133 research outputs found
ワカメ資化性イムノバイオティクスのイムノシンバイオティクスとしての利用性に関する基礎研究
Tohoku University課
An Adaptive Incremental Gradient Method With Support for Non-Euclidean Norms
Stochastic variance reduced methods have shown strong performance in solving
finite-sum problems. However, these methods usually require the users to
manually tune the step-size, which is time-consuming or even infeasible for
some large-scale optimization tasks. To overcome the problem, we propose and
analyze several novel adaptive variants of the popular SAGA algorithm.
Eventually, we design a variant of Barzilai-Borwein step-size which is tailored
for the incremental gradient method to ensure memory efficiency and fast
convergence. We establish its convergence guarantees under general settings
that allow non-Euclidean norms in the definition of smoothness and the
composite objectives, which cover a broad range of applications in machine
learning. We improve the analysis of SAGA to support non-Euclidean norms, which
fills the void of existing work. Numerical experiments on standard datasets
demonstrate a competitive performance of the proposed algorithm compared with
existing variance-reduced methods and their adaptive variants
Positional Information Matters for Invariant In-Context Learning: A Case Study of Simple Function Classes
In-context learning (ICL) refers to the ability of a model to condition on a
few in-context demonstrations (input-output examples of the underlying task) to
generate the answer for a new query input, without updating parameters. Despite
the impressive ICL ability of LLMs, it has also been found that ICL in LLMs is
sensitive to input demonstrations and limited to short context lengths. To
understand the limitations and principles for successful ICL, we conduct an
investigation with ICL linear regression of transformers. We characterize
several Out-of-Distribution (OOD) cases for ICL inspired by realistic LLM ICL
failures and compare transformers with DeepSet, a simple yet powerful
architecture for ICL. Surprisingly, DeepSet outperforms transformers across a
variety of distribution shifts, implying that preserving permutation invariance
symmetry to input demonstrations is crucial for OOD ICL. The phenomenon
specifies a fundamental requirement by ICL, which we termed as ICL invariance.
Nevertheless, the positional encodings in LLMs will break ICL invariance. To
this end, we further evaluate transformers with identical positional encodings
and find preserving ICL invariance in transformers achieves state-of-the-art
performance across various ICL distribution shiftsComment: Ongoing work; preliminary versio
Does Invariant Graph Learning via Environment Augmentation Learn Invariance?
Invariant graph representation learning aims to learn the invariance among
data from different environments for out-of-distribution generalization on
graphs. As the graph environment partitions are usually expensive to obtain,
augmenting the environment information has become the de facto approach.
However, the usefulness of the augmented environment information has never been
verified. In this work, we find that it is fundamentally impossible to learn
invariant graph representations via environment augmentation without additional
assumptions. Therefore, we develop a set of minimal assumptions, including
variation sufficiency and variation consistency, for feasible invariant graph
learning. We then propose a new framework Graph invAriant Learning Assistant
(GALA). GALA incorporates an assistant model that needs to be sensitive to
graph environment changes or distribution shifts. The correctness of the proxy
predictions by the assistant model hence can differentiate the variations in
spurious subgraphs. We show that extracting the maximally invariant subgraph to
the proxy predictions provably identifies the underlying invariant subgraph for
successful OOD generalization under the established minimal assumptions.
Extensive experiments on datasets including DrugOOD with various graph
distribution shifts confirm the effectiveness of GALA.Comment: NeurIPS 2023, 34 pages, 35 figure
Isolation and immunocharacterization of lactobacillus salivarius from the intestine of wakame-fed pigs to develop novel "Immunosynbiotics"
Emerging threats of antimicrobial resistance necessitate the exploration of effective alternatives for healthy livestock growth strategies. ?Immunosynbiotics?, a combination of immunoregulatory probiotics and prebiotics with synergistic effects when used together in feed, would be one of the most promising candidates. Lactobacilli are normal residents of the gastrointestinal tract of pigs, and many of them are able to exert beneficial immunoregulatory properties. On the other hand, wakame (Undaria pinnafida), an edible seaweed, has the potential to be used as an immunoregulatory prebiotic when added to livestock feed. Therefore, in order to develop a novel immunosynbiotic, we isolated and characterized immunoregulatory lactobacilli with the ability to utilize wakame. Following a month-long in vivo wakame feeding trial in 8-week-old Landrace pigs (n = 6), sections of intestinal mucous membrane were processed for bacteriological culture and followed by identification of pure colonies by 16S rRNA sequence. Each isolate was characterized in vitro in terms of their ability to assimilate to the wakame and to differentially modulate the expression of interleukin-6 (IL-6) and interferon beta (IFN-β) in the porcine intestinal epithelial (PIE) cells triggered by Toll-like receptor (TLR)-4 and TLR-3 activation, respectively. We demonstrated that feeding wakame to pigs significantly increased the lactobacilli population in the small intestine. We established a wakame-component adjusted culture media that allowed the isolation and characterization of a total of 128 Lactobacilli salivarius colonies from the gut of wakame-fed pigs. Interestingly, several L. salivarius isolates showed both high wakame assimilation ability and immunomodulatory capacities. Among the wakame assimilating isolates, L. salivarius FFIG71 showed a significantly higher capacity to upregulate the IL-6 expression, and L. salivarius FFIG131 showed significantly higher capacity to upregulate the IFN-β expression; these could be used as immunobiotic strains in combination with wakame for the development of novel immunologically active feeds for pigs.Fil: Masumizu, Yuki. Tohoku University; JapónFil: Zhou, Binghui. Tohoku University; JapónFil: Humayun Kober, AKM. Tohoku University; Japón. Chittagong Veterinary and Animal Sciences University; BangladeshFil: Islam, M. Aminul. Agricultural University; Bangladesh. Tohoku University; JapónFil: Iida, Hikaru. Tohoku University; JapónFil: Ikeda-Ohtsubo, Wakako. Tohoku University; JapónFil: Suda, Yoshihito. Department Of Food Agriculture, Miyagi University; JapónFil: Albarracín, Leonardo. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Centro de Referencia para Lactobacilos; Argentina. Tohoku University; Japón. Universidad Nacional de Tucumán; ArgentinaFil: Nochi, Tomonori. Tohoku University; JapónFil: Aso, Hisashi. Tohoku University; JapónFil: Suzuki, Keiichi. Tohoku University; JapónFil: Villena, Julio Cesar. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Centro de Referencia para Lactobacilos; Argentina. Tohoku University; JapónFil: Kitazawa, Haruki. Tohoku University; Japó
ITCH Nuclear Translocation and H1.2 Polyubiquitination Negatively Regulate the DNA Damage Response
The downregulation of the DNA damage response (DDR) enables aggressive tumors to achieve uncontrolled proliferation against replication stress, but the mechanisms underlying this process in tumors are relatively complex. Here, we demonstrate a mechanism through which a distinct E3 ubiquitin ligase, ITCH, modulates DDR machinery in triple-negative breast cancer (TNBC). We found that expression of a nuclear form of ITCH was significantly increased in human TNBC cell lines and tumor specimens. Phosphorylation of ITCH at Ser257 by AKT led to the nuclear localization of ITCH and ubiquitination of H1.2. The ITCH-mediated polyubiquitination of H1.2 suppressed RNF8/RNF168-dependent formation of 53BP1 foci, which plays important roles in DDR. Consistent with these findings, impaired ITCH nuclear translocation and H1.2 polyubiquitination sensitized cells to replication stress and limited cell growth and migration. AKT activation of ITCH-H1.2 axis may confer TNBC cells with a DDR repression to counteract the replication stress and increase cancer cell survivorship and growth potential
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