Mitigating the Position Bias of Transformer Models in Passage Re-Ranking

Supervised machine learning models and their evaluation strongly depends on the quality of the underlying dataset. When we search for a relevant piece of information it may appear anywhere in a given passage. However, we observe a bias in the position of the correct answer in the text in two popular Question Answering datasets used for passage re-ranking. The excessive favoring of earlier positions inside passages is an unwanted artefact. This leads to three common Transformer-based re-ranking models to ignore relevant parts in unseen passages. More concerningly, as the evaluation set is taken from the same biased distribution, the models overfitting to that bias overestimate their true effectiveness. In this work we analyze position bias on datasets, the contextualized representations, and their effect on retrieval results. We propose a debiasing method for retrieval datasets. Our results show that a model trained on a position-biased dataset exhibits a significant decrease in re-ranking effectiveness when evaluated on a debiased dataset. We demonstrate that by mitigating the position bias, Transformer-based re-ranking models are equally effective on a biased and debiased dataset, as well as more effective in a transfer-learning setting between two differently biased datasets

Charged pions from Ni on Ni collisions between 1 and 2 AGeV

Charged pions from Ni + Ni reactions at 1.05, 1.45 and 1.93 AGeV are measured with the FOPI detector. The mean $\pi^{\pm}$ multiplicities per mean number of participants increase with beam energy, in accordance with earlier studies of the Ar + KCl and La + La systems. The pion kinetic energy spectra have concave shape and are fitted by the superposition of two Boltzmann distributions with different temperatures. These apparent temperatures depend only weakly on bombarding energy. The pion angular distributions show a forward/backward enhancement at all energies, but not the $\Theta = 90^0$ enhancement which was observed in case of the Au + Au system. These features also determine the rapidity distributions which are therefore in disagreement with the hypothesis of one thermal source. The importance of the Coulomb interaction and of the pion rescattering by spectator matter in producing these phenomena is discussed.Comment: 22 pages, Latex using documentstyle[12pt,a4,epsfig], to appear in Z. Phys.

The Utility of ctDNA in Lung Cancer Clinical Research and Practice: A Systematic Review and Meta-Analysis of Clinical Studies.

This systematic review with embedded meta-analysis aimed to evaluate the clinical utility of circulating tumor DNA (ctDNA) in lung cancer. After screening and review of the Embase database search, 111 studies from 2015 to 2020 demonstrated ctDNA's value in prognostication/monitoring disease progression, mainly in patients with advanced/metastatic disease and non-small cell lung cancer. ctDNA positivity/detection at any time point was associated with shorter progression-free survival and overall survival, whereas ctDNA clearance/decrease during treatment was associated with a lower risk of progression and death. Validating these findings and addressing challenges regarding ctDNA testing integration into clinical practice will require further research

Multigene prognostic tests in breast cancer: past, present, future

There is growing consensus that multigene prognostic tests provide useful complementary information to tumor size and grade in estrogen receptor (ER)-positive breast cancers. The tests primarily rely on quantification of ER and proliferation-related genes and combine these into multivariate prediction models. Since ER-negative cancers tend to have higher proliferation rates, the prognostic value of current multigene tests in these cancers is limited. First-generation prognostic signatures (Oncotype DX, MammaPrint, Genomic Grade Index) are substantially more accurate to predict recurrence within the first 5 years than in later years. This has become a limitation with the availability of effective extended adjuvant endocrine therapies. Newer tests (Prosigna, EndoPredict, Breast Cancer Index) appear to possess better prognostic value for late recurrences while also remaining predictive of early relapse. Some clinical prediction problems are more difficult to solve than others: there are no clinically useful prognostic signatures for ER-negative cancers, and drug-specific treatment response predictors also remain elusive. Emerging areas of research involve the development of immune gene signatures that carry modest but significant prognostic value independent of proliferation and ER status and represent candidate predictive markers for immune-targeted therapies. Overall metrics of tumor heterogeneity and genome integrity (for example, homologue recombination deficiency score) are emerging as potential new predictive markers for platinum agents. The recent expansion of high-throughput technology platforms including low-cost sequencing of circulating and tumor-derived DNA and RNA and rapid reliable quantification of microRNA offers new opportunities to build extended prediction models across multiplatform data

Prevalence of PALB2 Mutations in Breast Cancer Patients in Multi-Ethnic Asian Population in Malaysia and Singapore

10.1371/journal.pone.0073638PLoS ONE88-POLN

Can the intake of antiparasitic secondary metabolites explain the low prevalence of hemoparasites among wild Psittaciformes?

Background: Parasites can exert selection pressure on their hosts through effects on survival, on reproductive success, on sexually selected ornament, with important ecological and evolutionary consequences, such as changes in population viability. Consequently, hemoparasites have become the focus of recent avian studies. Infection varies significantly among taxa. Various factors might explain the differences in infection among taxa, including habitat, climate, host density, the presence of vectors, life history and immune defence. Feeding behaviour can also be relevant both through increased exposure to vectors and consumption of secondary metabolites with preventative or therapeutic effects that can reduce parasite load. However, the latter has been little investigated. Psittaciformes (parrots and cockatoos) are a good model to investigate these topics, as they are known to use biological control against ectoparasites and to feed on toxic food. We investigated the presence of avian malaria parasites (Plasmodium), intracellular haemosporidians (Haemoproteus, Leucocytozoon), unicellular flagellate protozoans (Trypanosoma) and microfilariae in 19 Psittaciformes species from a range of habitats in the Indo-Malayan, Australasian and Neotropical regions. We gathered additional data on hemoparasites in wild Psittaciformes from the literature. We considered factors that may control the presence of hemoparasites in the Psittaciformes, compiling information on diet, habitat, and climate. Furthermore, we investigated the role of diet in providing antiparasitic secondary metabolites that could be used as self-medication to reduce parasite load. Results: We found hemoparasites in only two of 19 species sampled. Among them, all species that consume at least one food item known for its secondary metabolites with antimalarial, trypanocidal or general antiparasitic properties, were free from hemoparasites. In contrast, the infected parrots do not consume food items with antimalarial or even general antiparasitic properties. We found that the two infected species in this study consumed omnivorous diets. When we combined our data with data from studies previously investigating blood parasites in wild parrots, the positive relationship between omnivorous diets and hemoparasite infestation was confirmed. Individuals from open habitats were less infected than those from forests. Conclusions: The consumption of food items known for their secondary metabolites with antimalarial, trypanocidal or general antiparasitic properties, as well as the higher proportion of infected species among omnivorous parrots, could explain the low prevalence of hemoparasites reported in many vertebrates