Single-cell datasets often lack individual cell labels, making it challenging to identify cells associated with disease. To address this, we introduce Mixture Modeling for Multiple Instance Learning (MMIL), an expectation maximization method that enables the training and calibration of cell-level classifiers using patient-level labels. Our approach can be used to train e.g. lasso logistic regression models, gradient boosted trees, and neural networks. When applied to clinically-annotated, primary patient samples in Acute Myeloid Leukemia (AML) and Acute Lymphoblastic Leukemia (ALL), our method accurately identifies cancer cells, generalizes across tissues and treatment timepoints, and selects biologically relevant features. In addition, MMIL is capable of incorporating cell labels into model training when they are known, providing a powerful framework for leveraging both labeled and unlabeled data simultaneously. Mixture Modeling for MIL offers a novel approach for cell classification, with significant potential to advance disease understanding and management, especially in scenarios with unknown gold-standard labels and high dimensionality.

Single-cell technologies enable comprehensive profiling of diverse immune cell-types through the measurement of multiple genes or proteins per cell. In order to translate data from immune profiling assays into powerful diagnostics, machine learning approaches are used to compute per-sample immunological summaries, or featurizations that can be used as inputs to models for outcomes of interest. Current supervised learning approaches for computing per-sample representations are optimized based only on the outcome variable to be predicted and do not take into account clinically-relevant covariates that are likely to also be measured. Here we expand the optimization problem to also take into account such additional patient covariates to directly inform the learned per-sample representations. To do this, we introduce CytoCoSet, a set-based encoding method, which formulates a loss function with an additional triplet term penalizing samples with similar covariates from having disparate embedding results in per-sample representations. Overall, incorporating clinical covariates leads to improved prediction of clinical phenotypes.

Any supervised machine learning analysis is required to provide an estimate of the out-of-sample predictive performance. However, it is imperative to also provide a quantification of the uncertainty of this performance in the form of a confidence or credible interval (CI) and not just a point estimate. In an AutoML setting, estimating the CI is challenging due to the ``winner's curse", i.e., the bias of estimation due to cross-validating several machine learning pipelines and selecting the winning one. In this work, we perform a comparative evaluation of 9 state-of-the-art methods and variants in CI estimation in an AutoML setting on a corpus of real and simulated datasets. The methods are compared in terms of inclusion percentage (does a 95\% CI include the true performance at least 95\% of the time), CI tightness (tighter CIs are preferable as being more informative), and execution time. The evaluation is the first one that covers most, if not all, such methods and extends previous work to imbalanced and small-sample tasks. In addition, we present a variant, called BBC-F, of an existing method (the Bootstrap Bias Correction, or BBC) that maintains the statistical properties of the BBC but is more computationally efficient. The results support that BBC-F and BBC dominate the other methods in all metrics measured.

In this paper, we present a method using Deep Convolutional Neural Networks (DCNNs) to detect common glitches in video games. The problem setting consists of an image (800x800 RGB) as input to be classified into one of five defined classes, normal image, or one of four different kinds of glitches (stretched, low resolution, missing and placeholder textures). Using a supervised approach, we train a ShuffleNetV2 using generated data. This work focuses on detecting texture graphical anomalies achieving arguably good performance with an accuracy of 86.8\%, detecting 88\% of the glitches with a false positive rate of 8.7\%, and with the models being able to generalize and detect glitches even in unseen objects. We apply a confidence measure as well to tackle the issue with false positives as well as an effective way of aggregating images to achieve better detection in production. The main use of this work is the partial automatization of graphical testing in the final stages of video game development.

We present a method for expanding a dataset by incorporating knowledge from the wide distribution of pre-trained latent diffusion models. Data augmentations typically incorporate inductive biases about the image formation process into the training (e.g. translation, scaling, colour changes, etc.). Here, we go beyond simple pixel transformations and introduce the concept of instance-level data augmentation by repainting parts of the image at the level of object instances. The method combines a conditional diffusion model with depth and edge maps control conditioning to seamlessly repaint individual objects inside the scene, being applicable to any segmentation or detection dataset. Used as a data augmentation method, it improves the performance and generalization of the state-of-the-art salient object detection, semantic segmentation and object detection models. By redrawing all privacy-sensitive instances (people, license plates, etc.), the method is also applicable for data anonymization. We also release fully synthetic and anonymized expansions for popular datasets: COCO, Pascal VOC and DUTS.

Selective prediction minimizes incorrect predictions from vision-language models (VLMs) by allowing them to abstain from answering when uncertain. However, when deploying a vision-language system with low tolerance for inaccurate predictions, selective prediction may be over-cautious and abstain too frequently, even on many correct predictions. We introduce ReCoVERR, an inference-time algorithm to reduce the over-abstention of a selective vision-language system without increasing the error rate of the system's predictions. When the VLM makes a low-confidence prediction, instead of abstaining ReCoVERR tries to find relevant clues in the image that provide additional evidence for the prediction. ReCoVERR uses an LLM to pose related questions to the VLM, collects high-confidence evidences, and if enough evidence confirms the prediction the system makes a prediction instead of abstaining. ReCoVERR enables three VLMs (BLIP2, InstructBLIP, and LLaVA-1.5) to answer up to 20% more questions on the VQAv2 and A-OKVQA tasks without decreasing system accuracy, thus improving overall system reliability. Our code is available at https://github.com/tejas1995/ReCoVERR.

Noise is a fundamental problem in learning theory with huge effects in the application of Machine Learning (ML) methods, due to real world data tendency to be noisy. Additionally, introduction of malicious noise can make ML methods fail critically, as is the case with adversarial attacks. Thus, finding and developing alternatives to improve robustness to noise is a fundamental problem in ML. In this paper, we propose a method to deal with noise: mitigating its effect through the use of data abstractions. The goal is to reduce the effect of noise over the model's performance through the loss of information produced by the abstraction. However, this information loss comes with a cost: it can result in an accuracy reduction due to the missing information. First, we explored multiple methodologies to create abstractions, using the training dataset, for the specific case of numerical data and binary classification tasks. We also tested how these abstractions can affect robustness to noise with several experiments that explore the robustness of an Artificial Neural Network to noise when trained using raw data \emph{vs} when trained using abstracted data. The results clearly show that using abstractions is a viable approach for developing noise robust ML methods.

In this paper, we deal with bias mitigation techniques that remove specific data points from the training set to aim for a fair representation of the population in that set. Machine learning models are trained on these pre-processed datasets, and their predictions are expected to be fair. However, such approaches may exclude relevant data, making the attained subsets less trustworthy for further usage. To enhance the trustworthiness of prior methods, we propose additional requirements and objectives that the subsets must fulfill in addition to fairness: (1) group coverage, and (2) minimal data loss. While removing entire groups may improve the measured fairness, this practice is very problematic as failing to represent every group cannot be considered fair. In our second concern, we advocate for the retention of data while minimizing discrimination. By introducing a multi-objective optimization problem that considers fairness and data loss, we propose a methodology to find Pareto-optimal solutions that balance these objectives. By identifying such solutions, users can make informed decisions about the trade-off between fairness and data quality and select the most suitable subset for their application.

Optical continuous glucose monitoring (CGM) systems are emerging for personalized glucose management owing to their lower cost and prolonged durability compared to conventional electrochemical CGMs. Here, we report a computational CGM system, which integrates a biocompatible phosphorescence-based insertable biosensor and a custom-designed phosphorescence lifetime imager (PLI). This compact and cost-effective PLI is designed to capture phosphorescence lifetime images of an insertable sensor through the skin, where the lifetime of the emitted phosphorescence signal is modulated by the local concentration of glucose. Because this phosphorescence signal has a very long lifetime compared to tissue autofluorescence or excitation leakage processes, it completely bypasses these noise sources by measuring the sensor emission over several tens of microseconds after the excitation light is turned off. The lifetime images acquired through the skin are processed by neural network-based models for misalignment-tolerant inference of glucose levels, accurately revealing normal, low (hypoglycemia) and high (hyperglycemia) concentration ranges. Using a 1-mm thick skin phantom mimicking the optical properties of human skin, we performed in vitro testing of the PLI using glucose-spiked samples, yielding 88.8% inference accuracy, also showing resilience to random and unknown misalignments within a lateral distance of ~4.7 mm with respect to the position of the insertable sensor underneath the skin phantom. Furthermore, the PLI accurately identified larger lateral misalignments beyond 5 mm, prompting user intervention for re-alignment. The misalignment-resilient glucose concentration inference capability of this compact and cost-effective phosphorescence lifetime imager makes it an appealing wearable diagnostics tool for real-time tracking of glucose and other biomarkers.

This paper tackles the challenge of detecting unreliable behavior in regression algorithms, which may arise from intrinsic variability (e.g., aleatoric uncertainty) or modeling errors (e.g., model uncertainty). First, we formally introduce the notion of unreliability in regression, i.e., when the output of the regressor exceeds a specified discrepancy (or error). Then, using powerful tools for probabilistic modeling, we estimate the discrepancy density, and we measure its statistical diversity using our proposed metric for statistical dissimilarity. In turn, this allows us to derive a data-driven score that expresses the uncertainty of the regression outcome. We show empirical improvements in error detection for multiple regression tasks, consistently outperforming popular baseline approaches, and contributing to the broader field of uncertainty quantification and safe machine learning systems. Our code is available at https://zenodo.org/records/11281964.