Search Results (15)

This paper critically examines artificial intelligence applications in stock market forecasting, addressing significant gaps in the existing literature that often overlook the tension between theoretical market efficiency and empirical predictability. While numerous reviews catalog methodologies, they frequently fail to rigorously evaluate model performance across different market regimes or reconcile statistical significance with economic relevance. We analyze techniques ranging from traditional statistical models to advanced deep learning architectures, finding that ensemble methods like Extra Trees, Random Forest, and XGBoost consistently outperform single classifiers, achieving directional accuracy of up to 86% in specific market conditions. Our analysis reveals that hybrid approaches integrating multiple data sources demonstrate superior performance by capturing complementary market signals, yet many models showing statistical significance fail to generate economic value after accounting for transaction costs and market impact. By addressing methodological challenges including backtest overfitting, regime changes, and implementation constraints, we provide a novel comprehensive framework for rigorous model assessment that bridges the divide between academic research and practical implementation. This review makes three key contributions: (1) a reconciliation of the Efficient Market Hypothesis with AI-driven predictability through an adaptive market framework, (2) a multi-dimensional evaluation methodology that extends beyond classification accuracy to financial performance, and (3) an identification of promising research directions in explainable AI, transfer learning, causal modeling, and privacy-preserving techniques that address current limitations. Full article

We present Synesth, the most comprehensive and flexible tool for tree reconciliation that allows for events on syntenies (i.e., on sets of multiple genes), including duplications, transfers, fissions, and transient events going through unsampled species. This model allows for building histories that explicate the inconsistencies between a synteny tree and its associated species tree. We examine the combinatorial properties of this extended reconciliation model and study various associated parsimony problems. First, the infinite set of explicatory histories is reduced to a finite but exponential set of Pareto-optimal histories (in terms of counts of each event type), then to a polynomial set of Pareto-optimal event count vectors, and this eventually ends with minimum event cost histories given an event cost function. An inductive characterization of the solution space using different algebras for each granularity leads to efficient dynamic programming algorithms, ultimately ending with an $O\left(mn\right)$ time complexity algorithm for computing the cost of a minimum-cost history (m and n: number of nodes in the input synteny and species trees). This time complexity matches that of the fastest known algorithms for classical gene reconciliation with transfers. We show how Synesth can be applied to infer Pareto-optimal evolutionary scenarios for CRISPR-Cas systems in a set of bacterial genomes. Full article

Estimating the heterogeneity of base and precious metal mineralisation is a great challenge for mining engineers and geologists who undertake resource evaluation, grade control and reconciliation. The calculation of the minimum broken sample mass to represent a given lot of mineralisation at a given comminution size is based on the estimation of IH_L, the constant factor of constitution heterogeneity. IH_L can be derived by different heterogeneity testwork or calibration approaches. Three methodologies are well known in the mining industry: the standard heterogeneity test, the segregation free analysis, and the sampling tree experiment or duplicate sample analysis. However, the methodologies often show different results, especially when it comes to gold. These differences are due to many reasons. Assuming the variances added by sample preparation and analysis to be equivalent for all tests, the reasons for the differences may include the nugget effect (particularly the presence of coarse gold), the segregation effect and the procedure of collecting/splitting the samples when performing the tests. This paper analyses and compares two heterogeneity tests: the original heterogeneity test and the simplified segregation free analysis, both performed on mineralisation from different Brazilian operations. The results show clear differences between the tests, highlighting the complexity of estimating the heterogeneity of mineral deposits. The study reports the importance of using proper methodologies for constitution heterogeneity estimation so that minimum sample masses and relative standard deviations of the fundamental sampling error can be relied upon. It also provides recommendations for practitioners on the application of testwork/calibration studies. Full article

The paper solves the problem of constructing an evolutionary tree and the evolution of structures along it. This problem has long been posed and extensively researched; it is formulated and discussed below. As a result, we construct an exact cubic-time algorithm which outputs a tree with the minimum cost of embedding into it and of embedding it into a given network (Theorem 1). We construct an algorithm that outputs a minimum embedding of a tree into a network, taking into account incomplete linear sorting; the algorithm depends linearly on the number of nodes in the network and is exact if the sorting cost is not less than the sum of the duplication cost and the loss cost (Theorem 3). We construct an exact approximately quadratic-time algorithm which, for arbitrary costs of SCJ operations, solves the problem of reconstruction of given structures on any two-star tree (Theorem 4). We construct an exact algorithm which reduced the problem of DCJ reconstruction of given structures on any star to a logarithmic-length sequence of SAT problems, each of them being of approximately quadratic size (Theorem 5). The theorems have rigorous and complete proofs of correctness and complexity of the algorithms, and are accompanied by numerical examples and numerous explanatory illustrations, including flowcharts. Full article

As one of the most successful group of organisms, mammals occupy a variety of niches on Earth as a result of macroevolution. Transcription factors (TFs), the fundamental regulators of gene expression, may also have evolved. To examine the relationship between TFs and mammalian macroevolution, we analyzed 140,821 de novo-identified TFs and their birth and death histories from 96 mammalian species. Gene tree vs. species tree reconciliation revealed that placental mammals experienced an upsurge in TF losses around 100 million years ago (Mya) and also near the Cretaceous–Paleogene boundary (K–Pg boundary, 66 Mya). Early Euarchontoglires, Laurasiatheria and marsupials appeared between 100 and 95 Mya and underwent initial diversification. The K-Pg boundary was associated with the massive extinction of dinosaurs, which lead to adaptive radiation of mammals. Surprisingly, TF loss decelerated, rather than accelerated, molecular evolutionary rates of their target genes. As the rate of molecular evolution is affected by the mutation rate, the proportion of neutral mutations and the population size, the decrease in molecular evolution may reflect increased functional constraints to survive target genes. Full article

The rooting of phylogenetic trees permits important inferences about ancestral states and the polarity of evolutionary events. Recently, methods that reconcile discordance between gene-trees and species-trees—tree reconciliation methods—are becoming increasingly popular for rooting species trees. Rooting via reconciliation requires values for a particular parameter, the gene transfer to gene duplication ratio (T:D), which in current practice is estimated on the fly from discordances observed in the trees. To date, the accuracy of T:D estimates obtained by reconciliation analyses has not been compared to T:D estimates obtained by independent means, hence the effect of T:D upon inferences of species tree roots is altogether unexplored. Here we investigated the issue in detail by performing tree reconciliations of more than 10,000 gene trees under a variety of T:D ratios for two phylogenetic cases: a bacterial (prokaryotic) tree with 265 species and a fungal-metazoan (eukaryotic) tree with 31 species. We show that the T:D ratios automatically estimated by a current tree reconciliation method, ALE, generate virtually identical T:D ratios across bacterial genes and fungal-metazoan genes. The T:D ratios estimated by ALE differ 10- to 100-fold from robust, ALE-independent estimates from real data. More important is our finding that the root inferences using ALE in both datasets are strongly dependent upon T:D. Using more realistic T:D ratios, the number of roots inferred by ALE consistently increases and, in some cases, clearly incorrect roots are inferred. Furthermore, our analyses reveal that gene duplications have a far greater impact on ALE’s preferences for phylogenetic root placement than gene transfers or gene losses do. Overall, we show that obtaining reliable species tree roots with ALE is only possible when gene duplications are abundant in the data and the number of falsely inferred gene duplications is low. Finding a sufficient sample of true gene duplications for rooting species trees critically depends on the T:D ratios used in the analyses. T:D ratios, while being important parameters of genome evolution in their own right, affect the root inferences with tree reconciliations to an unanticipated degree. Full article

Desertification has become one of the most pronounced ecological disasters, affecting arid and semi-arid areas of Nigeria. This phenomenon is more pronounced in the northern region, particularly the eleven frontline states of Nigeria, sharing borders with the Niger Republic. This has been attributed to a range of natural and anthropogenic factors. Rampant felling of trees for fuelwood, unsustainable agriculture, overgrazing, coupled with unfavourable climatic conditions are among the key factors that aggravate the desertification phenomenon. This study applied geospatial analysis to explore land use/land cover changes and detect major conversions from ecologically active land covers to sand dunes. Results indicate that areas covered by sand dunes (a major indicator of desertification) have doubled over the 25 years under consideration (1990 to 2015). Even though 0.71 km² of dunes was converted to vegetation, indicative of the success of various international, national, local and individual afforestation efforts, conversely about 10.1 km² of vegetation were converted to sand dunes, implying around 14 times more deforestation compared to afforestation. On average, our results revealed that the sand dune in the study area is progressing at a mean annual rate of 15.2 km² annually. The land cover conversion within the 25-year study period was from vegetated land to farmlands. Comparing the progression of a sand dune with climate records of the study area and examining the relationship between indicators of climate change and desertification suggested a mismatch between both processes, as increasing rainfall and lower temperatures observed in 1994, 2005, 2012, and 2014 did not translate into positive feedbacks for desertification in the study area. Likewise, the mean annual Normalized Difference Vegetation Index (NDVI) from 2000 to 2015 shows a deviation between vegetation peaks, mean temperatures and rainfall. On average, our results reveal that the sand dune is progressing at a mean annual rate of about 15.2 km² in the study area. Based on this study’s land cover change, trend and conversion assessment, visual reconciliation of climate records of land cover data, statistical analysis, observations from ground-truthing, as well as previous literature, it can be inferred that desertification in Nigeria is less a function of climate change, but more a product of human activities driven by poverty, population growth and failed government policies. Further projections by this study also reveal a high probability of more farmlands being converted to sand dunes by the years 2030 and 2045 if current practices prevail. Full article

Phylogenetic reconciliation is a fundamental method in the study of pairs of coevolving species. This paper provides an overview of the underlying theory of reconciliation in the context of host-symbiont cophylogenetics, identifying some of the major challenges to users of these methods, such as selecting event costs and selecting representative reconciliations. Next, recent advances to address these challenges are discussed followed by a discussion of several established and recent software tools. Full article

Duplication-Transfer-Loss (DTL) reconciliation is a widely used computational technique for understanding gene family evolution and inferring horizontal gene transfer (transfer for short) in microbes. However, most existing models and implementations of DTL reconciliation cannot account for the effect of unsampled or extinct species lineages on the evolution of gene families, likely affecting their accuracy. Accounting for the presence and possible impact of any unsampled species lineages, including those that are extinct, is especially important for inferring and studying horizontal transfer since many genes in the species lineages represented in the reconciliation analysis are likely to have been acquired through horizontal transfer from unsampled lineages. While models of DTL reconciliation that account for transfer from unsampled lineages have already been proposed, they use a relatively simple framework for transfer from unsampled lineages and cannot explicitly infer the location on the species tree of each unsampled or extinct lineage associated with an identified transfer event. Furthermore, there does not yet exist any systematic studies to assess the impact of accounting for unsampled lineages on the accuracy of DTL reconciliation. In this work, we address these deficiencies by (i) introducing an extended DTL reconciliation model, called the DTLx reconciliation model, that accounts for unsampled and extinct species lineages in a new, more functional manner compared to existing models, (ii) showing that optimal reconciliations under the new DTLx reconciliation model can be computed just as efficiently as under the fastest DTL reconciliation model, (iii) providing an efficient algorithm for sampling optimal DTLx reconciliations uniformly at random, (iv) performing the first systematic simulation study to assess the impact of accounting for unsampled lineages on the accuracy of DTL reconciliation, and (v) comparing the accuracies of inferring transfers from unsampled lineages under our new model and the only other previously proposed parsimony-based model for this problem. Full article

Syntenies are genomic segments of consecutive genes identified by a certain conservation in gene content and order. The notion of conservation may vary from one definition to another, the more constrained requiring identical gene contents and gene orders, while more relaxed definitions just require a certain similarity in gene content, and not necessarily in the same order. Regardless of the way they are identified, the goal is to characterize homologous genomic regions, i.e., regions deriving from a common ancestral region, reflecting a certain gene co-evolution that can enlighten important functional properties. In addition of being able to identify them, it is also necessary to infer the evolutionary history that has led from the ancestral segment to the extant ones. In this field, most algorithmic studies address the problem of inferring rearrangement scenarios explaining the disruption in gene order between segments with the same gene content, some of them extending the evolutionary model to gene insertion and deletion. However, syntenies also evolve through other events modifying their content in genes, such as duplications, losses or horizontal gene transfers, i.e., the movement of genes from one species to another. Although the reconciliation approach between a gene tree and a species tree addresses the problem of inferring such events for single-gene families, little effort has been dedicated to the generalization to segmental events and to syntenies. This paper reviews some of the main algorithmic methods for inferring ancestral syntenies and focus on those integrating both gene orders and gene trees. Full article

This paper is an investigation of the divine feminine power as depicted in the texts of Hispanic mystics from Sufi, Hebrew, and Christian traditions. This work is intended to investigate the origin and subsequent development of a transcendent reconciliation of polarity, its diverse manifestations, and the attainment of a common goal, the quintessential of the Perfect Human Being. The architect of the encounter that leads to Union is “Sophia”. She is the Secret. Only those who are able to discern Her own immeasurable dimension may contemplate the Lady who dwells in the sacred geometry of the abyss. Sophia is linked to the hermetic Word, She is allusive, clandestine, poetic, and pregnant with symbols, gnostic resonances, and musical murmurs that conduct the “traveler” through dwellings and stations towards an ancient Sophianic knowledge that leads to the “germinal vesicle”, the “inner wine cellar”, to the Initium, to the Motherland. She is the Mater filius sapientae, who through an alchemical transmutation becomes a song to the absent Sophia whose Presence can only be intuited. Present throughout the Creation, Sophia is the axis around which the poetics of the Taryuman al-ashwaq rotates and the kabbalistic Tree of Life is structured. Full article

Mammals have variable numbers (1300–2000) of transcription factors (TFs), but the reasons for this large variation are unclear. To investigate general TF patterns, we de novo identified 156,906 TFs from 96 mammalian species. We identified more than 500 human isolated TFs that are rarely reported in human TF-to-TF networks. Mutations in the genes of these TFs were less lethal than those of connected TFs. Consequently, these isolated TFs are more tolerant of changes and have become unique during speciation. They may also serve as a source of variation for TF evolution. Reconciliation of TF-family phylogenetic trees with a mammalian species tree revealed an average of 37.8% TF gains and 15.0% TF losses over 177 million years, which implies that isolated TFs are pervasive in mammals. Compared with non-TF interacting genes, TF-interacting genes have unique TF profiles and have higher expression levels in mice than in humans. Different expression levels of the same TF-interacting gene contribute to species-specific phenotypes. Formation and loss of isolated TFs enabling unique TF profiles may provide variable switches that adjust divergent expression profiles of target genes to generate species-specific phenotypes, thereby making species unique. Full article

In the reconciliation problem, we are given two phylogenetic trees. A species tree represents the evolutionary history of a group of species, and a gene tree represents the history of a family of related genes within these species. A reconciliation maps nodes of the gene tree to the corresponding points of the species tree, and thus helps to interpret the gene family history. In this paper, we study the case when both trees are unrooted and their edge lengths are known exactly. The goal is to root them and to find a reconciliation that agrees with the edge lengths. We show a linear-time algorithm for finding the set of all possible root locations, which is a significant improvement compared to the previous $O(N^{3}logN)$ algorithm. Full article

Conflict and environmental degradation in the Democratic Republic of the Congo are interrelated and complex. The authors conducted a case study of a community-based environmental restoration project in Eastern Congo and provide early results which suggest a link between community environmental action and multidimensional outcomes such as peace and reconciliation. The project examined in this study is based on a framework (Theory of Change) which networks communities through autonomous savings groups, churches, mosques, schools, and a community leadership network with the goal of catalyzing sustainable farming, reforestation, and community forest management. The primary project input was training, and the resulting voluntary community action included tree planting and the management of common forest areas. A mixed-methods approach was used to evaluate project results comparing two watersheds, and included a difference in differences analysis, participatory workshops, remote sensing analysis, and community activity reports. Positive change was observed in the treatment watershed in terms of ecosystem health and household economic condition. Results suggest a possible influence on peace conditions which, while fragile, offers hope for continued restorative action by communities. This study provides evidence that a community-based approach to environmental restoration may have a positive influence on multidimensional issues such as forests, watershed health, economic well-being, and peace. Full article

Characterizing the mechanisms of duplicate gene retention using phylogenetic methods requires models that are consistent with different biological processes. The interplay between complex biological processes and necessarily simpler statistical models leads to a complex modeling problem. A discussion of the relationship between biological processes, existing models for duplicate gene retention and data is presented. Existing models are then extended in deriving two new birth/death models for phylogenetic application in a gene tree/species tree reconciliation framework to enable probabilistic inference of the mechanisms from model parameterization. The goal of this work is to synthesize a detailed discussion of modeling duplicate genes to address biological questions, moving from previous work to future trajectories with the aim of generating better models and better inference. Full article