Analysis of Approximate Message Passing with a Class of Non-Separable Denoisers

Approximate message passing (AMP) is a class of efficient algorithms for solving high-dimensional linear regression tasks where one wishes to recover an unknown signal \beta_0 from noisy, linear measurements y = A \beta_0 + w. When applying a separable denoiser at each iteration, the performance of AMP (for example, the mean squared error of its estimates) can be accurately tracked by a simple, scalar iteration referred to as state evolution. Although separable denoisers are sufficient if the unknown signal has independent and identically distributed entries, in many real-world applications, like image or audio signal reconstruction, the unknown signal contains dependencies between entries. In these cases, a coordinate-wise independence structure is not a good approximation to the true prior of the unknown signal. In this paper we assume the unknown signal has dependent entries, and using a class of non-separable sliding-window denoisers, we prove that a new form of state evolution still accurately predicts AMP performance. This is an early step in understanding the role of non-separable denoisers within AMP, and will lead to a characterization of more general denoisers in problems including compressive image reconstruction.Comment: 37 pages, 1 figure. A shorter version of this paper to appear in the proceedings of ISIT 201

Uptake of Improved Technologies in the Semi-arid Tropics of West Africa: Why is Agricultural Transformation Lagging Behind?

During the last 3 decades, donors and governments have invested in the development and dissemination of new technologies in the semi-arid tropics of West Africa. Though a wide range of improved technologies has been developed, adoption remains low without a significant impact on crop productivity, rural income and poverty. Agricultural transformation as occurred in East Asia has not yet occurred in the semi-arid tropics of West Africa. This paper uses data from a regional survey of rural households in 3 countries in West Africa (Burkina Faso, Mali, and Niger) to identify the determinants of uptake of improved technologies. Limited productivity gain is found to be a major constraint to the uptake of technologies. In addition, poorly functioning institutions, lack of information or poor exposure of farmers to agricultural innovations, and poor functioning or missing markets have also hindered the uptake of many new technologies.institutions, technology, markets, road infrastructure, information, agricultural productivity, International Development,

Impact of ICRISAT Research on Australian Agriculture

Research and Development/Tech Change/Emerging Technologies,

PI3K inhibition enhances the anti-tumor effect of eribulin in triple negative breast cancer

Loss of the tumor suppressor phosphatase and tensin homolog (PTEN) is commonly observed in triple negative breast cancer (TNBC), leading to activation of the phosphoinositide 3-kinase (PI3K) signaling to promote tumor cell growth and chemotherapy resistance. In this study, we investigated whether adding a pan-PI3K inhibitor could improve the cytotoxic effect of eribulin, a non-taxane microtubule inhibitor, in TNBC patient-derived xenograft models (PDX) with loss of PTEN, and the underlying molecular mechanisms. Three TNBC-PDX models (WHIM6, WHIM12 and WHIM21), all with loss of PTEN expression, were tested for their response to BKM120 and eribulin, alone or in combinatio

Clinical challenges in the management of hormone receptor-positive, human epidermal growth factor receptor 2-negative metastatic breast cancer: A literature review

Endocrine therapy (ET) is integral to the treatment of hormone receptor-positive (HR+), human epidermal growth factor receptor 2-negative (HER2-) metastatic breast cancer (MBC). Aromatase inhibitors (AIs; e.g., anastrozole, letrozole, exemestane), selective estrogen receptor modulators (e.g., tamoxifen), and the selective estrogen receptor degrader, fulvestrant, inhibit tumor cell proliferation by targeting ER signaling. However, the efficacy of ET could be limited by intrinsic and acquired resistance mechanisms, which has prompted the development of targeted agents and combination strategies. In recent years, the treatment landscape for HR+, HER2- MBC has evolved rapidly. AIs, historically the first-line treatment for postmenopausal patients with HR+, HER2- MBC, have been challenged by more effective ET, such as fulvestrant alone or in combination with an AI, and the cyclin-dependent kinase (CDK)4/6 inhibitors, which have increasingly become the new standard of care. For endocrine-resistant disease (≥ second-line), clinical trials demonstrated that the mammalian target of rapamycin inhibitor, everolimus, enhanced the efficacy of exemestane or fulvestrant after progression on an AI. CDK4/6 inhibitors in combination with fulvestrant have demonstrated superior progression-free survival and overall survival versus fulvestrant alone. Recently, the combination of fulvestrant with alpelisib in phosphatidylinositol-4,5-bisphosphate 3-kinase (PIK3CA) mutated HR+, HER2- MBC following progression on or after ET was approved, based on the SOLAR-1 study. However, the optimal sequencing of treatments is unknown, especially following disease progression on a CDK4/6 inhibitor. This review aims to provide practical guidance for the management of HR+, HER2- MBC based on available data and the utility of genomic biomarkers, including germline breast cancer genes 1 and 2 (BRCA1/2) mutations, and somatic estrogen receptor alpha gene (ESR1), HER2, and PIK3CA mutations

Collective Action for Integrated Community Watershed Management in Semi-Arid India: Analysis of Multiple Livelihood Impacts and the Drivers of Change

Spatial and temporal attributes of watersheds and associated market failures require institutional arrangements for coordinating use and management of natural resources. Effective collective action (CA) for watershed management has the potential to provide multiple economic and environmental benefits - tangible and non-tangible - to rural communities. This allows smallholder farmers to jointly invest in management practices that provide collective benefits to community members. The functions of the group can also extend to include provision of new services like collective marketing of products and essential inputs. While watershed management contributes to resource productivity and sustainability, increased commercialization and market access open opportunities to diversify into high-value crops, creating incentives for agricultural intensification. However, evaluating the multi-faceted impacts of integrated watershed management interventions is complicated by problems of measurement, valuation and attribution. While, more rigorous methods for evaluating such impacts in the context of developing countries are beginning to emerge, this study employs a mix of qualitative and quantitative methods for evaluating these multi-faceted impacts from a case study of a watershed project in semi-arid India. Results from qualitative insights are confirmed through econometric analyses and empirical measurements using proper count erfactuals. The study analyses the drought mitigation, economic and environmental gains along with linked benefits for commercialization of production and increased farmer participation in markets.Resource /Energy Economics and Policy,

Inferring TF activities and activity regulators from gene expression data with constraints from TF perturbation data

MOTIVATION: The activity of a transcription factor (TF) in a sample of cells is the extent to which it is exerting its regulatory potential. Many methods of inferring TF activity from gene expression data have been described, but due to the lack of appropriate large-scale datasets, systematic and objective validation has not been possible until now. RESULTS: We systematically evaluate and optimize the approach to TF activity inference in which a gene expression matrix is factored into a condition-independent matrix of control strengths and a condition-dependent matrix of TF activity levels. We find that expression data in which the activities of individual TFs have been perturbed are both necessary and sufficient for obtaining good performance. To a considerable extent, control strengths inferred using expression data from one growth condition carry over to other conditions, so the control strength matrices derived here can be used by others. Finally, we apply these methods to gain insight into the upstream factors that regulate the activities of yeast TFs Gcr2, Gln3, Gcn4 and Msn2. AVAILABILITY AND IMPLEMENTATION: Evaluation code and data are available at https://doi.org/10.5281/zenodo.4050573. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online