Daily Papers

Parametric body models are central to many human-centric tasks, yet existing models often rely on costly 3D scans and learned shape spaces that are proprietary and demographically narrow. We introduce Anny, a simple, fully differentiable, and scan-free human body model grounded in anthropometric knowledge from the MakeHuman community. Anny defines a continuous, interpretable shape space, where phenotype parameters (e.g. gender, age, height, weight) control blendshapes spanning a wide range of human forms -- across ages (from infants to elders), body types, and proportions. Calibrated using WHO population statistics, it provides realistic and demographically grounded human shape variation within a single unified model. Thanks to its openness and semantic control, Anny serves as a versatile foundation for 3D human modeling -- supporting millimeter-accurate scan fitting, controlled synthetic data generation, and Human Mesh Recovery (HMR). We further introduce Anny-One, a collection of 800k photorealistic humans generated with Anny, showing that despite its simplicity, HMR models trained with Anny can match the performance of those trained with scan-based body models, while remaining interpretable and broadly representative. The Anny body model and its code are released under the Apache 2.0 license, making Anny an accessible foundation for human-centric 3D modeling.

Phenomenological modeling of variable stars allows determination of a set of the parameters, which are needed for classification in the "General Catalogue of Variable Stars" and similar catalogs. We apply a recent method NAV ("New Algol Variable") to eclipsing binary stars of different types. Although all periodic functions may be represented as Fourier series with an infinite number of coefficients, this is impossible for a finite number of the observations. Thus one may use a restricted Fourier series, i.e. a trigonometric polynomial (TP) of order s either for fitting the light curve, or to make a periodogram analysis. However, the number of parameters needed drastically increases with decreasing width of minimum. In the NAV algorithm, the special shape of minimum is used, so the number of parameters is limited to 10 (if the period and initial epoch are fixed) or 12 (not fixed). We illustrate the NAV method by application to a recently discovered Algol-type eclipsing variable 2MASS J11080308-6145589 (in the field of previously known variable star RS Car) and compare results to that obtained using the TP fits. For this system, the statistically optimal number of parameters is 44, but the fit is still worse than that of the NAV fit. Application to the system GSC 3692-00624 argues that the NAV fit is better than the TP one even for the case of EW-type stars with much wider eclipses. Model parameters are listed.

We introduce a general, flexible, parametric survival modelling framework which encompasses key shapes of hazard function (constant, increasing, decreasing, up-then-down, down-then-up), various common survival distributions (log-logistic, Burr type XII, Weibull, Gompertz), and includes defective distributions (i.e., cure models). This generality is achieved using four basic distributional parameters: two scale-type parameters and two shape parameters. Generalising to covariate dependence, the scale-type regression components correspond to accelerated failure time (AFT) and proportional hazards (PH) models. Therefore, this general formulation unifies the most popular survival models which allows us to consider the practical value of possible modelling choices for survival data. Furthermore, in line with our proposed flexible baseline distribution, we advocate the use of multi-parameter regression in which more than one distributional parameter depends on covariates - rather than the usual convention of having a single covariate-dependent (scale) parameter. While many choices are available, we suggest introducing covariates through just one or other of the two scale parameters, which covers AFT and PH models, in combination with a `power' shape parameter, which allows for more complex non-AFT/non-PH effects, while the other shape parameter remains covariate-independent, and handles automatic selection of the baseline distribution. We explore inferential issues in simulations, both with and without a covariate, with particular focus on evidence concerning the need, or otherwise, to include both AFT and PH parameters. We illustrate the efficacy of our modelling framework by investigating differences between treatment groups using data from a lung cancer study and a melanoma study. Censoring is accommodated throughout.

Phenomenological characteristics of the sample of the Algol-type stars are revised using a recently developed NAV ("New Algol Variable") algorithm (2012Ap.....55..536A, 2012arXiv 1212.6707A) and compared to that obtained using common methods of Trigonometric Polynomial Fit (TP) or local Algebraic Polynomial (A) fit of a fixed or (alternately) statistically optimal degree (1994OAP.....7...49A, 2003ASPC..292..391A). The computer program NAV is introduced, which allows to determine the best fit with 7 "linear" and 5 "non-linear" parameters and their error estimates. The number of parameters is much smaller than for the TP fit (typically 20-40, depending on the width of the eclipse, and is much smaller (5-20) for the W UMa and beta Lyrae - type stars. This causes more smooth approximation taking into account the reflection and ellipsoidal effects (TP2) and generally different shapes of the primary and secondary eclipses. An application of the method to two-color CCD photometry to the recently discovered eclipsing variable 2MASS J18024395 + 4003309 = VSX J180243.9 +400331 (2015JASS...32..101A) allowed to make estimates of the physical parameters of the binary system based on the phenomenological parameters of the light curve. The phenomenological parameters of the light curves were determined for the sample of newly discovered EA and EW - type stars (VSX J223429.3+552903, VSX J223421.4+553013, VSX J223416.2+553424, US-NO-B1.0 1347-0483658, UCAC3-191-085589, VSX J180755.6+074711= UCAC3 196-166827). Despite we have used original observations published by the discoverers, the accuracy estimates of the period using the NAV method are typically better than the original ones.

Wheat varieties show a large diversity of traits and phenotypes. Linking them to genetic variability is essential for shorter and more efficient wheat breeding programs. Newly desirable wheat variety traits include disease resistance to reduce pesticide use, adaptation to climate change, resistance to heat and drought stresses, or low gluten content of grains. Wheat breeding experiments are documented by a large body of scientific literature and observational data obtained in-field and under controlled conditions. The cross-referencing of complementary information from the literature and observational data is essential to the study of the genotype-phenotype relationship and to the improvement of wheat selection. The scientific literature on genetic marker-assisted selection describes much information about the genotype-phenotype relationship. However, the variety of expressions used to refer to traits and phenotype values in scientific articles is a hinder to finding information and cross-referencing it. When trained adequately by annotated examples, recent text mining methods perform highly in named entity recognition and linking in the scientific domain. While several corpora contain annotations of human and animal phenotypes, currently, no corpus is available for training and evaluating named entity recognition and entity-linking methods in plant phenotype literature. The Triticum aestivum trait Corpus is a new gold standard for traits and phenotypes of wheat. It consists of 540 PubMed references fully annotated for trait, phenotype, and species named entities using the Wheat Trait and Phenotype Ontology and the species taxonomy of the National Center for Biotechnology Information. A study of the performance of tools trained on the Triticum aestivum trait Corpus shows that the corpus is suitable for the training and evaluation of named entity recognition and linking.

We report on analysis of the two-color VR CCD observations of the newly discovered variable 2MASS J18024395+4003309=VSX J180243.9+400331 obtained using the 1-m telescope of the Mt. Lemmon Observatory (LOAO) in the field of the intermediate polar V1323 Her. The extended version of this conference talk we published in 2015JASS...32..127A. The variability was reported in 2012OAP....25..150A, and the object was monitored. The two-color observations covered all phase interval. The object is classified as an Algol-type variable with tidally distorted components, and shows an asymmetry of the maxima (the O\'Connell effect). For phenomenological modeling, we used the trigonometric polynomial approximation of statistically optimal degree, and a recent method "NAV" (New Algol Variable) using local specific shapes for the eclipse. Methodological aspects are described, especially for the case of few color observations. Estimates of the physical parameters based on analysis of phenomenological parameters, are presented.

We conducted more than 1.3 million comparisons of iris patterns encoded from images collected at two Nigerian universities, which constitute the newly available African Human Iris (AFHIRIS) database. The purpose was to discover whether ethnic differences in iris structure and appearance such as the textural feature size, as contrasted with an all-Chinese image database or an American database in which only 1.53% were of African-American heritage, made a material difference for iris discrimination. We measured a reduction in entropy for the AFHIRIS database due to the coarser iris features created by the thick anterior layer of melanocytes, and we found stochastic parameters that accurately model the relevant empirical distributions. Quantile-Quantile analysis revealed that a very small change in operational decision thresholds for the African database would compensate for the reduced entropy and generate the same performance in terms of resistance to False Matches. We conclude that despite demographic difference, individuality can be robustly discerned by comparison of iris patterns in this West African population.

State-of-the-art space science missions increasingly rely on automation due to spacecraft complexity and the costs of human oversight. The high volume of data, including scientific and telemetry data, makes manual inspection challenging. Machine learning offers significant potential to meet these demands. The Euclid space telescope, in its survey phase since February 2024, exemplifies this shift. Euclid's success depends on accurate monitoring and interpretation of housekeeping telemetry and science-derived data. Thousands of telemetry parameters, monitored as time series, may or may not impact the quality of scientific data. These parameters have complex interdependencies, often due to physical relationships (e.g., proximity of temperature sensors). Optimising science operations requires careful anomaly detection and identification of hidden parameter states. Moreover, understanding the interactions between known anomalies and physical quantities is crucial yet complex, as related parameters may display anomalies with varied timing and intensity. We address these challenges by analysing temperature anomalies in Euclid's telemetry from February to August 2024, focusing on eleven temperature parameters and 35 covariates. We use a predictive XGBoost model to forecast temperatures based on historical values, detecting anomalies as deviations from predictions. A second XGBoost model predicts anomalies from covariates, capturing their relationships to temperature anomalies. We identify the top three anomalies per parameter and analyse their interactions with covariates using SHAP (Shapley Additive Explanations), enabling rapid, automated analysis of complex parameter relationships. Our method demonstrates how machine learning can enhance telemetry monitoring, offering scalable solutions for other missions with similar data challenges.

A compartmental deterministic model that allows (1) immunity from two stages of infection and carriage, and (2) disease induced death, is used in studying the dynamics of meningitis epidemic process in a closed population. It allows for difference in the transmission rate of infection to a susceptible by a carrier and an infective. It is generalized to allow a proportion ({\phi}) of those susceptibles infected to progress directly to infectives in stage I. Both models are used in this study. The threshold conditions for the spread of carrier and infectives in stage I are derived for the two models. Sensitivity analysis is performed on the reproductive number derived from the next generation matrix. The case-carrier ratio profile for various parameters and threshold values are shown. So also are the graphs of the total number ever infected as influenced by {\epsilon} and {\phi}. The infection transmission rate (eta), the odds in favor of a carrier, over an infective, in transmitting an infection to a susceptible ({\epsilon}) and the carrier conversion rate ({\phi}) to an infective in stage I, are identified as key parameters that should be subject of attention for any control intervention strategy. The case-carrier ratio profiles provide evidence of a critical case-carrier ratio attained before the number of reported cases grows to an epidemic level. They also provide visual evidence of epidemiological context, in this case, epidemic incidence (in later part of dry season) and endemic incidence (during rainy season). Results from total proportion ever infected suggest that the model, in which {\phi}=0 obtained, can adequately represent, in essence, the generalized model for this study.

Prototype-based neural networks offer interpretable predictions by comparing inputs to learned, representative signal patterns anchored in training data. While such models have shown promise in the classification of physiological data, it remains unclear whether their prototypes capture an underlying structure that aligns with broader clinical phenotypes. We use a prototype-based deep learning model trained for multi-label ECG classification using the PTB-XL dataset. Then without modification we performed inference on the MIMIC-IV clinical database. We assess whether individual prototypes, trained solely for classification, are associated with hospital discharge diagnoses in the form of phecodes in this external population. Individual prototypes demonstrate significantly stronger and more specific associations with clinical outcomes compared to the classifier's class predictions, NLP-extracted concepts, or broader prototype classes across all phecode categories. Prototype classes with mixed significance patterns exhibit significantly greater intra-class distances (p < 0.0001), indicating the model learned to differentiate clinically meaningful variations within diagnostic categories. The prototypes achieve strong predictive performance across diverse conditions, with AUCs ranging from 0.89 for atrial fibrillation to 0.91 for heart failure, while also showing substantial signal for non-cardiac conditions such as sepsis and renal disease. These findings suggest that prototype-based models can support interpretable digital phenotyping from physiologic time-series data, providing transferable intermediate phenotypes that capture clinically meaningful physiologic signatures beyond their original training objectives.

Tissue phenotyping is a fundamental task in learning objective characterizations of histopathologic biomarkers within the tumor-immune microenvironment in cancer pathology. However, whole-slide imaging (WSI) is a complex computer vision in which: 1) WSIs have enormous image resolutions with precludes large-scale pixel-level efforts in data curation, and 2) diversity of morphological phenotypes results in inter- and intra-observer variability in tissue labeling. To address these limitations, current efforts have proposed using pretrained image encoders (transfer learning from ImageNet, self-supervised pretraining) in extracting morphological features from pathology, but have not been extensively validated. In this work, we conduct a search for good representations in pathology by training a variety of self-supervised models with validation on a variety of weakly-supervised and patch-level tasks. Our key finding is in discovering that Vision Transformers using DINO-based knowledge distillation are able to learn data-efficient and interpretable features in histology images wherein the different attention heads learn distinct morphological phenotypes. We make evaluation code and pretrained weights publicly-available at: https://github.com/Richarizardd/Self-Supervised-ViT-Path.

We review the method NAV (New Algol Variable) first introduced in 2012Ap.....55..536A, which uses the locally-dependent shapes of eclipses in an addition to the trigonometric polynomial of the second order (which typically describes the "out-of-eclipse" part of the light curve with effects of reflection, ellipticity and O'Connell). Eclipsing binary stars are believed to show distinct eclipses only if belonging to the EA type. With a decreasing eclipse width, the statistically optimal value of the trigonometric polynomial s (2003ASPC..292..391A) drastically increases from ~2 for elliptic (EL) variables without eclipses, ~6-8 for EW and up to ~30-50 for some EA with narrow eclipses. In this case of large number of parameters, the smoothing curve becomes very noisy and apparent waves (the Gibbs phenomenon) may be seen. The NAV set of the parameters may be used for classification in the GCVS, VSX and similar catalogs. The maximal number of parameters is m=12, which corresponds to s=5, if correcting both the period and the initial epoch. We have applied the method to few stars, also in a case of multi-color photometry (2015JASS...32..127A), when it is possible to use the phenomenological parameters from the NAV fit to estimate physical parameters using statistical dependencies. We conclude that the NAV approximation is better than the TP one even for the case of EW-type stars with much wider eclipses. It may also be used to determine timings (see 2005ASPC..335...37A for a review of methods) or to determine parameters in the case of variable period, using a complete light curve modeling the phase variations. The method is illustrated on 2MASS J11080447-6143290 (EA-type), USNO-B1.0 1265-0306001 and USNO-B1.0 1266-0313413 (EW-type) and compared to various other methods from the literature.

A crucial step within secondary analysis of electronic health records (EHRs) is to identify the patient cohort under investigation. While EHRs contain medical billing codes that aim to represent the conditions and treatments patients may have, much of the information is only present in the patient notes. Therefore, it is critical to develop robust algorithms to infer patients' conditions and treatments from their written notes. In this paper, we introduce a dataset for patient phenotyping, a task that is defined as the identification of whether a patient has a given medical condition (also referred to as clinical indication or phenotype) based on their patient note. Nursing Progress Notes and Discharge Summaries from the Intensive Care Unit of a large tertiary care hospital were manually annotated for the presence of several high-context phenotypes relevant to treatment and risk of re-hospitalization. This dataset contains 1102 Discharge Summaries and 1000 Nursing Progress Notes. Each Discharge Summary and Progress Note has been annotated by at least two expert human annotators (one clinical researcher and one resident physician). Annotated phenotypes include treatment non-adherence, chronic pain, advanced/metastatic cancer, as well as 10 other phenotypes. This dataset can be utilized for academic and industrial research in medicine and computer science, particularly within the field of medical natural language processing.

Hypertension remains a global health concern with a rising prevalence, necessitating effective monitoring and understanding of blood pressure (BP) dynamics. This study delves into the wealth of information derived from BP measurement, a crucial approach in informing our understanding of hypertensive trends. Numerous studies have reported on the relationship between BP variation and various factors. In this research, we leveraged an extensive dataset comprising 75 million records spanning two decades, offering a unique opportunity to explore and analyze BP variations across demographic features such as age, race, and gender. Our findings revealed that gender-based BP variation was not statistically significant, challenging conventional assumptions. Interestingly, systolic blood pressure (SBP) consistently increased with age, while diastolic blood pressure (DBP) displayed a distinctive peak in the forties age group. Moreover, our analysis uncovered intriguing similarities in the distribution of BP among some of the racial groups. This comprehensive investigation contributes to the ongoing discourse on hypertension and underscores the importance of considering diverse demographic factors in understanding BP variations. Our results provide valuable insights that may inform personalized healthcare approaches tailored to specific demographic profiles.

A comparative analysis of the special shapes (patterns, profiles) of the eclipses applied for the phenomenological modeling of the light curves of eclipsing binary stars is conducted. Families of functions are considered, generalizing local approximations (Andronov, 2010, 2012) and the functions theoretically unlimited in a width, based on a Gaussian (Mikulasek, 2015). For an analysis, the light curve of the star V0882 Car = 2MASS J11080308 - 6145589 of the classic Algol - subtype (\beta Persei) is used. By analyzing dozens of modified functions with additional parameters, it was chosen the 14 best ones according to the criterion of the least sum of squares of deviations. The best are the functions with an additional parameter, describing profiles, which are limited in phase.

Objective: We investigate whether deep learning techniques for natural language processing (NLP) can be used efficiently for patient phenotyping. Patient phenotyping is a classification task for determining whether a patient has a medical condition, and is a crucial part of secondary analysis of healthcare data. We assess the performance of deep learning algorithms and compare them with classical NLP approaches. Materials and Methods: We compare convolutional neural networks (CNNs), n-gram models, and approaches based on cTAKES that extract pre-defined medical concepts from clinical notes and use them to predict patient phenotypes. The performance is tested on 10 different phenotyping tasks using 1,610 discharge summaries extracted from the MIMIC-III database. Results: CNNs outperform other phenotyping algorithms in all 10 tasks. The average F1-score of our model is 76 (PPV of 83, and sensitivity of 71) with our model having an F1-score up to 37 points higher than alternative approaches. We additionally assess the interpretability of our model by presenting a method that extracts the most salient phrases for a particular prediction. Conclusion: We show that NLP methods based on deep learning improve the performance of patient phenotyping. Our CNN-based algorithm automatically learns the phrases associated with each patient phenotype. As such, it reduces the annotation complexity for clinical domain experts, who are normally required to develop task-specific annotation rules and identify relevant phrases. Our method performs well in terms of both performance and interpretability, which indicates that deep learning is an effective approach to patient phenotyping based on clinicians' notes.

Speech patterns have been identified as potential diagnostic markers for neuropsychiatric conditions. However, most studies only compare a single clinical group to healthy controls, whereas clinical practice often requires differentiating between multiple potential diagnoses (multiclass settings). To address this, we assembled a dataset of repeated recordings from 420 participants (67 with major depressive disorder, 106 with schizophrenia and 46 with autism, as well as matched controls), and tested the performance of a range of conventional machine learning models and advanced Transformer models on both binary and multiclass classification, based on voice and text features. While binary models performed comparably to previous research (F1 scores between 0.54-0.75 for autism spectrum disorder, ASD; 0.67-0.92 for major depressive disorder, MDD; and 0.71-0.83 for schizophrenia); when differentiating between multiple diagnostic groups performance decreased markedly (F1 scores between 0.35-0.44 for ASD, 0.57-0.75 for MDD, 0.15-0.66 for schizophrenia, and 0.38-0.52 macro F1). Combining voice and text-based models yielded increased performance, suggesting that they capture complementary diagnostic information. Our results indicate that models trained on binary classification may learn to rely on markers of generic differences between clinical and non-clinical populations, or markers of clinical features that overlap across conditions, rather than identifying markers specific to individual conditions. We provide recommendations for future research in the field, suggesting increased focus on developing larger transdiagnostic datasets that include more fine-grained clinical features, and that can support the development of models that better capture the complexity of neuropsychiatric conditions and naturalistic diagnostic assessment.

We introduce phi-3-mini, a 3.8 billion parameter language model trained on 3.3 trillion tokens, whose overall performance, as measured by both academic benchmarks and internal testing, rivals that of models such as Mixtral 8x7B and GPT-3.5 (e.g., phi-3-mini achieves 69% on MMLU and 8.38 on MT-bench), despite being small enough to be deployed on a phone. The innovation lies entirely in our dataset for training, a scaled-up version of the one used for phi-2, composed of heavily filtered web data and synthetic data. The model is also further aligned for robustness, safety, and chat format. We also provide some initial parameter-scaling results with a 7B and 14B models trained for 4.8T tokens, called phi-3-small and phi-3-medium, both significantly more capable than phi-3-mini (e.g., respectively 75% and 78% on MMLU, and 8.7 and 8.9 on MT-bench).

Discovering evolutionary traits that are heritable across species on the tree of life (also referred to as a phylogenetic tree) is of great interest to biologists to understand how organisms diversify and evolve. However, the measurement of traits is often a subjective and labor-intensive process, making trait discovery a highly label-scarce problem. We present a novel approach for discovering evolutionary traits directly from images without relying on trait labels. Our proposed approach, Phylo-NN, encodes the image of an organism into a sequence of quantized feature vectors -- or codes -- where different segments of the sequence capture evolutionary signals at varying ancestry levels in the phylogeny. We demonstrate the effectiveness of our approach in producing biologically meaningful results in a number of downstream tasks including species image generation and species-to-species image translation, using fish species as a target example.

We open-source a state-of-the-art 7.5B-parameter generative model series named PhoGPT for Vietnamese, which includes the base pre-trained monolingual model PhoGPT-7B5 and its instruction-following variant, PhoGPT-7B5-Instruct. In addition, we also demonstrate its superior performance compared to previous open-source models through a human evaluation experiment. GitHub: https://github.com/VinAIResearch/PhoGPT

We made a comparative analysis of numerical methods for multidimensional optimization. The main parameter is a number of computations of the test function to reach necessary accuracy, as it is computationally "slow". For complex functions, analytic differentiation by many parameters can cause problems associated with a significant complication of the program and thus slowing its operation. For comparison, we used the methods: "brute force" (or minimization on a regular grid), Monte Carlo, steepest descent, conjugate gradients, Brent's method (golden section search), parabolic interpolation etc. The Monte-Carlo method was applied to the eclipsing binary system AM Leo.

As the most basic application and implementation of deep learning, image classification has grown in popularity. Various datasets are provided by renowned data science communities for benchmarking machine learning algorithms and pre-trained models. The ASSIRA Cats & Dogs dataset is one of them and is being used in this research for its overall acceptance and benchmark standards. A comparison of various pre-trained models is demonstrated by using different types of optimizers and loss functions. Hyper-parameters are changed to gain the best result from a model. By applying this approach, we have got higher accuracy without major changes in the training model. To run the experiment, we used three different computer architectures: a laptop equipped with NVIDIA GeForce GTX 1070, a laptop equipped with NVIDIA GeForce RTX 3080Ti, and a desktop equipped with NVIDIA GeForce RTX 3090. The acquired results demonstrate supremacy in terms of accuracy over the previously done experiments on this dataset. From this experiment, the highest accuracy which is 99.65% is gained using the NASNet Large.

The quantitative prediction of the intensity of rainfall events (light or heavy) has remained a challenge in Numerical Weather Prediction (NWP) models. For the first time the mean coefficient of diffusional growth rates are calculated using an Eulerian-Lagrangian particle-based small-scale model on in situ airborne measurement data of Cloud Aerosol Interaction and Precipitation Enhancement Experiment (CAIPEEX) during monsoon over Indian sub-continent. The results show that diffusional growth rates varies in the range of 0.00025 - 0.0015(cm/s). The generic problem of the overestimation of light rain in NWP models might be related with the choice of cm in the model. It is also shown from DNS experiment using Eulerian-Lagrangian particle-based small-scale model that the relative dispersion is constrained with average values in the range of ~ 0.2 - 0.37 (~ 0.1- 0.26) in less humid (more humid) conditions. This is in agreement with in situ airborne observation (dispersion ~ 0.36) and previous study over Indian sub-continent. The linear relationship between relative dispersion and cloud droplet number concentration (NC) is obtained from this study using CAIPEEX observation over Indian subcontinent. The dispersion based autoconversion-scheme for Indian region must be useful for the Indian summer monsoon precipitation calculation in the general circulation model. The present study also provide valuable guidance for the parameterization of effective radius, important for radiation scheme.

Plant traits such as leaf carbon content and leaf mass are essential variables in the study of biodiversity and climate change. However, conventional field sampling cannot feasibly cover trait variation at ecologically meaningful spatial scales. Machine learning represents a valuable solution for plant trait prediction across ecosystems, leveraging hyperspectral data from remote sensing. Nevertheless, trait prediction from hyperspectral data is challenged by label scarcity and substantial domain shifts (\eg across sensors, ecological distributions), requiring robust cross-domain methods. Here, we present GreenHyperSpectra, a pretraining dataset encompassing real-world cross-sensor and cross-ecosystem samples designed to benchmark trait prediction with semi- and self-supervised methods. We adopt an evaluation framework encompassing in-distribution and out-of-distribution scenarios. We successfully leverage GreenHyperSpectra to pretrain label-efficient multi-output regression models that outperform the state-of-the-art supervised baseline. Our empirical analyses demonstrate substantial improvements in learning spectral representations for trait prediction, establishing a comprehensive methodological framework to catalyze research at the intersection of representation learning and plant functional traits assessment. All code and data are available at: https://github.com/echerif18/HyspectraSSL.

Tissue phenotyping is a fundamental computational pathology (CPath) task in learning objective characterizations of histopathologic biomarkers in anatomic pathology. However, whole-slide imaging (WSI) poses a complex computer vision problem in which the large-scale image resolutions of WSIs and the enormous diversity of morphological phenotypes preclude large-scale data annotation. Current efforts have proposed using pretrained image encoders with either transfer learning from natural image datasets or self-supervised pretraining on publicly-available histopathology datasets, but have not been extensively developed and evaluated across diverse tissue types at scale. We introduce UNI, a general-purpose self-supervised model for pathology, pretrained using over 100 million tissue patches from over 100,000 diagnostic haematoxylin and eosin-stained WSIs across 20 major tissue types, and evaluated on 33 representative CPath clinical tasks in CPath of varying diagnostic difficulties. In addition to outperforming previous state-of-the-art models, we demonstrate new modeling capabilities in CPath such as resolution-agnostic tissue classification, slide classification using few-shot class prototypes, and disease subtyping generalization in classifying up to 108 cancer types in the OncoTree code classification system. UNI advances unsupervised representation learning at scale in CPath in terms of both pretraining data and downstream evaluation, enabling data-efficient AI models that can generalize and transfer to a gamut of diagnostically-challenging tasks and clinical workflows in anatomic pathology.

Recent space-borne and ground-based observations provide photometric measurements as time series. The effect of interstellar dust extinction in the near-infrared range is only 10% of that measured in the V band. However, the sensitivity of the light curve shape to the physical parameters in the near-infrared is much lower. So, interpreting these types of data sets requires new approaches like the different large-scale surveys, which create similar problems with big data. Using a selected data set, we provide a method for applying routines implemented in R to extract most information of measurements to determine physical parameters, which can also be used in automatic classification schemes and pipeline processing. We made a multivariate classification of 131 Cepheid light curves (LC) in J, H, and K colors, where all the LCs were represented in 20D parameter space in these colors separately. Performing a Principal Component Analysis (PCA), we got an orthogonal coordinate system and squared Euclidean distances between LCs, with 6 significant eigenvalues, reducing the 20-dimension to 6. We also estimated the optimal number of partitions of similar objects and found it to be equal to 7 in each color; their dependence on the period, absolute magnitude, amplitude, and metallicity are also discussed. We computed the Spearman rank correlations, showing that periods and absolute magnitudes correlate with the first three PCs significantly. The first two PC are also found to have a relationship with the amplitude, but the metallicity effects are only marginal. The method shown can be generalized and implemented in unsupervised classification schemes and analysis of mixed and biased samples. The analysis of our Classical Cepheid near-infrared LC sample showed that the J, H, K curves are insufficient for determination of stellar metallicity, with mass being the key factor shaping them.

The phenomenological parameters of eclipsing binary stars, which are the prototypes of the EA, EB and EW systems are determined using the expert complex of computer programs, which realizes the NAV ("New Algol Variable") algorithm (Andronov 2010, 2012) and its possible modifications are discussed, as well as constrains for estimates of some physical parameters of the systems in a case of photometric observations only, such as the degree of eclipse, ratio of the mean surface brightnesses of the components. The half-duration of the eclipse is 0.0617(7), 0.1092(18) and 0.1015(7) for Algol, beta Lyrae and W UMa, respectively. The brightness ratio is 6.8pm1.0, 4.9pm1.0 and 1.15pm0.13. These results show that the eclipses have distinct begin and end not only in EA (as generally assumed), but also in EB and EW - type systems as well. The algorithm may be applied to classification and study of the newly discovered (or poorly studied) eclipsing variables based on own observations or that obtained using photometric surveys.

The basic body shape (i.e., the body shape in T-pose) of a person does not change within a single video. However, most SOTA human mesh estimation (HME) models output a slightly different, thus inconsistent basic body shape for each video frame. Furthermore, we find that SOTA 3D human pose estimation (HPE) models outperform HME models regarding the precision of the estimated 3D keypoint positions. We solve the problem of inconsistent body shapes by leveraging anthropometric measurements like taken by tailors from humans. We create a model called A2B that converts given anthropometric measurements to basic body shape parameters of human mesh models. We obtain superior and consistent human meshes by combining the A2B model results with the keypoints of 3D HPE models using inverse kinematics. We evaluate our approach on challenging datasets like ASPset or fit3D, where we can lower the MPJPE by over 30 mm compared to SOTA HME models. Further, replacing estimates of the body shape parameters from existing HME models with A2B results not only increases the performance of these HME models, but also guarantees consistent body shapes.

We present the findings of "The Alzheimer's Disease Prediction Of Longitudinal Evolution" (TADPOLE) Challenge, which compared the performance of 92 algorithms from 33 international teams at predicting the future trajectory of 219 individuals at risk of Alzheimer's disease. Challenge participants were required to make a prediction, for each month of a 5-year future time period, of three key outcomes: clinical diagnosis, Alzheimer's Disease Assessment Scale Cognitive Subdomain (ADAS-Cog13), and total volume of the ventricles. The methods used by challenge participants included multivariate linear regression, machine learning methods such as support vector machines and deep neural networks, as well as disease progression models. No single submission was best at predicting all three outcomes. For clinical diagnosis and ventricle volume prediction, the best algorithms strongly outperform simple baselines in predictive ability. However, for ADAS-Cog13 no single submitted prediction method was significantly better than random guesswork. Two ensemble methods based on taking the mean and median over all predictions, obtained top scores on almost all tasks. Better than average performance at diagnosis prediction was generally associated with the additional inclusion of features from cerebrospinal fluid (CSF) samples and diffusion tensor imaging (DTI). On the other hand, better performance at ventricle volume prediction was associated with inclusion of summary statistics, such as the slope or maxima/minima of biomarkers. TADPOLE's unique results suggest that current prediction algorithms provide sufficient accuracy to exploit biomarkers related to clinical diagnosis and ventricle volume, for cohort refinement in clinical trials for Alzheimer's disease. However, results call into question the usage of cognitive test scores for patient selection and as a primary endpoint in clinical trials.

Pulmonary Hypertension (PH) is a severe disease characterized by an elevated pulmonary artery pressure. The gold standard for PH diagnosis is measurement of mean Pulmonary Artery Pressure (mPAP) during an invasive Right Heart Catheterization. In this paper, we investigate noninvasive approach to PH detection utilizing Magnetic Resonance Imaging, Computer Models and Machine Learning. We show using the ablation study, that physics-informed feature engineering based on models of blood circulation increases the performance of Gradient Boosting Decision Trees-based algorithms for classification of PH and regression of values of mPAP. We compare results of regression (with thresholding of estimated mPAP) and classification and demonstrate that metrics achieved in both experiments are comparable. The predicted mPAP values are more informative to the physicians than the probability of PH returned by classification models. They provide the intuitive explanation of the outcome of the machine learning model (clinicians are accustomed to the mPAP metric, contrary to the PH probability).

Practical identifiability is a critical concern in data-driven modeling of mathematical systems. In this paper, we propose a novel framework for practical identifiability analysis to evaluate parameter identifiability in mathematical models of biological systems. Starting with a rigorous mathematical definition of practical identifiability, we demonstrate its equivalence to the invertibility of the Fisher Information Matrix. Our framework establishes the relationship between practical identifiability and coordinate identifiability, introducing a novel metric that simplifies and accelerates the evaluation of parameter identifiability compared to the profile likelihood method. Additionally, we introduce new regularization terms to address non-identifiable parameters, enabling uncertainty quantification and improving model reliability. To guide experimental design, we present an optimal data collection algorithm that ensures all model parameters are practically identifiable. Applications to Hill functions, neural networks, and dynamic biological models demonstrate the feasibility and efficiency of the proposed computational framework in uncovering critical biological processes and identifying key observable variables.

This is the 1st part of the dissertation for my master degree and compares the power consumption using the default floating point (32bit) and Nvidia mixed precision (16bit and 32bit) while training a classification ML model. A custom PC with specific hardware was built to perform the experiments, and different ML hyper-parameters, such as batch size, neurons, and epochs, were chosen to build Deep Neural Networks (DNN). Additionally, various software was used during the experiments to collect the power consumption data in Watts from the Graphics Processing Unit (GPU), Central Processing Unit (CPU), Random Access Memory (RAM) and manually from a wattmeter connected to the wall. A benchmarking test with default hyper parameter values for the DNN was used as a reference, while the experiments used a combination of different settings. The results were recorded in Excel, and descriptive statistics were chosen to calculate the mean between the groups and compare them using graphs and tables. The outcome was positive when using mixed precision combined with specific hyper-parameters. Compared to the benchmarking, the optimisation for the classification reduced the power consumption between 7 and 11 Watts. Similarly, the carbon footprint is reduced because the calculation uses the same power consumption data. Still, a consideration is required when configuring hyper-parameters because it can negatively affect hardware performance. However, this research required inferential statistics, specifically ANOVA and T-test, to compare the relationship between the means. Furthermore, tests indicated no statistical significance of the relationship between the benchmarking and experiments. However, a more extensive implementation with a cluster of GPUs can increase the sample size significantly, as it is an essential factor and can change the outcome of the statistical analysis.

Genome-wide association study (GWAS) tests single nucleotide polymorphism (SNP) markers across the genome to localize the underlying causal variant of a trait. Because causal variants are seldom observed directly, a surrogate model based on genotyped markers are widely considered. Although many methods estimating the parameters of the surrogate model have been proposed, the connection between the surrogate model and the true causal model is yet investigated. In this work, we establish the connection between the surrogate model and the true causal model. The connection shows that population structure is accounted in GWAS by modelling the variant of interest and not the trait. Such observation explains how environmental confounding can be partially corrected using genetic covariates and why the previously claimed connection between PC correction and linear mixed models is incorrect.

Learning the underlying dynamics of single cells from snapshot data has gained increasing attention in scientific and machine learning research. The destructive measurement technique and cell proliferation/death result in unpaired and unbalanced data between snapshots, making the learning of the underlying dynamics challenging. In this paper, we propose joint Velocity-Growth Flow Matching (VGFM), a novel paradigm that jointly learns state transition and mass growth of single-cell populations via flow matching. VGFM builds an ideal single-cell dynamics containing velocity of state and growth of mass, driven by a presented two-period dynamic understanding of the static semi-relaxed optimal transport, a mathematical tool that seeks the coupling between unpaired and unbalanced data. To enable practical usage, we approximate the ideal dynamics using neural networks, forming our joint velocity and growth matching framework. A distribution fitting loss is also employed in VGFM to further improve the fitting performance for snapshot data. Extensive experimental results on both synthetic and real datasets demonstrate that VGFM can capture the underlying biological dynamics accounting for mass and state variations over time, outperforming existing approaches for single-cell dynamics modeling.

Straight line equation y=mx with slope m, when singularly perturbed as ay^3+y=mx with a positive parameter a, results in S-shaped curves or S-curves on a real plane. As arightarrow 0, we get back y=mx which is a cumulative distribution function of a continuous uniform distribution that describes the occurrence of every event in an interval to be equally probable. As arightarrowinfty, the derivative of y has finite support only at y=0 resembling a degenerate distribution. Based on these arguments, in this work, we propose that these S-curves can represent maximum entropy uniform distribution to a zero entropy single value. We also argue that these S-curves are superposable as they are only parametrically nonlinear but fundamentally linear. So far, the superposed forms have been used to capture the patterns of natural systems such as nonlinear dynamics of biological growth and kinetics of enzyme reactions. Here, we attempt to use the S-curve and its superposed form as statistical models. We fit the models on a classical dataset containing flower measurements of iris plants and analyze their usefulness in pattern recognition. Based on these models, we claim that any non-uniform pattern can be represented as a singular perturbation to uniform distribution. However, our parametric estimation procedure have some limitations such as sensitivity to initial conditions depending on the data at hand.

Post-training quantization (PTQ) is a neural network compression technique that converts a full-precision model into a quantized model using lower-precision data types. Although it can help reduce the size and computational cost of deep neural networks, it can also introduce quantization noise and reduce prediction accuracy, especially in extremely low-bit settings. How to determine the appropriate quantization parameters (e.g., scaling factors and rounding of weights) is the main problem facing now. Existing methods attempt to determine these parameters by minimize the distance between features before and after quantization, but such an approach only considers local information and may not result in the most optimal quantization parameters. We analyze this issue and ropose PD-Quant, a method that addresses this limitation by considering global information. It determines the quantization parameters by using the information of differences between network prediction before and after quantization. In addition, PD-Quant can alleviate the overfitting problem in PTQ caused by the small number of calibration sets by adjusting the distribution of activations. Experiments show that PD-Quant leads to better quantization parameters and improves the prediction accuracy of quantized models, especially in low-bit settings. For example, PD-Quant pushes the accuracy of ResNet-18 up to 53.14% and RegNetX-600MF up to 40.67% in weight 2-bit activation 2-bit. The code is released at https://github.com/hustvl/PD-Quant.

Hypertension, defined as blood pressure (BP) that is above normal, holds paramount significance in the realm of public health, as it serves as a critical precursor to various cardiovascular diseases (CVDs) and significantly contributes to elevated mortality rates worldwide. However, many existing BP measurement technologies and standards might be biased because they do not consider clinical outcomes, comorbidities, or demographic factors, making them inconclusive for diagnostic purposes. There is limited data-driven research focused on studying the variance in BP measurements across these variables. In this work, we employed GPT-35-turbo, a large language model (LLM), to automatically extract the mean and standard deviation values of BP for both males and females from a dataset comprising 25 million abstracts sourced from PubMed. 993 article abstracts met our predefined inclusion criteria (i.e., presence of references to blood pressure, units of blood pressure such as mmHg, and mention of biological sex). Based on the automatically-extracted information from these articles, we conducted an analysis of the variations of BP values across biological sex. Our results showed the viability of utilizing LLMs to study the BP variations across different demographic factors.

This paper presents a NeRF-based framework for point cloud (PCD) reconstruction, specifically designed for indoor high-throughput plant phenotyping facilities. Traditional NeRF-based reconstruction methods require cameras to move around stationary objects, but this approach is impractical for high-throughput environments where objects are rapidly imaged while moving on conveyors or rotating pedestals. To address this limitation, we develop a variant of NeRF-based PCD reconstruction that uses a single stationary camera to capture images as the object rotates on a pedestal. Our workflow comprises COLMAP-based pose estimation, a straightforward pose transformation to simulate camera movement, and subsequent standard NeRF training. A defined Region of Interest (ROI) excludes irrelevant scene data, enabling the generation of high-resolution point clouds (10M points). Experimental results demonstrate excellent reconstruction fidelity, with precision-recall analyses yielding an F-score close to 100.00 across all evaluated plant objects. Although pose estimation remains computationally intensive with a stationary camera setup, overall training and reconstruction times are competitive, validating the method's feasibility for practical high-throughput indoor phenotyping applications. Our findings indicate that high-quality NeRF-based 3D reconstructions are achievable using a stationary camera, eliminating the need for complex camera motion or costly imaging equipment. This approach is especially beneficial when employing expensive and delicate instruments, such as hyperspectral cameras, for 3D plant phenotyping. Future work will focus on optimizing pose estimation techniques and further streamlining the methodology to facilitate seamless integration into automated, high-throughput 3D phenotyping pipelines.

We introduce a new family of physics-inspired generative models termed PFGM++ that unifies diffusion models and Poisson Flow Generative Models (PFGM). These models realize generative trajectories for N dimensional data by embedding paths in N{+}D dimensional space while still controlling the progression with a simple scalar norm of the D additional variables. The new models reduce to PFGM when D{=}1 and to diffusion models when D{to}infty. The flexibility of choosing D allows us to trade off robustness against rigidity as increasing D results in more concentrated coupling between the data and the additional variable norms. We dispense with the biased large batch field targets used in PFGM and instead provide an unbiased perturbation-based objective similar to diffusion models. To explore different choices of D, we provide a direct alignment method for transferring well-tuned hyperparameters from diffusion models (D{to} infty) to any finite D values. Our experiments show that models with finite D can be superior to previous state-of-the-art diffusion models on CIFAR-10/FFHQ 64{times}64 datasets, with FID scores of 1.91/2.43 when D{=}2048/128. In class-conditional setting, D{=}2048 yields current state-of-the-art FID of 1.74 on CIFAR-10. In addition, we demonstrate that models with smaller D exhibit improved robustness against modeling errors. Code is available at https://github.com/Newbeeer/pfgmpp

Chronotype compares individuals' circadian phase to others. It contextualizes mental health risk assessments and detection of social jet lag, which can hamper mental health and cognitive performance. Existing ways of determining chronotypes, such as Dim Light Melatonin Onset (DLMO) or the Morningness-Eveningness Questionnaire (MEQ), are limited by being discrete in time and time-intensive to update, meaning they rarely capture real-world variability across time. Chronotyping users based on a daily planner app might augment existing methods to enable assessment continuously and at scale. This paper reports the construction of a supervised binary classifier that attempts to demonstrate the feasibility of this approach. 1,460 registered users from the Owaves app opted in by filling out the MEQ survey between July 14, 2022, and May 1, 2023. 142 met the eligibility criteria. We used multimodal app data from individuals identified as morning and evening types from MEQ data, basing the classifier on app time series data. This included daily timing for 8 main lifestyle activity types: exercise, sleep, social interactions, meal times, relaxation, work, play, and miscellaneous, as defined in the app. The timing of activities showed substantial change across time, as well as heterogeneity by activity type. Our novel chronotyping classifier was able to predict the morningness and eveningness of its users with an ROC AUC of 0.70. Our findings demonstrate the feasibility of chronotype classification from multimodal, real-world app data, while highlighting fundamental challenges to applying discrete and fixed labels to complex, dynamic, multimodal behaviors. Our findings suggest a potential for real-time monitoring of shifts in chronotype specific to different causes (i.e. types of activity), which could feasibly be used to support future, prospective mental health support research.

Modern foundation models rely heavily on using scaling laws to guide crucial training decisions. Researchers often extrapolate the optimal architecture and hyper parameters settings from smaller training runs by describing the relationship between, loss, or task performance, and scale. All components of this process vary, from the specific equation being fit, to the training setup, to the optimization method. Each of these factors may affect the fitted law, and therefore, the conclusions of a given study. We discuss discrepancies in the conclusions that several prior works reach, on questions such as the optimal token to parameter ratio. We augment this discussion with our own analysis of the critical impact that changes in specific details may effect in a scaling study, and the resulting altered conclusions. Additionally, we survey over 50 papers that study scaling trends: while 45 of these papers quantify these trends using a power law, most under-report crucial details needed to reproduce their findings. To mitigate this, we we propose a checklist for authors to consider while contributing to scaling law research.

A database of images of approximately 960 unique plants belonging to 12 species at several growth stages is made publicly available. It comprises annotated RGB images with a physical resolution of roughly 10 pixels per mm. To standardise the evaluation of classification results obtained with the database, a benchmark based on f_{1} scores is proposed. The dataset is available at https://vision.eng.au.dk/plant-seedlings-dataset

We consider the solvable neural scaling model with three parameters: data complexity, target complexity, and model-parameter-count. We use this neural scaling model to derive new predictions about the compute-limited, infinite-data scaling law regime. To train the neural scaling model, we run one-pass stochastic gradient descent on a mean-squared loss. We derive a representation of the loss curves which holds over all iteration counts and improves in accuracy as the model parameter count grows. We then analyze the compute-optimal model-parameter-count, and identify 4 phases (+3 subphases) in the data-complexity/target-complexity phase-plane. The phase boundaries are determined by the relative importance of model capacity, optimizer noise, and embedding of the features. We furthermore derive, with mathematical proof and extensive numerical evidence, the scaling-law exponents in all of these phases, in particular computing the optimal model-parameter-count as a function of floating point operation budget.

Objective: fMRI and derived measures such as functional connectivity (FC) have been used to predict brain age, general fluid intelligence, psychiatric disease status, and preclinical neurodegenerative disease. However, it is not always clear that all demographic confounds, such as age, sex, and race, have been removed from fMRI data. Additionally, many fMRI datasets are restricted to authorized researchers, making dissemination of these valuable data sources challenging. Methods: We create a variational autoencoder (VAE)-based model, DemoVAE, to decorrelate fMRI features from demographics and generate high-quality synthetic fMRI data based on user-supplied demographics. We train and validate our model using two large, widely used datasets, the Philadelphia Neurodevelopmental Cohort (PNC) and Bipolar and Schizophrenia Network for Intermediate Phenotypes (BSNIP). Results: We find that DemoVAE recapitulates group differences in fMRI data while capturing the full breadth of individual variations. Significantly, we also find that most clinical and computerized battery fields that are correlated with fMRI data are not correlated with DemoVAE latents. An exception are several fields related to schizophrenia medication and symptom severity. Conclusion: Our model generates fMRI data that captures the full distribution of FC better than traditional VAE or GAN models. We also find that most prediction using fMRI data is dependent on correlation with, and prediction of, demographics. Significance: Our DemoVAE model allows for generation of high quality synthetic data conditioned on subject demographics as well as the removal of the confounding effects of demographics. We identify that FC-based prediction tasks are highly influenced by demographic confounds.

Hyperparameter tuning is one of the essential steps to guarantee the convergence of machine learning models. We argue that intuition about the optimal choice of hyperparameters for stochastic gradient descent can be obtained by studying a neural network's phase diagram, in which each phase is characterised by distinctive dynamics of the singular values of weight matrices. Taking inspiration from disordered systems, we start from the observation that the loss landscape of a multilayer neural network with mean squared error can be interpreted as a disordered system in feature space, where the learnt features are mapped to soft spin degrees of freedom, the initial variance of the weight matrices is interpreted as the strength of the disorder, and temperature is given by the ratio of the learning rate and the batch size. As the model is trained, three phases can be identified, in which the dynamics of weight matrices is qualitatively different. Employing a Langevin equation for stochastic gradient descent, previously derived using Dyson Brownian motion, we demonstrate that the three dynamical regimes can be classified effectively, providing practical guidance for the choice of hyperparameters of the optimiser.

Automatic analysis of the enormous sets of images is a critical task in life sciences. This faces many challenges such as: algorithms are highly parameterized, significant human input is intertwined, and lacking a standard meta-visualization approach. This paper proposes an alternative iterative approach for optimizing input parameters, saving time by minimizing the user involvement, and allowing for understanding the workflow of algorithms and discovering new ones. The main focus is on developing an interactive visualization technique that enables users to analyze the relationships between sampled input parameters and corresponding output. This technique is implemented as a prototype called Veni Vidi Vici, or "I came, I saw, I conquered." This strategy is inspired by the mathematical formulas of numbering computable functions and is developed atop ImageJ, a scientific image processing program. A case study is presented to investigate the proposed framework. Finally, the paper explores some potential future issues in the application of the proposed approach in parameter space analysis in visualization.

Interrogating the evolution of biological changes at early stages of life requires longitudinal profiling of molecules, such as DNA methylation, which can be challenging with children. We introduce a probabilistic and longitudinal machine learning framework based on multi-mean Gaussian processes (GPs), accounting for individual and gene correlations across time. This method provides future predictions of DNA methylation status at different individual ages while accounting for uncertainty. Our model is trained on a birth cohort of children with methylation profiled at ages 0-4, and we demonstrated that the status of methylation sites for each child can be accurately predicted at ages 5-7. We show that methylation profiles predicted by multi-mean GPs can be used to estimate other phenotypes, such as epigenetic age, and enable comparison to other health measures of interest. This approach encourages epigenetic studies to move towards longitudinal design for investigating epigenetic changes during development, ageing and disease progression.

The study emphasizes the challenge of finding the optimal trade-off between bias and variance, especially as hyperparameter optimization increases in complexity. Through empirical analysis, three hyperparameter tuning algorithms Tree-structured Parzen Estimator (TPE), Genetic Search, and Random Search are evaluated across regression and classification tasks. The results show that nonlinear models, with properly tuned hyperparameters, significantly outperform linear models. Interestingly, Random Search excelled in regression tasks, while TPE was more effective for classification tasks. This suggests that there is no one-size-fits-all solution, as different algorithms perform better depending on the task and model type. The findings underscore the importance of selecting the appropriate tuning method and highlight the computational challenges involved in optimizing machine learning models, particularly as search spaces expand.

The teaching career shares common global characteristics, such as internal promotion, performance evaluation, recruitment of top candidates, continuous training, specialization, and peer learning. This study aims to describe the factors associated with the value placed on the teaching career in Peru. A total of 28217 public school teachers were analyzed using data from the 2020 National Teacher Survey. A variable measuring the "value of the teaching career" was constructed using eight indicators and categorized as low, medium, or high. Another variable, vision of the future, was classified as pessimistic, conformist, or optimistic. This observational, cross-sectional, and analytical study included variables related to in-service training, working conditions, professional recognition, and sociodemographic characteristics. Among the teachers surveyed, 45.8 % expressed an optimistic outlook on the future of the profession, 48 % held a conformist view, and only 6.2 % reported a pessimistic perspective. A generalized linear model revealed that the value placed on the teaching career was significantly associated with male gender (p = 0.002), a professional career (p < 0.001), an optimistic outlook (p = 0.033), and working at the primary level (p < 0.001). It was concluded that Peruvian teachers predominantly hold conformist or optimistic views of their profession. This highlights the need to reinforce merit-based advancement, competency-based training, intrinsic motivation, and ongoing professional development

This research utilized three types of artificial neural network (ANN) methodologies, namely Backpropagation Neural Network (BPNN) with varied training, transfer, divide, and learning functions; Radial Basis Function Neural Network (RBFNN); and General Regression Neural Network (GRNN), to forecast the severity of stem rust. It considered parameters such as mean maximum temperature, mean minimum temperature, mean rainfall, mean average temperature, mean relative humidity, and different wheat varieties. The statistical analysis revealed that GRNN demonstrated effective predictive capability and required less training time compared to the other models. Additionally, the results indicated that total seasonal rainfall positively influenced the development of wheat stem rust. Keywords: Wheat stem rust, Back propagation neural network, Radial Basis Function Neural Network, General Regression Neural Network.

Student's grade retention is a key issue faced by many education systems, especially those in developing countries. In this paper, we seek to gauge the relevance of students' personality traits in predicting grade retention in Brazil. For that, we used data collected in 2012 and 2017, in the city of Sertaozinho, countryside of the state of Sao Paulo, Brazil. The surveys taken in Sertaozinho included several socioeconomic questions, standardized tests, and a personality test. Moreover, students were in grades 4, 5, and 6 in 2012. Our approach was based on training machine learning models on the surveys' data to predict grade retention between 2012 and 2017 using information from 2012 or before, and then using some strategies to quantify personality traits' predictive power. We concluded that, besides proving to be fairly better than a random classifier when isolated, personality traits contribute to prediction even when using socioeconomic variables and standardized tests results.

Understanding the biological mechanism of disease is critical for medicine, and in particular drug discovery. AI-powered analysis of genome-scale biological data hold great potential in this regard. The increasing availability of single-cell RNA sequencing data has enabled the development of large foundation models for disease biology. However, existing foundation models either do not improve or only modestly improve over task-specific models in downstream applications. Here, we explored two avenues for improving the state-of-the-art. First, we scaled the pre-training dataset to 116 million cells, which is larger than those used by previous models. Second, we leveraged the availability of large-scale biological annotations as a form of supervision during pre-training. We trained the TEDDY family of models comprising six transformer-based state-of-the-art single-cell foundation models with 70 million, 160 million, and 400 million parameters. We vetted our models on two downstream evaluation tasks -- identifying the underlying disease state of held-out donors not seen during training and distinguishing healthy cells from diseased ones for disease conditions and donors not seen during training. Scaling experiments showed that performance improved predictably with both data volume and parameter count. Our models showed substantial improvement over existing work on the first task and more muted improvements on the second.

A ubiquitous feature of data of our era is their extra-large sizes and dimensions. Analyzing such high-dimensional data poses significant challenges, since the feature dimension is often much larger than the sample size. This thesis introduces robust and computationally efficient methods to address several common challenges associated with high-dimensional data. In my first manuscript, I propose a coherent approach to variable screening that accommodates nonlinear associations. I develop a novel variable screening method that transcends traditional linear assumptions by leveraging mutual information, with an intended application in neuroimaging data. This approach allows for accurate identification of important variables by capturing nonlinear as well as linear relationships between the outcome and covariates. Building on this foundation, I develop new optimization methods for sparse estimation using nonconvex penalties in my second manuscript. These methods address notable challenges in current statistical computing practices, facilitating computationally efficient and robust analyses of complex datasets. The proposed method can be applied to a general class of optimization problems. In my third manuscript, I contribute to robust modeling of high-dimensional correlated observations by developing a mixed-effects model based on Tsallis power-law entropy maximization and discussed the theoretical properties of such distribution. This model surpasses the constraints of conventional Gaussian models by accommodating a broader class of distributions with enhanced robustness to outliers. Additionally, I develop a proximal nonlinear conjugate gradient algorithm that accelerates convergence while maintaining numerical stability, along with rigorous statistical properties for the proposed framework.

Although deep learning has produced dazzling successes for applications of image, speech, and video processing in the past few years, most trainings are with suboptimal hyper-parameters, requiring unnecessarily long training times. Setting the hyper-parameters remains a black art that requires years of experience to acquire. This report proposes several efficient ways to set the hyper-parameters that significantly reduce training time and improves performance. Specifically, this report shows how to examine the training validation/test loss function for subtle clues of underfitting and overfitting and suggests guidelines for moving toward the optimal balance point. Then it discusses how to increase/decrease the learning rate/momentum to speed up training. Our experiments show that it is crucial to balance every manner of regularization for each dataset and architecture. Weight decay is used as a sample regularizer to show how its optimal value is tightly coupled with the learning rates and momentums. Files to help replicate the results reported here are available.

Early identification of sensitive cancer cell lines is essential for accelerating biomarker discovery and elucidating drug mechanism of action. Given the efficiency and low cost of small-scale drug screens relative to extensive omics profiling, we compared drug-response panel (DRP) descriptors against omics features for predictive capacity using gradient boosting tree models across the GDSC and CCLE drug response datasets. DRP descriptors consistently outperformed omics data across key performance metrics, with variable performance across different drugs. Using complementary explainability approaches, we confirmed known MAPK-inhibitor sensitivity signatures, and identified novel potential biomarker candidates for MEK1/2 and BTK/MNK inhibitors. Lastly, to demonstrate the utility of this approach in distinguishing phenotypes, we applied our models to the breast cancer line MCF7 versus the non-tumorigenic MCF10A, and successfully identified compounds that selectively inhibit MCF7 while sparing the non-tumorigenic MCF10A. This methodology, developed using focused drug and cell line panels, supports early-stage drug development by facilitating rational cell line selection and compound prioritisation, enabling more efficient biomarker identification and candidate assessment.

Introduction: Blood vessels can be non-invasively visualized from a digital fundus image (DFI). Several studies have shown an association between cardiovascular risk and vascular features obtained from DFI. Recent advances in computer vision and image segmentation enable automatising DFI blood vessel segmentation. There is a need for a resource that can automatically compute digital vasculature biomarkers (VBM) from these segmented DFI. Methods: In this paper, we introduce a Python Vasculature BioMarker toolbox, denoted PVBM. A total of 11 VBMs were implemented. In particular, we introduce new algorithmic methods to estimate tortuosity and branching angles. Using PVBM, and as a proof of usability, we analyze geometric vascular differences between glaucomatous patients and healthy controls. Results: We built a fully automated vasculature biomarker toolbox based on DFI segmentations and provided a proof of usability to characterize the vascular changes in glaucoma. For arterioles and venules, all biomarkers were significant and lower in glaucoma patients compared to healthy controls except for tortuosity, venular singularity length and venular branching angles. Conclusion: We have automated the computation of 11 VBMs from retinal blood vessel segmentation. The PVBM toolbox is made open source under a GNU GPL 3 license and is available on physiozoo.com (following publication).

Convolutional Neural Networks (CNN) have gained great success in many artificial intelligence tasks. However, finding a good set of hyperparameters for a CNN remains a challenging task. It usually takes an expert with deep knowledge, and trials and errors. Genetic algorithms have been used in hyperparameter optimizations. However, traditional genetic algorithms with fixed-length chromosomes may not be a good fit for optimizing deep learning hyperparameters, because deep learning models have variable number of hyperparameters depending on the model depth. As the depth increases, the number of hyperparameters grows exponentially, and searching becomes exponentially harder. It is important to have an efficient algorithm that can find a good model in reasonable time. In this article, we propose to use a variable length genetic algorithm (GA) to systematically and automatically tune the hyperparameters of a CNN to improve its performance. Experimental results show that our algorithm can find good CNN hyperparameters efficiently. It is clear from our experiments that if more time is spent on optimizing the hyperparameters, better results could be achieved. Theoretically, if we had unlimited time and CPU power, we could find the optimized hyperparameters and achieve the best results in the future.

Dirichlet Process mixture models (DPMM) in combination with Gaussian kernels have been an important modeling tool for numerous data domains arising from biological, physical, and social sciences. However, this versatility in applications does not extend to strong theoretical guarantees for the underlying parameter estimates, for which only a logarithmic rate is achieved. In this work, we (re)introduce and investigate a metric, named Orlicz-Wasserstein distance, in the study of the Bayesian contraction behavior for the parameters. We show that despite the overall slow convergence guarantees for all the parameters, posterior contraction for parameters happens at almost polynomial rates in outlier regions of the parameter space. Our theoretical results provide new insight in understanding the convergence behavior of parameters arising from various settings of hierarchical Bayesian nonparametric models. In addition, we provide an algorithm to compute the metric by leveraging Sinkhorn divergences and validate our findings through a simulation study.