state-of-the-art baselines on the next item recommendation task. We also demonstrate how each of the model components, slow input feature, and fast ones play a role in achieving the best results in next item prediction and learning users' representations.

International audience

Finding a set of users of interest serves several applications in behavioral analytics. Often times, identifying users requires to explore the data and gradually choose potential targets. This is a special case of Exploratory Data Analysis (EDA), an iterative and tedious process. In this paper, we formalize and solve the problem of guided exploration of user groups whose purpose is to find target users. We model exploration as an iterative decision-making process, where an agent is shown a set of groups, chooses users from those groups, and selects the best action to move to the next step. To solve our problem, we apply reinforcement learning to discover an efficient exploration strategy from a simulated agent experience, and propose to use the learned strategy to recommend an exploration policy that can be applied to the same task for any dataset. Our framework accepts a wide class of exploration actions and does not need to gather exploration logs. Our experiments show that the agent naturally captures manual exploration by human analysts, and succeeds to learn an interpretable and transferable exploration policy.

Service-based technology is becoming widespread, and many service oriented platforms are available with different characteristics and constraints, making them incompatible. Consequently, designing, developing and executing an application using services running on different platforms is a challenging task if not impossible. A first challenge is to provide an ideal and virtual SOC platform; ideal because it subsumes the actual real SOA platforms, virtual because it delegates the execution to these real platforms. But since ldquoidealrdquo depends on the domain; the second challenge is to provide extensibility mechanisms allowing to define what ideal means in a given domain and to provide the engineering support for the design and development of service-based application dedicated to such domains. The paper describes how we addressed these challenges, and to what extent they have been met.

The goal of operational Business Intelligence (BI) is to help organizations improve the efficiency of their business by giving every "operational worker" insights needed to make better operational decisions, and aligning day-to-day operations with strategic goals. Operational BI reporting contributes to this goal by embedding analytics and reporting information into workflow applications so that the business user has all required information (contextual and business data) in order to make good decisions. EII systems facilitate the construction of operational BI reports by enabling the creation and querying of customized virtual database schemas over a set of distributed and heterogeneous data sources with a low TCO. Queries over these virtual databases feed the operational BI reports. We describe the characteristics of operational BI reporting applications and show that they increase the complexity of the source to target mapping defined between source data and virtual databases. We show that this complexity yields the execution of "mega queries", i.e., queries with possible a 1,000 tables in their FROM clause. We present some key optimization methods that have been successfully implemented in SAP Business Objects Data Federator system to deal with mega queries.

The Home Network is a pervasive environment by nature. Its openness to dynamic distributed and heterogeneous devices brings great challenges in home application design. We present here an open architecture for home service development. Distribution and heterogeneity are managed by service-oriented drivers leveraging the “service platform” concept. Our project provides an open source driver combining Web Services and OSGi standards to compose home services. Performance test results illustrate the service-oriented design.

Le Select is a research prototype of an EII (Enterprise Information Integration) system (also known as a mediation system), which was developed from 1998 to 2001 at INRIA (France). Le Select was then transferred to a start-up company named Medience, which was purchased in 2005 by Business Objects. Under its new brand, the EII system now called "Data Federator" is a master piece of Business Objects' Enterprise Information Management (EIM) offering. During this period of nearly ten years, the EII system has been rewritten almost three times, not only for industrializing its code, but mainly because the system was confronted to customer needs that required modifications in order to address functional needs that were not anticipated. The aim of this presentation is to review these main transformations of the system and relate them to Business Intelligence application requirements. We emphasize a few problems such as designing complex views, data cleaning, and query optimization strategies for "narrow" and "mega" queries. The presentation makes extensive use of customer cases to illustrate our purpose. We conclude with a list of open issues.

There are many examples where cooperation among scientists takes place by exchanging scientific resources, such as data, programs and mathematical models. This is particularly true for environmental applications. Finding the right resource to apply in an environmental problem is a difficult task. Usually, this decision is based on previous experience. Scientists have to cooperate in order to solve such problems. To facilitate the exchange, reuse and dissemination of information we propose an architecture for managing distributed scientific resources. Our proposal combines a mediation-based heterogeneous distributed database system and an enhanced metadata support system for effective management of distributed scientific models and data.

Projet CARAVEL

@@@@ groups together matching pairs with a high similarity value by applying a given grouping criteria (e.g. by transitive closure). Finally, ging collapses each individual cluster into a tuple of the resulting data source. AJAX provides @@@@ for specifying data cleaning programs, which consists of SQL statements enriched with a set of specific primitives to express these transformations.

In contemporary organizations, inaccurate, invalid, out-of-date or incomplete data may have a heavy financial, or even social impact. Consequently, the problem arises how to design and construct data warehouses, which satisfy specific, well-defined quality criteria. The basic issues raised in this context are the need for a methodology for quality design for data warehouses, the modeling and the measurement of the quality of the data warehouse. The panelists discuss their experience -through research and practical industrial projects- to provide specific solutions to problems of quality, both as technology and methodology providers.

Many distributed database applications need to replicate data to improve data availability and query response time. The two phase commit protocol guarantees mutual consistency of replicated data but does not provide good performance. Lazy replication has been used as an alternative solution in several types of applications such as online financial transactions and telecommunication systems. In this case, mutual consistency is relaxed and the concept of freshness is used to measure the deviation between replica copies. We propose two update propagation strategies that improve freshness. Both of them use immediate propagation: updates to a primary copy are propagated towards a slave node as soon as they are detected at the master node without waiting for the commitment of the update transaction. We study the behavior of our strategies and show that they improve data freshness with respect to the deferred approach.

The efficiency of dynamic dispatch is a major impediment to the adoption of multimethods in object-oriented languages. In this article, we propose a simple multimethod dispatch scheme based on compressed dispatch tables. This scheme is applicable to any object-oriented language using a method precedence order that satisfies a specific monotonous property (e.g., as Cecil and Dylan) and guarantees that dynamic dispatch is performed in constant time, the latter being a major requirement for some languages and applications. We provide efficient algorithms to build the dispatch tables, provide their worst-case complexity, and demonstrate the effectiveness of our scheme by real measurements performed on two large object-oriented applications. Finally, we provide a detailed comparison of our technique with other existing techniques.

Active database systems are now in widespread use. The use of triggers in these systems, however, is difficult because of the complex interaction between triggers, transactions, and application programs. Repeated calculations of rules may incur costly redundant computations in rule conditions and actions. In this paper, we focus on active relational database systems supporting SQL triggers. In this context, we provide a powerful and complete solution to eliminate redundant computations of SQL triggers when they are costly. We define a model to describe programs, rules and their interactions. We provide algorithms to extract invariant subqueries from trigger's condition and action. We define heuristics to memorize the most “profitable” invariants. Finally, we develop a rewriting technique that enables to generate and execute the optimized code of SQL triggers.

Chopping transactions into pieces is good for performance but may lead to nonserializable executions. Many researchers have reacted to this fact by either inventing new concurrency-control mechanisms, weakening serializability, or both. We adopt a different approach. We assume a user who —has access only to user-level tools such as (1) choosing isolation degrees 1ndash;4, (2) the ability to execute a portion of a transaction using multiversion read consistency, and (3) the ability to reorder the instructions in transaction programs; and —knows the set of transactions that may run during a certain interval (users are likely to have such knowledge for on-line or real-time transactional applications). Given this information, our algorithm finds the finest chopping of a set of transactions TranSet with the following property: If the pieces of the chopping execute serializably, then TranSet executes serializably . This permits users to obtain more concurrency while preserving correctness. Besides obtaining more intertransaction concurrency, chopping transactions in this way can enhance intratransaction parallelism. The algorithm is inexpensive, running in O(n×(e+m)) time, once conflicts are identified, using a naive implementation, where n is the number of concurrent transactions in the interval, e is the number of edges in the conflict graph among the transactions, and m is the maximum number of accesses of any transaction. This makes it feasible to add as a tuning knob to real systems.

Optimizing method dispatch is a central issue in object-oriented language implementation. The dispatch table scheme, used for example by C++, is the only implementation of method dispatch that offers constant time performance. This property is the main asset of dispatch tables and a major requirement for some languages. However, the major drawback of dispatch tables is the space they require. Reducing the size of dispatch tables has been studied in the case of mono-methods with techniques such as coloring. In the case of multi-methods, dispatch tables are practically unusable as they grow as a power of the number of arguments. In this paper, we propose an algorithm to compress the dispatch tables of multi-methods by analyzing their signatures.

Chopping transactions into pieces is good for performance but may lead to non-serializable executions. Many researchers have reacted to this fact by either inventing new concurrency control mechanisms, weakening serializability, or both. We adopt a different approach.

The use of non-deterministic database languages is motivated using pragmatic and theoretical considerations. It is shown that non-determinism resolves some difficulties concerning the expressive power of deterministic languages: there are non-deterministic languages expressing low complexity classes of queries/updates, whereas no such deterministic languages exist. Various mechanisms yielding non-determinism are reviewed. The focus is on two closely related families of non-deterministic languages. The first consists of extensions of Datalog with negations in bodies and/or heads of rules, with non-deterministic fixpoint semantics. The second consists of non-deterministic extensions of first-order logic and fixpoint logics, using the witness operator. The ability of the various non-deterministic languages to express deterministic transformation is characterized. In particular, non-deterministic languages expressing exactly the queries/updates computable in polynomial time are exhibited, whereas it is conjectured that no analogous deterministic language exists. The connection between non-deterministic languages and determinism is also explored. Several problems of practical interest are examined, such as checking (statically or dynamically) if a given program is deterministic, detecting coincidence of deterministic and non-deterministic semantics, and verifying termination for non-deterministic programs.

Deductive databases provide a formal framework to study rule-based query languages that are extensions of first-order logic. However, deductive database languages and their current implementations do not seem appropriate for improving the development of real applications or even sample of them. Our goal is to make deductive database technology practical. The design and implementation of the RDL1 system, presented in this paper, constitute a step toward this goal. Our approach is based on the integration of a production rule language within a relational database system, the development of a rule-based programming environment and the support of system extensibility using Abstract Data Types. We discuss important practical experience gained during the implementation of the system. Also, comparisons with related work such as LDL, STARBURST and POSTGRES are given.

ASSYST (Applied Sentencing System) was developed so that judges, prosecutors, defense attorneys, probation officers and other key members of the Federal criminal justice system could easily compute, record, archive and examine the implications of Guidelines promulgated by the United States Sentencing Commission [1].

The authors consider the problem of integrating a powerful production rule language, called RDLI, with a relational DBMS. A rule in RDLI is composed of a condition part which is a relational calculus expression and an action part which is a sequence of updates over a database. The semantics of a RDLI rule is presented according to a binary relation over databases states. Then, they introduce a general compilation technique for transforming producing rules in an execution model, the PCN, based on predicate transition networks (PrTN). The features of this model are its descriptive power and its query optimization support.>

Tnls paper presents a powerful integrrty subsystem, which is implemented in the SABRE database system. The specification language is simple. Tne enforcement algorithm is general, in particular, it handles referential dependency and temporal assertions. Specialized strategies efficiently treat each class of assertions. The system automatically manages integrity checkpoints. Also, an efficient method is described for processing assertions involving aggregates. An analysis exhibits the value of the algorithms. It 1s shown that, in general, this method is better than the query modification method for domain assertions. Measures have also been done for giving the cost added for controlling integrity in comparison with the cost of the request itself.