Learning Timescales in MTRNNs

We test the viability of having learnable timescales in multi-timescales recurrent neural networks

The GB Virus C (GBV-C) NS3 Serine Protease Inhibits HIV-1 Replication in a CD4+ T Lymphocyte Cell Line without Decreasing HIV Receptor Expression

Introduction: Persistent infection with GBV-C (GB Virus C), a non-pathogenic virus related to hepatitis C virus (HCV), prolongs survival in HIV infection. Two GBV-C proteins, NS5A and E2, have been shown previously to inhibit HIV replication in vitro. We investigated whether the GBV-C NS3 serine protease affects HIV replication. Results: GBV-C NS3 protease expressed in a human CD4+ T lymphocyte cell line significantly inhibited HIV replication. Addition of NS4A or NS4A/4B coding sequence to GBV-C NS3 increased the effect on HIV replication. Inhibition of HI

Sustainable computational science: the ReScience initiative

Computer science o ers a large set of tools for prototyping, writing, running, testing, validating, sharing and reproducing results, however computational science lags behind. In the best case, authors may provide their source code as a compressed archive and they may feel con dent their research is reproducible. But this is not exactly true. Jonathan Buckheit and David Donoho proposed more than two decades ago that an article about computational results is advertising, not scholarship. e actual scholarship is the full so ware environment, code, and data that produced the result. is implies new work ows, in particular in peer-reviews. Existing journals have been slow to adapt: source codes are rarely requested, hardly ever actually executed to check that they produce the results advertised in the article. ReScience is a peer-reviewed journal that targets computational research and encourages the explicit replication of already published research, promoting new and open-source implementations in order to ensure that the original research can be replicated from its description. To achieve this goal, the whole publishing chain is radically di erent from other traditional scienti c journals. ReScience resides on GitHub where each new implementation of a computational study is made available together with comments, explanations, and so ware tests

A Cooperative Interaction between Nontranslated RNA Sequences and NS5A Protein Promotes In Vivo Fitness of a Chimeric Hepatitis C/GB Virus B

GB virus B (GBV-B) is closely related to hepatitis C virus (HCV), infects small non-human primates, and is thus a valuable surrogate for studying HCV. Despite significant differences, the 5′ nontranslated RNAs (NTRs) of these viruses fold into four similar structured domains (I-IV), with domains II-III-IV comprising the viral internal ribosomal entry site (IRES). We previously reported the in vivo rescue of a chimeric GBV-B (vGB/IIIHC) containing HCV sequence in domain III, an essential segment of the IRES. We show here that three mutations identified within the vGB/IIIHC genome (within the 3′NTR, upstream of the poly(U) tract, and NS5A coding sequence) are necessary and sufficient for production of this chimeric virus following intrahepatic inoculation of synthetic RNA in tamarins, and thus apparently compensate for the presence of HCV sequence in domain III. To assess the mechanism(s) underlying these compensatory mutations, and to determine whether 5′NTR subdomains participating in genome replication do so in a virus-specific fashion, we constructed and evaluated a series of chimeric subgenomic GBV-B replicons in which various 5′NTR subdomains were substituted with their HCV homologs. Domains I and II of the GBV-B 5′NTR could not be replaced with HCV sequence, indicating that they contain essential, virus-specific RNA replication elements. In contrast, domain III could be swapped with minimal loss of genome replication capacity in cell culture. The 3′NTR and NS5A mutations required for rescue of the related chimeric virus in vivo had no effect on replication of the subgenomic GBneoD/IIIHC RNA in vitro. The data suggest that in vivo fitness of the domain III chimeric virus is dependent on a cooperative interaction between the 5′NTR, 3′NTR and NS5A at a step in the viral life cycle subsequent to genome replication, most likely during particle assembly. Such a mechanism may be common to all hepaciviruses

Re-run, Repeat, Reproduce, Reuse, Replicate: Transforming Code into Scientific Contributions

Scientific code is different from production software. Scientific code, by producing results that are then analyzed and interpreted, participates in the elaboration of scientific conclusions. This imposes specific constraints on the code that are often overlooked in practice. We articulate, with a small example, five characteristics that a scientific code in computational science should possess: re-runnable, repeatable, reproducible, reusable, and replicable. The code should be executable (re-runnable) and produce the same result more than once (repeatable); it should allow an investigator to reobtain the published results (reproducible) while being easy to use, understand and modify (reusable), and it should act as an available reference for any ambiguity in the algorithmic descriptions of the article (replicable)

Morphological Development at the Evolutionary Timescale: Robotic Developmental Evolution

Evolution and development operate at different timescales; generations for the one, a lifetime for the other. These two processes, the basis of much of life on earth, interact in many non-trivial ways, but their temporal hierarchy-evolution overarching development-is observed for most multicellular life forms. When designing robots, however, this tenet lifts: It becomes-however natural-a design choice. We propose to inverse this temporal hierarchy and design a developmental process happening at the phylogenetic timescale. Over a classic evolutionary search aimed at finding good gaits for tentacle 2D robots, we add a developmental process over the robots\u27 morphologies. Within a generation, the morphology of the robots does not change. But from one generation to the next, the morphology develops. Much like we become bigger, stronger, and heavier as we age, our robots are bigger, stronger, and heavier with each passing generation. Our robots start with baby morphologies, and a few thousand generations later, end-up with adult ones. We show that this produces better and qualitatively different gaits than an evolutionary search with only adult robots, and that it prevents premature convergence by fostering exploration. In addition, we validate our method on voxel lattice 3D robots from the literature and compare it to a recent evolutionary developmental approach. Our method is conceptually simple, and it can be effective on small or large populations of robots, and intrinsic to the robot and its morphology, not the task or environment. Furthermore, by recasting the evolutionary search as a learning process, these results can be viewed in the context of developmental learning robotics

Behavioral Diversity Generation in Autonomous Exploration through Reuse of Past Experience

International audienceThe production of behavioral diversity – producing a diversity of effects – is an essential strategy for robots exploring the world when facing situations where interaction possibilities are unknown or non-obvious. It allows to discover new aspects of the environment that cannot be inferred or deduced from available knowledge. However, creating behavioral diversity in situations where it is most crucial – new and unknown ones – is far from trivial. In particular in large and redundant sensorimotor spaces, only small areas are interesting to explore for any practical purpose. When the environment does not provide clues or gradient toward those areas, trying to discover those areas relies on chance. To address this problem, we introduce a method to create behavioral diversity in a new sensorimotor task by re-enacting actions that allowed to produce behavioral diversity in a previous task, along with a measure that quantifies this diversity. We show that our method can learn how to interact with an object by reusing experience from another, that it adapts to instances of morphological changes and of dissimilarity between tasks, and how scaffolding behaviors can emerge by simply switching the attention of the robot to different parts of the environment. Finally, we show that the method can robustly use simulated experiences and crude cognitive models to generate behavioral diversity in real robots

rougier/one-critic-two-actors: Version 1.2

Supporting material for the article "One critic, two actors