Objectives: Unsupervised learning with electronic health record (EHR) data has shown promise for phenotype discovery, but approaches typically disregard existing clinical information, limiting interpretability. We operationalize a Bayesian latent class framework for phenotyping that incorporates domain-specific knowledge to improve clinical meaningfulness of EHR-derived phenotypes and illustrate its utility by identifying an asthma sub-phenotype informed by features of Type 2 (T2) inflammation. Materials and methods: We illustrate a framework for incorporating clinical knowledge into a Bayesian latent class model via informative priors to guide unsupervised clustering toward clinically relevant subgroups. This approach models missingness, accounting for potential missing-not-at-random patterns, and provides patient-level probabilities for phenotype assignment with uncertainty. Using reusable and flexible code, we applied the model to a large asthma EHR cohort, specifying informative priors for T2 inflammation-related features and weakly informative priors for other clinical variables, allowing the data to inform posterior distributions. Results and Conclusion: Using encounter data from January 2017 to February 2024 for 44,642 adult asthma patients, we found a bimodal posterior distribution of phenotype assignment, indicating clear class separation. The T2 inflammation-informed class (38.7%) was characterized by elevated eosinophil levels and allergy markers, plus high healthcare utilization and medication use, despite weakly informative priors on the latter variables. These patterns suggest an "uncontrolled T2-high" sub-phenotype. This demonstrates how our Bayesian latent class modeling approach supports hypothesis generation and cohort identification in EHR-based studies of heterogeneous diseases without well-established phenotype definitions.

Close-range laser scanning provides detailed 3D captures of forest stands but requires efficient software for processing 3D point cloud data and extracting individual trees. Although recent studies have introduced deep learning methods for tree instance segmentation, these approaches require large annotated datasets and substantial computational resources. As a resource-efficient alternative, we present a revised version of the treeX algorithm, an unsupervised method that combines clustering-based stem detection with region growing for crown delineation. While the original treeX algorithm was developed for personal laser scanning (PLS) data, we provide two parameter presets, one for ground-based laser scanning (stationary terrestrial - TLS and PLS), and one for UAV-borne laser scanning (ULS). We evaluated the method on six public datasets (FOR-instance, ForestSemantic, LAUTx, NIBIO MLS, TreeLearn, Wytham Woods) and compared it to six open-source methods (original treeX, treeiso, RayCloudTools, ForAINet, SegmentAnyTree, TreeLearn). Compared to the original treeX algorithm, our revision reduces runtime and improves accuracy, with instance detection F$_1$-score gains of +0.11 to +0.49 for ground-based data. For ULS data, our preset achieves an F$_1$-score of 0.58, whereas the original algorithm fails to segment any correct instances. For TLS and PLS data, our algorithm achieves accuracy similar to recent open-source methods, including deep learning. Given its algorithmic design, we see two main applications for our method: (1) as a resource-efficient alternative to deep learning approaches in scenarios where the data characteristics align with the method design (sufficient stem visibility and point density), and (2) for the semi-automatic generation of labels for deep learning models. To enable broader adoption, we provide an open-source Python implementation in the pointtree package.

OpenAI is giving free ChatGPT users limited access to its Deep Research tool without the need to pay for it. In addition, the company has expanded the tool's limits for all users by rolling out a lightweight version of it powered by its o4-mini model. It says the o4-mini Deep Research feature produces slightly shorter responses, but is "nearly as smart, more cost-efficient and delivers similarly high-quality results" as the original version. OpenAI previously released the tool for use by paying Pro, Plus, Team, Edu and Enterprise subscribers. But even they have a limited number of Deep Research queries per month.

Node embedding algorithms produce low-dimensional latent representations of nodes in a graph. These embeddings are often used for downstream tasks, such as node classification and link prediction. In this paper, we investigate the following two questions: (Q1) Can we explain each embedding dimension with human-understandable graph features (e.g. degree, clustering coefficient and PageRank). (Q2) How can we modify existing node embedding algorithms to produce embeddings that can be easily explained by human-understandable graph features? We find that the answer to Q1 is yes and introduce a new framework called XM (short for eXplain eMbedding) to answer Q2. A key aspect of XM involves minimizing the nuclear norm of the generated explanations. We show that by minimizing the nuclear norm, we minimize the lower bound on the entropy of the generated explanations. We test XM on a variety of real-world graphs and show that XM not only preserves the performance of existing node embedding methods, but also enhances their explainability.

The potential of Machine Learning Control (MLC) in HVAC systems is hindered by its opaque nature and inference mechanisms, which is challenging for users and modelers to fully comprehend, ultimately leading to a lack of trust in MLC-based decision-making. To address this challenge, this paper investigates and explores Interpretable Machine Learning (IML), a branch of Machine Learning (ML) that enhances transparency and understanding of models and their inferences, to improve the credibility of MLC and its industrial application in HVAC systems. Specifically, we developed an innovative framework that combines the principles of Shapley values and the in-context learning feature of Large Language Models (LLMs). While the Shapley values are instrumental in dissecting the contributions of various features in ML models, LLM provides an in-depth understanding of rule-based parts in MLC; combining them, LLM further packages these insights into a coherent, human-understandable narrative. The paper presents a case study to demonstrate the feasibility of the developed IML framework for model predictive control-based precooling under demand response events in a virtual testbed. The results indicate that the developed framework generates and explains the control signals in accordance with the rule-based rationale.

Today I am happy to announce that a new tidymodels-centric version of my free, online, interactive course, Supervised Machine Learning: Case Studies in R, has been published! This is at least the third version of this course I've built at this point but I believe it to be the best, in terms of how it communicates machine learning concepts and how useful to your real-world problems the demonstrated code will be. Similar to the last time I launched this course, it provides four case studies using data from the real world for you to practice your predictive modeling skills. One question we sometimes field from R users is about choosing to use tidymodels vs. caret. The original version of my course mostly used caret, and caret is a stable and broadly used framework for modeling and machine learning in R.

A music mashup combines audio elements from two or more songs to create a new work. To reduce the time and effort required to make them, researchers have developed algorithms that predict the compatibility of audio elements. Prior work has focused on mixing unaltered excerpts, but advances in source separation enable the creation of mashups from isolated stems (e.g., vocals, drums, bass, etc.). In this work, we take advantage of separated stems not just for creating mashups, but for training a model that predicts the mutual compatibility of groups of excerpts, using self-supervised and semi-supervised methods. Specifically, we first produce a random mashup creation pipeline that combines stem tracks obtained via source separation, with key and tempo automatically adjusted to match, since these are prerequisites for high-quality mashups. To train a model to predict compatibility, we use stem tracks obtained from the same song as positive examples, and random combinations of stems with key and/or tempo unadjusted as negative examples. To improve the model and use more data, we also train on "average" examples: random combinations with matching key and tempo, where we treat them as unlabeled data as their true compatibility is unknown. To determine whether the combined signal or the set of stem signals is more indicative of the quality of the result, we experiment on two model architectures and train them using semi-supervised learning technique. Finally, we conduct objective and subjective evaluations of the system, comparing them to a standard rule-based system.

Predictive power has always been the main research focus of learning algorithms. While the general approach for these algorithms is to consider all possible attributes in a dataset to best predict the response of interest, an important branch of research is focused on sparse learning. Indeed, in many practical settings we believe that only an extremely small combination of different attributes affect the response. However even sparse-learning methods can still preserve a high number of attributes in high-dimensional settings and possibly deliver inconsistent prediction performance. The latter methods can also be hard to interpret for researchers and practitioners, a problem which is even more relevant for the ``black-box''-type mechanisms of many learning approaches. Finally, there is often a problem of replicability since not all data-collection procedures measure (or observe) the same attributes and therefore cannot make use of proposed learners for testing purposes. To address all the previous issues, we propose to study a procedure that combines screening and wrapper methods and aims to find a library of extremely low-dimensional attribute combinations (with consequent low data collection and storage costs) in order to (i) match or improve the predictive performance of any particular learning method which uses all attributes as an input (including sparse learners); (ii) provide a low-dimensional network of attributes easily interpretable by researchers and practitioners; and (iii) increase the potential replicability of results due to a diversity of attribute combinations defining strong learners with equivalent predictive power. We call this algorithm ``Sparse Wrapper AlGorithm'' (SWAG).

One of the oldest Greek myths, the story of Pandora was first recorded more than 2,500 years ago, in the time of Homer. In the original telling, Pandora was not some innocent girl who succumbed to the temptation to open a forbidden jar. Rather, as the poet Hesiod tells us, Pandora was "made, not born." Having been commissioned by all-powerful Zeus and designed to his cruel specifications by Hephaestus, the god of invention, Pandora was a lifelike android created to look like a bewitching maiden. Her purpose was to entrap mortals as a manifestation of kalos kakon: "evil hidden in beauty."

What makes humans so good at solving seemingly complex video games? Unlike computers, humans bring in a great deal of prior knowledge about the world, enabling efficient decision making. This paper investigates the role of human priors for solving video games. Given a sample game, we conduct a series of ablation studies to quantify the importance of various priors on human performance. We do this by modifying the video game environment to systematically mask different types of visual information that could be used by humans as priors. We find that removal of some prior knowledge causes a drastic degradation in the speed with which human players solve the game, e.g. from 2 minutes to over 20 minutes. Furthermore, our results indicate that general priors, such as the importance of objects and visual consistency, are critical for efficient game-play.