Single-cell RNA sequencing (scRNA-seq) provides unprecedented insights into cellular heterogeneity, enabling detailed analysis of complex biological systems at single-cell resolution. However, the high dimensionality and technical noise inherent in scRNA-seq data pose significant analytical challenges. While current embedding methods focus primarily on gene expression levels, they often overlook crucial gene-gene interactions that govern cellular identity and function. To address this limitation, we present a novel embedding approach that integrates both gene expression profiles and data-driven gene-gene interactions. Our method first constructs a Cell-Leaf Graph (CLG) using random forest models to capture regulatory relationships between genes, while simultaneously building a K-Nearest Neighbor Graph (KNNG) to represent expression similarities between cells. These graphs are then combined into an Enriched Cell-Leaf Graph (ECLG), which serves as input for a graph neural network to compute cell embeddings. By incorporating both expression levels and gene-gene interactions, our approach provides a more comprehensive representation of cellular states. Extensive evaluation across multiple datasets demonstrates that our method enhances the detection of rare cell populations and improves downstream analyses such as visualization, clustering, and trajectory inference. This integrated approach represents a significant advance in single-cell data analysis, offering a more complete framework for understanding cellular diversity and dynamics.

Identifying influential nodes in complex networks is a fundamental task in network analysis with wide-ranging applications across domains. While deep learning has advanced node influence detection, existing supervised approaches remain constrained by their reliance on labeled data, limiting their applicability in real-world scenarios where labels are scarce or unavailable. While contrastive learning demonstrates significant potential for performance enhancement, existing approaches predominantly rely on multiple-embedding generation to construct positive/negative sample pairs. To overcome these limitations, we propose ReCC (\textit{r}egular \textit{e}quivalence-based \textit{c}ontrastive \textit{c}lustering), a novel deep unsupervised framework for influential node identification. We first reformalize influential node identification as a label-free deep clustering problem, then develop a contrastive learning mechanism that leverages regular equivalence-based similarity, which captures structural similarities between nodes beyond local neighborhoods, to generate positive and negative samples. This mechanism is integrated into a graph convolutional network to learn node embeddings that are used to differentiate influential from non-influential nodes. ReCC is pre-trained using network reconstruction loss and fine-tuned with a combined contrastive and clustering loss, with both phases being independent of labeled data. Additionally, ReCC enhances node representations by combining structural metrics with regular equivalence-based similarities. Extensive experiments demonstrate that ReCC outperforms state-of-the-art approaches across several benchmarks.

Dementia (DEM) is a growing global health challenge, underscoring the need for early and accurate diagnosis. Electroencephalography (EEG) provides a non-invasive window into brain activity, but conventional methods struggle to capture its transient complexity. We present the \textbf{EEG Microstate Analysis Framework (EEG-MSAF)}, an end-to-end pipeline that leverages EEG microstates discrete, quasi-stable topographies to identify DEM-related biomarkers and distinguish DEM, mild cognitive impairment (MCI), and normal cognition (NC). EEG-MSAF comprises three stages: (1) automated microstate feature extraction, (2) classification with machine learning (ML), and (3) feature ranking using Shapley Additive Explanations (SHAP) to highlight key biomarkers. We evaluate on two EEG datasets: the public Chung-Ang University EEG (CAUEEG) dataset and a clinical cohort from Thessaloniki Hospital. Our framework demonstrates strong performance and generalizability. On CAUEEG, EEG-MSAF-SVM achieves \textbf{89\% $\pm$ 0.01 accuracy}, surpassing the deep learning baseline CEEDNET by \textbf{19.3\%}. On the Thessaloniki dataset, it reaches \textbf{95\% $\pm$ 0.01 accuracy}, comparable to EEGConvNeXt. SHAP analysis identifies mean correlation and occurrence as the most informative metrics: disruption of microstate C (salience/attention network) dominates DEM prediction, while microstate F, a novel default-mode pattern, emerges as a key early biomarker for both MCI and DEM. By combining accuracy, generalizability, and interpretability, EEG-MSAF advances EEG-based dementia diagnosis and sheds light on brain dynamics across the cognitive spectrum.

Existing agents for solving tasks such as ML engineering rely on prompting powerful language models. As a result, these agents do not improve with more experience. In this paper, we show that agents backed by weaker models that improve via reinforcement learning (RL) can outperform agents backed by much larger, but static models. We identify two major challenges with RL in this setting. First, actions can take a variable amount of time (e.g., executing code for different solutions), which leads to asynchronous policy gradient updates that favor faster but suboptimal solutions. To tackle variable-duration actions, we propose duration-aware gradient updates in a distributed asynchronous RL framework to amplify high-cost but high-reward actions. Second, using only test split performance as a reward provides limited feedback. A program that is nearly correct is treated the same as one that fails entirely. To address this, we propose environment instrumentation to offer partial credit, distinguishing almost-correct programs from those that fail early (e.g., during data loading). Environment instrumentation uses a separate static language model to insert print statement to an existing program to log the agent's experimental progress, from which partial credit can be extracted as reward signals for learning. Our experimental results on MLEBench suggest that performing gradient updates on a much smaller model (Qwen2.5-3B) trained with RL outperforms prompting a much larger model (Claude-3.5-Sonnet) with agent scaffolds, by an average of 22% across 12 Kaggle tasks.

Human cognition is profoundly shaped by the environments in which it unfolds. Yet, it remains an open question whether learning and decision making can be explained as a principled adaptation to the statistical structure of real-world tasks. We introduce ecologically rational analysis, a computational framework that unifies the normative foundations of rational analysis with ecological grounding. Leveraging large language models to generate ecologically valid cognitive tasks at scale, and using meta-learning to derive rational models optimized for these environments, we develop a new class of learning algorithms: Ecologically Rational Meta-learned Inference (ERMI). ERMI internalizes the statistical regularities of naturalistic problem spaces and adapts flexibly to novel situations, without requiring hand-crafted heuristics or explicit parameter updates. We show that ERMI captures human behavior across 15 experiments spanning function learning, category learning, and decision making, outperforming several established cognitive models in trial-by-trial prediction. Our results suggest that much of human cognition may reflect adaptive alignment to the ecological structure of the problems we encounter in everyday life.

Neural network pruning has emerged as a promising approach for deploying LLMs in low-resource scenarios while preserving downstream task performance. However, for the first time, we reveal that such pruning disrupts LLMs' internal activation features crucial for lie detection, where probing classifiers (typically small logistic regression models) trained on these features assess the truthfulness of LLM-generated statements. This discovery raises a crucial open question: how can we prune LLMs without sacrificing these critical lie detection capabilities? Our investigation further reveals that naively adjusting layer-wise pruning sparsity based on importance inadvertently removes crucial weights, failing to improve lie detection performance despite its reliance on the most crucial LLM layer. To address this issue, we propose Truthful Pruning aligned by Layer-wise Outliers (TPLO), which places greater emphasis on layers with more activation outliers and stronger discriminative features simultaneously. This preserves LLMs' original performance while retaining critical features of inner states needed for robust lie detection. Moreover, we introduce a prompting rule to enrich the TruthfulQA benchmark for better calibrating LLM pruning. Empirical results show that our approach improves the hallucination detection for pruned LLMs (achieving 88% accuracy at 50% sparsity) and enhances their performance on TruthfulQA.

Real-time monitoring of power consumption in cities and micro-grids through the Internet of Things (IoT) can help forecast future demand and optimize grid operations. But moving all consumer-level usage data to the cloud for predictions and analysis at fine time scales can expose activity patterns. Federated Learning~(FL) is a privacy-sensitive collaborative DNN training approach that retains data on edge devices, trains the models on private data locally, and aggregates the local models in the cloud. But key challenges exist: (i) clients can have non-independently identically distributed~(non-IID) data, and (ii) the learning should be computationally cheap while scaling to 1000s of (unseen) clients. In this paper, we develop and evaluate several optimizations to FL training across edge and cloud for time-series demand forecasting in micro-grids and city-scale utilities using DNNs to achieve a high prediction accuracy while minimizing the training cost. We showcase the benefit of using exponentially weighted loss while training and show that it further improves the prediction of the final model. Finally, we evaluate these strategies by validating over 1000s of clients for three states in the US from the OpenEIA corpus, and performing FL both in a pseudo-distributed setting and a Pi edge cluster. The results highlight the benefits of the proposed methods over baselines like ARIMA and DNNs trained for individual consumers, which are not scalable.

This work demonstrates a proof-of-principle for using uncertainty-aware architectures, in combination with active learning techniques and an in-the-loop physics simulation code as a data labeller, to construct efficient datasets for data-driven surrogate model generation. Building off of a previous proof-of-principle successfully demonstrating training set reduction on static pre-labelled datasets, using the ADEPT framework, this strategy was applied again to the plasma turbulent transport problem within tokamak fusion plasmas, specifically the QuaLiKiz quasilinear electrostatic gyrokinetic turbulent transport code. While QuaLiKiz provides relatively fast evaluations, this study specifically targeted small datasets to serve as a proxy for more expensive codes, such as CGYRO or GENE. The newly implemented algorithm uses the SNGP architecture for the classification component of the problem and the BNN-NCP architecture for the regression component, training models for all turbulent modes (ITG, TEM, ETG) and all transport fluxes ($Q_e$, $Q_i$, $Γ_e$, $Γ_i$, and $Π_i$) described by the general QuaLiKiz output. With 45 active learning iterations, moving from a small initial training set of $10^{2}$ to a final set of $10^{4}$, the resulting models reached a $F_1$ classification performance of ~0.8 and a $R^2$ regression performance of ~0.75 on an independent test set across all outputs. This extrapolates to reaching the same performance and efficiency as the previous ADEPT pipeline, although on a problem with 1 extra input dimension. While the improvement rate achieved in this implementation diminishes faster than expected, the overall technique is formulated with components that can be upgraded and generalized to many surrogate modeling applications beyond plasma turbulent transport predictions.

The explosive growth of complex datasets across various modalities necessitates advanced analytical tools that not only group data effectively but also provide human-understandable insights into the discovered structures. We introduce HERCULES (Hierarchical Embedding-based Recursive Clustering Using LLMs for Efficient Summarization), a novel algorithm and Python package designed for hierarchical k-means clustering of diverse data types, including text, images, and numeric data (processed one modality per run). HERCULES constructs a cluster hierarchy by recursively applying k-means clustering, starting from individual data points at level 0. A key innovation is its deep integration of Large Language Models (LLMs) to generate semantically rich titles and descriptions for clusters at each level of the hierarchy, significantly enhancing interpretability. The algorithm supports two main representation modes: `direct' mode, which clusters based on original data embeddings or scaled numeric features, and `description' mode, which clusters based on embeddings derived from LLM-generated summaries. Users can provide a `topic\_seed' to guide LLM-generated summaries towards specific themes. An interactive visualization tool facilitates thorough analysis and understanding of the clustering results. We demonstrate HERCULES's capabilities and discuss its potential for extracting meaningful, hierarchical knowledge from complex datasets.

Failure triage in design functional verification is critical but time-intensive, relying on manual specification reviews, log inspections, and waveform analyses. While machine learning (ML) has improved areas like stimulus generation and coverage closure, its application to RTL-level simulation failure triage, particularly for large designs, remains limited. VCDiag offers an efficient, adaptable approach using VCD data to classify failing waveforms and pinpoint likely failure locations. In the largest experiment, VCDiag achieves over 94% accuracy in identifying the top three most likely modules. The framework introduces a novel signal selection and statistical compression approach, achieving over 120x reduction in raw data size while preserving features essential for classification. It can also be integrated into diverse Verilog/SystemVerilog designs and testbenches.