Concurrent Programs Research Articles

Scalable transcriptomics analysis with Dask: applications in data science and machine learning

BackgroundGene expression studies are an important tool in biological and biomedical research. The signal carried in expression profiles helps derive signatures for the prediction, diagnosis and prognosis of different diseases. Data science and specifically machine learning have many applications in gene expression analysis. However, as the dimensionality of genomics datasets grows, scalable solutions become necessary.MethodsIn this paper we review the main steps and bottlenecks in machine learning pipelines, as well as the main concepts behind scalable data science including those of concurrent and parallel programming. We discuss the benefits of the Dask framework and how it can be integrated with the Python scientific environment to perform data analysis in computational biology and bioinformatics.ResultsThis review illustrates the role of Dask for boosting data science applications in different case studies. Detailed documentation and code on these procedures is made available at https://github.com/martaccmoreno/gexp-ml-dask.ConclusionBy showing when and how Dask can be used in transcriptomics analysis, this review will serve as an entry point to help genomic data scientists develop more scalable data analysis procedures.

Matching Logic Based on Ownership Transfer

We combine “ownership transfer” with matching logic to reason about fault-free partial correctness of shared-memory concurrent programs. As we all know, what really gives separation logic (concurrent separation logic) an edge is the ownership transfer of the heap. Inspired by this, we use matching logic to realize variable ownership (permission) and its transfer mechanism, which reveals the hidden principle behind “protected variables” of resource and “rely set” in extended CSL. In addition, variable ownership can replace Dijkstra’s semaphore blocking technique to achieve the critical section. Soundness is important to us, we provide a semantic model that supports the separation property and demonstrate the soundness of our logic based on trace semantics.

Strong Sleptsov nets are Turing complete

It is known that a Sleptsov net, with multiple firing of a transition at a step, runs exponentially faster than a Petri net, opening prospects for its application as a graphical language of concurrent programming. We provide a classification of place-transition nets based on firability rules considering general definitions and their strong and weak variants. We introduce and study a strong Sleptsov net, where a transition with the maximal firing multiplicity fires at a step, and prove that it is Turing complete. We follow the proof pattern of Peterson which he applied to prove that an inhibitor Petri net is Turing complete by simulating a Shepherdson and Sturgis register machine. The central construct of our proof is a strong Sleptsov net that checks whether a register value (place marking) equals zero.

A comparison of the university mathematics learning environment with its high school equivalent.

In light of rising college student debt, many states now offer multiple options for students to earn college credit while still in high school. Concurrent enrollment programs, which allow qualified high school teachers to teach college credit-bearing classes in the high school, are one such option. Because concurrent enrollment classes teach college-level material at college-level rigor, they offer an ideal way to compare the secondary and tertiary learning environments across identical academic expectations. This study sought to compare the university mathematics environment with its concurrent enrollment counterpart. The WIHIC was found to be valid and reliable for the university population. The comparison of 242 students in university classrooms with 260 students in concurrent enrollment classrooms revealed a statistical difference, with the concurrent enrollment setting scoring higher in Involvement, Teacher Support, and Student Cohesion and the university setting scoring higher in Task Orientation. This implies that earning college credit in a secondary setting is a viable, and possibly even preferable, alternative to earning it in a university setting. We examine the discrepancy in scores-particularly the large discrepancy in Task Orientation-and discuss the benefit of the flipped classroom as one path to improving the university learning environment.

Bio‐inspired optimization to support the test data generation of concurrent software

SummaryConcurrent programming is increasingly present in modern applications. Although it provides higher performance and better use of available resources, the mechanisms of interaction between processes/threads result in a greater challenge for software testing activity. The nondeterminism present in those applications is one of the main issues during the test activity since the same test input can produce different possible execution paths, which may or not contain defects. The test data automatic generation can alleviate this problem, ensuring higher speed and reliability in software testing activity. This paper explores the automatic test data generation for concurrent programs through Genetic Algorithm, a bioinspired optimization technique, and proposes a test data generation approach for concurrent programs, called BioConcST, and a new operator for the selection of test subjects, called FuzzyST, which uses fuzzy logic. The approaches were evaluated in an experimental study towards their validation. The results showed that BioConcST is more promising than the other approaches at all analyzed levels. FuzzyST, together with Elitism and Tournament operators, provided the best results; however, it proved more suitable for concurrent programs of higher complexity.

Overweight and Obese Adult Patients Show Larger Benefits from Concurrent Training Compared with Pharmacological Metformin Treatment on Insulin Resistance and Fat Oxidation.

Metformin, a drug widely used to treat insulin resistance, and training that combines aerobic and strength exercise modalities (i.e., concurrent training) may improve insulin sensitivity. However, there is a paucity of clinical trials investigating the effects of concurrent training, particularly on insulin resistance and fat oxidation in overweight and obese patients. Furthermore, only a few studies have compared the effects of concurrent training with metformin treatment. Therefore, the aim of this study was to examine the effects of a 12-week concurrent training program versus pharmaceutical treatment with metformin on maximum fat oxidation, glucose metabolism, and insulin resistance in overweight or obese adult patients. Male and female patients with insulin resistance were allocated by convenience to a concurrent training group (n = 7 (2 males); age = 32.9 ± 8.3 years; body mass index = 30 ± 4.0 kg·m-2) or a metformin group (n = 7 (2 males); age = 34.4 ± 14.0 years; body mass index = 34.4 ± 6.0 kg·m-2). Before and after the interventions, all participants were assessed for total body mass, body mass index, fat mass, fat-free mass, maximum oxygen consumption, maximal fat oxidization during exercise, fasting glucose, and insulin resistance through the homeostatic model assessment (HOMA-IR). Due to non-normal distribution of the variable maximal fat oxidation, the Mann-Whitney U test was applied and revealed better maximal fat oxidization (Δ = 308%) in the exercise compared with the metformin group (Δ = -30.3%; p = 0.035). All other outcome variables were normally distributed, and significant group-by-time interactions were found for HOMA-IR (p < 0.001, Δ = -84.5%), fasting insulin (p < 0.001, Δ = -84.6%), and increased maximum oxygen consumption (p = 0.046, Δ = 12.3%) in favor of the exercise group. Similar changes were found in both groups for the remaining dependent variables. Concurrent training seems to be more effective compared with pharmaceutical metformin treatment to improve insulin resistance and fat oxidation in overweight and obese adult patients with insulin resistance. The rather small sample size calls for more research in this area.

Reversing an imperative concurrent programming language

We introduce a method of reversing the execution of imperative concurrent programs. Given an irreversible program, we describe the process of producing two versions. The first performs forward execution and saves information necessary for reversal. The second uses this saved information to simulate reversal. We propose using identifiers to capture statement execution order, and to use this to correctly undo data races via backtracking reversibility. We prove this reversibility to be correct, showing that the initial program state is restored and that all saved information is used (garbage-clean). • Reversal of a concurrent imperative programming language that stores minimal data to undo irreversible steps • Identifiers assigned to statements as they execute that determines reverse control flow and ensures correct reversibility • Proof of correctness confirms the method of reversal restores program states and does not produce garbage • Reversibility illustrated on an implementation of a parallel sorting algorithm, with forward and reverse execution described

The Influence of Exercise, Lifestyle Behavior Components, and Physical Fitness on Maternal Weight Gain, Postpartum Weight Retention, and Excessive Gestational Weight Gain.

This study examines (a)the influence of exercise, lifestyle behavior components (sedentary time, physical activity, and sleep and dietary patterns), and physical fitness on maternal weight gain, postpartum weight retention, and excessive gestational weight gain and (b)whether exercise protects against the adverse effects of impaired metabolism and nonoptimal body composition related to excessive gestational weight gain. Subjects were assigned to either a supervised concurrent (aerobic + resistance) exercise program followed 3days/week (n = 47) or a control group (n = 54). Sedentary time, physical activity, sleep and dietary patterns (assessed by accelerometry and questionnaires), muscle strength (handgrip test), and cardiorespiratory fitness (Bruce test) were determined at gestational Weeks 16 and 33 (early-middle and late pregnancy, respectively), and at 6 weeks postpartum. Weight gain and weight retention were calculated using recorded weights at prepregnancy, early-middle, and late pregnancy, and at 6weeks postpartum. Birth complications, maternal postpartum body composition, cardiometabolic, and inflammatory markers in maternal and umbilical cord arterial and venous blood, and in colostrum, and mature milk were also recorded. The exercise intervention reduced late weight gain (B = -2.7, SE = 0.83, p = .003) and weight retention (B = -2.85, SE = 1.3, p = .03), independent of any lifestyle behavior component or physical fitness, but did not prevent excessive weight gain. Increasing cardiorespiratory fitness, muscle strength, and sleep duration were associated with a smaller mean weight gain and lower excessive weight gain values (p < .05). Among the participants who experienced excessive weight gain, those who were exercisers had a lower body mass index and systemic tumor necrosis factor-alpha concentration, lower umbilical cord venous tumor necrosis factor-alpha and arterial interferon gamma levels, higher cord arterial interleukin-10 levels, and improved placental function compared with controls (p < .05). In summary, exercise may help optimize gestational weight gain and weight retention, and may attenuate the impaired phenotype related to excessive weight gain. Increasing cardiorespiratory fitness, muscle strength, and sleep duration might help to prevent excessive weight gain during pregnancy.

Automated replication of tuple spaces via static analysis

• Data replication may improve the efficiency of a distributed system. • Implementing replication manually requires a significant effort. • We propose an experimental technique for automated replication of tuple spaces. • We combine program transformation and static analysis, preserving strong consistency. • Transformed programs exhibit desirable properties (e.g. reduced non-local accesses). Coordination languages for tuple spaces can offer significant advantages in the specification and implementation of distributed systems, but often do require manual programming effort to ensure consistency. We propose an experimental technique for automated replication of tuple spaces in distributed systems. The system of interest is modelled as a concurrent Go program where different threads represent the behaviour of the separate components, each owning its own local tuple repository. We automatically transform the initial program by combining program transformation and static analysis, so that tuples are replicated depending on the components' read-write access patterns. In this way, we turn the initial system into a replicated one where the replication of tuples is automatically achieved, while avoiding unnecessary replication overhead. Custom static analyses may be plugged in easily in our prototype implementation. We see this as a first step towards developing a fully-fledged framework to support designers to quickly evaluate many classes of replication-based systems under different consistency levels.

Vertical Saltwater Intrusion in Coastal Aquifers Driven by Episodic Flooding: A Review

AbstractLow‐elevation coastal areas are increasingly vulnerable to seawater flooding as sea levels rise and the frequency and intensity of large storms increase with climate change. Seawater flooding can lead to the salinization of fresh coastal aquifers by vertical saltwater intrusion (SWI). Vertical SWI is often overlooked in coastal zone threat assessments despite the risk it poses to critical freshwater resources and salt‐intolerant ecosystems that sustain coastal populations. This review synthesizes field and modeling approaches for investigating vertical SWI and the practical and theoretical understanding of salinization and flushing processes obtained from prior studies. The synthesis explores complex vertical SWI dynamics that are influenced by density‐dependent flow and oceanic, hydrologic, geologic, climatic, and anthropogenic forcings acting on coastal aquifers across spatial and temporal scales. Key knowledge gaps, management challenges, and research opportunities are identified to help advance our understanding of the vulnerability of fresh coastal groundwater. Past modeling studies often focus on idealized aquifer systems, and thus future work could consider more diverse geologic, climatic, and topographic environments. Concurrent field and modeling programs should be sustained over time to capture interactions between physical processes, repeated salinization and flushing events, and delayed aquifer responses. Finally, this review highlights the need for improved coordination and knowledge translation across disciplines (e.g., coastal engineering, hydrogeology, oceanography, social science) to gain a more holistic understanding of vertical SWI. There also needs to be more education of communities, policy makers, and managers to motivate societal action to address coastal groundwater vulnerability in a changing climate.

Consistency-preserving propagation for SMT solving of concurrent program verification

The happens-before orders have been widely adopted to model thread interleaving behaviors of concurrent programs. A dedicated ordering theory solver, usually composed of theory propagation, consistency checking, and conflict clause generation, plays a central role in concurrent program verification. We propose a novel preventive reasoning approach that automatically preserves the ordering consistency and makes consistency checking and conflict clause generation omissible. We implement our approach in a prototype tool and conduct experiments on credible benchmarks; results reveal a significant improvement over existing state-of-the-art concurrent program verifiers.

A concurrent program logic with a future and history

Verifying fine-grained optimistic concurrent programs remains an open problem. Modern program logics provide abstraction mechanisms and compositional reasoning principles to deal with the inherent complexity. However, their use is mostly confined to pencil-and-paper or mechanized proofs. We devise a new separation logic geared towards the lacking automation. While local reasoning is known to be crucial for automation, we are the first to show how to retain this locality for (i) reasoning about inductive properties without the need for ghost code, and (ii) reasoning about computation histories in hindsight. We implemented our new logic in a tool and used it to automatically verify challenging concurrent search structures that require inductive properties and hindsight reasoning, such as the Harris set.

A bunch of sessions: a propositions-as-sessions interpretation of bunched implications in channel-based concurrency

The emergence of propositions-as-sessions, a Curry-Howard correspondence between propositions of Linear Logic and session types for concurrent processes, has settled the logical foundations of message-passing concurrency. Central to this approach is the resource consumption paradigm heralded by Linear Logic. In this paper, we investigate a new point in the design space of session type systems for message-passing concurrent programs. We identify O’Hearn and Pym’s Logic of Bunched Implications (BI) as a fruitful basis for an interpretation of the logic as a concurrent programming language. This leads to a treatment of non-linear resources that is radically different from existing approaches based on Linear Logic. We introduce a new π-calculus with sessions, called πBI; its most salient feature is a construct called spawn, which expresses new forms of sharing that are induced by structural principles in BI. We illustrate the expressiveness of πBI and lay out its fundamental theory: type preservation, deadlock-freedom, and weak normalization results for well-typed processes; an operationally sound and complete typed encoding of an affine λ-calculus; and a non-interference result for access of resources.

Model checking for a multi-execution memory model

Multi-execution memory models, such as Promising and Weakestmo, are an advanced class of weak memory consistency models that justify certain outcomes of a concurrent program by considering multiple candidate executions collectively. While this key characteristic allows them to support effective compilation to hardware models and a wide range of compiler optimizations, it makes reasoning about them substantially more difficult. In particular, we observe that Promising and Weakestmo inhibit effective model checking because they allow some suprisingly weak behaviors that cannot be generated by examining one execution at a time. We therefore introduce Weakestmo2, a strengthening of Weakestmo by constraining its multi-execution nature, while preserving the important properties of Weakestmo: DRF theorems, compilation to hardware models, and correctness of local program transformations. Our strengthening rules out a class of surprisingly weak program behaviors, which we attempt to characterize with the help of two novel properties: load buffering race freedom and certification locality. In addition, we develop WMC, a model checker for Weakestmo2 with performance close to that of the best tools for per-execution models.

Concurrent size

The size of a data structure (i.e., the number of elements in it) is a widely used property of a data set. However, for concurrent programs, obtaining a correct size efficiently is non-trivial. In fact, the literature does not offer a mechanism to obtain a correct (linearizable) size of a concurrent data set without resorting to inefficient solutions, such as taking a full snapshot of the data structure to count the elements, or acquiring one global lock in all update and size operations. This paper presents a methodology for adding a concurrent linearizable size operation to sets and dictionaries with a relatively low performance overhead. Theoretically, the proposed size operation is wait-free with asymptotic complexity linear in the number of threads (independently of data-structure size). Practically, we evaluated the performance overhead by adding size to various concurrent data structures in Java−a skip list, a hash table and a tree. The proposed linearizable size operation executes faster by orders of magnitude compared to the existing option of taking a snapshot, while incurring a throughput loss of 1%−20% on the original data structure’s operations.

CAAT: consistency as a theory

We propose a family of logical theories for capturing an abstract notion of consistency and show how to build a generic and efficient theory solver that works for all members in the family. The theories can be used to model the influence of memory consistency models on the semantics of concurrent programs. They are general enough to precisely capture important examples like TSO, POWER, ARMv8, RISC-V, RC11, IMM, and the Linux kernel memory model. To evaluate the expressiveness of our theories and the performance of our solver, we integrate them into a lazy SMT scheme that we use as a backend for a bounded model checking tool. An evaluation against related verification tools shows, besides flexibility, promising performance on challenging programs under complex memory models.

Selective androgen receptor modulation for muscle weakness in chronic obstructive pulmonary disease: a randomised control trial

BackgroundSelective androgen receptor modulators (SARMs) increase muscle mass via the androgen receptor. This phase 2A trial investigated the effects of a SARM, GSK2881078, in conjunction with exercise, on leg strength...

Description and Outcomes of an Innovative Concurrent Hospice-Dialysis Program.

Compared with the general Medicare population, patients with ESKD have worse quality metrics for end-of-life care, including a higher percentage experiencing hospitalizations and in-hospital deaths and a lower percentage referred to hospice. We developed a Concurrent Hospice and Dialysis Program in which patients may receive palliative dialysis alongside hospice services. The Program aims to improve access to quality end-of-life care and, ultimately, improve the experiences of patients, caregivers, and clinicians. We sought to describe (1) the Program and (2) enrollment and utilization characteristics of Program participants. We conducted a quantitative description of demographics, patient characteristics, and utilization of Program enrollees. Of 43 total enrollees, 44% received at least one dialysis treatment, whereas 56% received no dialysis. The median (range) hospice length of stay was 9 (1-76) days for all participants and 13 (4-76) days for those who received at least one dialysis treatment. The average number of dialysis treatments was 3.5 (range 1-9) for hemodialysis and 19.2 (range 3-65) for peritoneal dialysis. Sixty-five percent of enrollees died at home, 23% in inpatient hospice, and 12% in a nursing facility; no patients died in the hospital. Our 3-year experience with the Program demonstrated that enrollees had a longer median hospice stay than the previously reported 5-day median for patients with ESKD. Most patients received no further dialysis treatments despite the option to continue dialysis. Our experience provides evidence to support future work testing the effectiveness of such clinical programs to improve patient and utilization outcomes.

The Discourje project: run-time verification of communication protocols in Clojure

To simplify shared-memory concurrent programming, languages have started to offer core support for high-level communications primitives, in the form of message passing though channels, in addition to lower-level synchronisation primitives. Yet, a growing body of evidence suggests that channel-based programming abstractions also have their issues. The Discourje project aims to help programmers cope with channels and concurrency bugs in Clojure programs, based on dynamic analysis. The idea is that programmers write not only implementations of communication protocols in their Clojure programs, but also specifications. Discourje then offers a run-time verification library to ensure that channel actions in implementations are safe relative to specifications. The aim of this paper is to provide a comprehensive overview of the current state of Discourje, including case studies, theoretical foundations, and practical aspects.

Indexed and fibered structures for partial and total correctness assertions

AbstractHoare Logic has a long tradition in formal verification and has been continuously developed and used to verify a broad class of programs, including sequential, object-oriented, and concurrent programs. Here we focus on partial and total correctness assertions within the framework of Hoare logic and show that a comprehensive categorical analysis of its axiomatic semantics needs the languages of indexed and fibered category theory. We consider Hoare formulas with local, finite contexts, of program and logical variables. The structural features of Hoare assertions are presented in an indexed setting, while the logical features of deduction are modeled in the fibered one.