Building trainable taggers in a web-based, UIMA-supported NLP workbench

Argo is a web-based NLP and text mining workbench with a convenient graphical user interface for designing and executing processing workflows of various complexity. The workbench is intended for specialists and nontechnical audiences alike, and provides the ever expanding library of analytics compliant with the Unstructured Information Management Architecture, a widely adopted interoperability framework. We explore the flexibility of this framework by demonstrating workflows involving three processing components capable of performing self-contained machine learning-based tagging. The three components are responsible for the three distinct tasks of 1) generating observations or features, 2) training a statistical model based on the generated features, and 3) tagging unlabelled data with the model. The learning and tagging components are based on an implementation of conditional random fields (CRF); whereas the feature generation component is an analytic capable of extending basic token information to a comprehensive set of features. Users define the features of their choice directly from Argo’s graphical interface, without resorting to programming (a commonly used approach to feature engineering). The experimental results performed on two tagging tasks, chunking and named entity recognition, showed that a tagger with a generic set of features built in Argo is capable of competing with taskspecific solutions.

Sex can be dangerous: Acoustically-orienting parasitoids on field crickets (Orthoptera: Gryllidae)

The Orthopterists\u27 Society generously awarded me grants in 1995 and 1997 to conduct research on Teleogryllus oceanicus (Orthoptera: Gryllidae) on the Big Island of Hawaii. Here I report results to date from fieldwork conducted in the past few years

Sex differences in metabolic rates in field crickets and their dipteran parasitoids

Sex differences in metabolic rate (MR) can result from dimorphism in the performance of energetically demanding activities. Male crickets (Teleogryllus oceanicus) engage in costly calling and aggressive activity not performed by females. Consistent with this difference, we found higher maximal MR, factorial scope, and fat content in males than females. T. oceanicus song is also costly because it attracts the parasitoid fly Ormia ochracea. Parasitized crickets had reduced maximal MR consistent with a metabolic cost to harboring larvae. This cost was greater for females, either because females invest more heavily into reproduction at the expense of metabolic capacity, or because males are under stronger selection to respond to infection. Little is known about O. ochracea outside of its auditory system and parasitic lifestyle. We observed greater resting MR in male flies, possibly reflecting a sex difference in the requirement for metabolic power output, because male flies perform potentially costly mating behavior not seen in females. We found a positive relationship between larval density within a cricket and pupal resting MR, suggesting that crickets in good condition are able to both harbor more larvae and produce larvae with higher resting MR. These results reveal a complex interplay between the metabolism of crickets and their fly parasitoids

Environmental and genetic influences on mating strategies along a replicated food availability gradient in guppies (\u3cem\u3ePoecilia reticulata\u3c/em\u3e)

Food availability is expected to influence the relative cost of different mating tactics, but little attention has been paid to this potential source of adaptive geographic variation in behavior. Associations between the frequency of different mating tactics and resource availability could arise because tactic use responds directly to food intake (phenotypic plasticity), because populations exposed to different average levels of food availability have diverged genetically in tactic use, or both. Different populations of guppies (Poecilia reticulata) in Trinidad experience different average levels of food availability. We combined field observations with laboratory “common garden” and diet experiments to examine how this environmental gradient has influenced the evolution of male mating tactics. Three independent components of variation in male behavior were found in the field: courtship versus foraging, dominance interactions, and interference competition versus searching for mates. Compared with low-food-availability sites, males at high-food-availability sites devoted more effort to interference competition. This difference disappeared in the common garden experiment, which suggests that it was caused by phenotypic plasticity and not genetic divergence. In the diet experiment, interference competition was more frequent and intense among males raised on the greater of two food levels, but this was only true for fish descended from sites with low food availability. Thus, the association between interference competition and food availability in the field can be attributed to a genetically variable norm of reaction. Genetically variable norms of reaction with respect to food intake were found for the other two behavioral components as well and are discussed in relation to the patterns observed in the field. Our results indicate that food availability gradients are an important, albeit complex, source of geographic variation in male mating strategies

Sex–specific effects of carotenoid intake on the immunological response to allografts in guppies (\u3cem\u3ePoecilia reticulata\u3c/em\u3e)

Rarely are the evolutionary origins of mate preferences known, but, recently, the preference of female guppies (Poecilia reticulata) for males with carotenoid‐based sexual coloration has been linked to a sensory bias that may have originally evolved for detecting carotenoid‐rich fruits. If carotenoids enhance the immune systems of these fishes, as has been suggested for other species, this could explain the origin of the attraction to orange fruits as well as the maintenance of the female preference for orange males. We used the classic immunological technique of tissue grafting to assay a component of the immune response of guppies raised on two different dietary levels of carotenoids. Individual scales were transplanted between pairs of unrelated fishes, creating reciprocal allografts. Transplanted scales were scored on a six‐point rejection scale every day for 10 days. Five days later, the same pairs of fishes received a second set of allografts and were scored again. Compared with low‐carotenoid‐diet males, high‐carotenoid‐diet males mounted a significantly stronger rejection response to the second allograft but not to the first allograft. High‐carotenoid‐diet females, however, showed no improvement in graft rejection compared with low‐carotenoid‐diet females. To our knowledge, this is the first experimental evidence for sex‐specific effects of carotenoid consumption on the immune system of a species with carotenoid‐based sexual coloration. These results are consistent with the hypothesis that the mate preference for carotenoid coloration is maintained by the benefits to females of choosing healthy mates, but they cast doubt on the idea that the benefits of carotenoid consumption, per se, could account for the origin of the preference. The sex‐specificity of carotenoid effects on allograft rejection in guppies provides indirect support for the general hypothesis that males pay an immunological cost for sexual ornamentation

Thalidomide attenuates nitric oxide mediated angiogenesis by blocking migration of endothelial cells

BACKGROUND: Thalidomide is an immunomodulatory agent, which arrests angiogenesis. The mechanism of anti-angiogenic activity of thalidomide is not fully understood. As nitric oxide is involved in angiogenesis, we speculate a cross-talk between thalidomide and nitric oxide signaling pathway to define angiogenesis. The aim of present study is to understand the mechanistic aspects of thalidomide-mediated attenuation of angiogenesis induced by nitric oxide at the cellular level. METHODS: To study the cellular mechanism of thalidomide-mediated blocking of angiogenesis triggered by nitric oxide, we used two endothelial cell based models: 1) wound healing and 2) tube formation using ECV 304, an endothelial cell line. These cell-based models reflect pro-angiogenic events in vivo. We also studied the effects of thalidomide on nitric oxide mediated egg yolk angiogenesis. Thalidomide could block the formation of blood vessels both in absence and presence of nitric oxide. Thalidomide effects on migration of, and actin polymerization in, ECV 304 cells were studied at the single cell level using live cell imaging techniques and probes to detect nitric oxide. RESULTS: Results demonstrate that thalidomide blocks nitric oxide-mediated angiogenesis in egg yolk model and also reduces the number of tubes formed in endothelial cell monolayers. We also observed that thalidomide arrests wound healing in presence and absence of nitric oxide in a dose-dependent fashion. Additionally, thalidomide promotes actin polymerization and antagonizes the formation of membrane extensions triggered by nitric oxide in endothelial cells. Experiments targeting single tube structure with thalidomide, followed by nitric oxide treatment, show that the tube structures are insensitive to thalidomide and nitric oxide. These observations suggest that thalidomide interferes with nitric oxide-induced migration of endothelial cells at the initial phase of angiogenesis before cells co-ordinate themselves to form organized tubes in endothelial cells and thereby inhibits angiogenesis. CONCLUSION: Thalidomide exerts inhibitory effects on nitric oxide-mediated angiogenesis by altering sub-cellular actin polymerization pattern, which leads to inhibition of endothelial cell migration

Feature Extraction Techniques in Medical Imaging: A Systematic Review

With the surge in the development of various applications in the field of Computer Vision and Digital Image Processing, a significant amount of medical pictures are being produced. Thus, the patient-specific scan pictures represent the boundless volume of data that requires careful organization and supervision to assist clinical decision support systems. Now that retrieval, classification, segmentation, and other procedures have been completed, these devices assist doctors to uncover serious illnesses including skin conditions, tumors, and cancer. This imaging largely depends on characteristics to detect the afflicted region and perform the diagnosis visually. The authors of this paper present an overview of numerous feature extraction approaches used to extract features from medical images obtained via different modalities, but only used a handful of these techniques for this job and provided the findings

From Molecules to Materials: Pre-training Large Generalizable Models for Atomic Property Prediction

Foundation models have been transformational in machine learning fields such as natural language processing and computer vision. Similar success in atomic property prediction has been limited due to the challenges of training effective models across multiple chemical domains. To address this, we introduce Joint Multi-domain Pre-training (JMP), a supervised pre-training strategy that simultaneously trains on multiple datasets from different chemical domains, treating each dataset as a unique pre-training task within a multi-task framework. Our combined training dataset consists of $\sim$120M systems from OC20, OC22, ANI-1x, and Transition-1x. We evaluate performance and generalization by fine-tuning over a diverse set of downstream tasks and datasets including: QM9, rMD17, MatBench, QMOF, SPICE, and MD22. JMP demonstrates an average improvement of 59% over training from scratch, and matches or sets state-of-the-art on 34 out of 40 tasks. Our work highlights the potential of pre-training strategies that utilize diverse data to advance property prediction across chemical domains, especially for low-data tasks