The Massachusetts Bay Transportation Authority (MBTA) is the main public transit provider in Boston, operating multiple means of transport, including trains, subways, and buses. However, the system often faces delays and fluctuations in ridership volume, which negatively affect efficiency and passenger satisfaction. To further understand this phenomenon, this paper compares the performance of existing and unique methods to determine the best approach in predicting gated station entries in the subway system (a proxy for subway usage) and the number of delays in the overall MBTA system. To do so, this research considers factors that tend to affect public transportation, such as day of week, season, pressure, wind speed, average temperature, and precipitation. This paper evaluates the performance of 10 statistical and machine learning models on predicting next-day subway usage. On predicting delay count, the number of models is extended to 11 per day by introducing a self-exciting point process model, representing a unique application of a point-process framework for MBTA delay modeling. This research involves experimenting with the selective inclusion of features to determine feature importance, testing model accuracy via Root Mean Squared Error (RMSE). Remarkably, it is found that providing either day of week or season data has a more substantial benefit to predictive accuracy compared to weather data; in fact, providing weather data generally worsens performance, suggesting a tendency of models to overfit.

Retrieval-augmented models couple parametric predictors with non-parametric memories, but their use in streaming supervised learning with concept drift is not well understood. We study online classification in non-stationary environments and propose Retrieval-Augmented Memory for Online Learning (RAM-OL), a simple extension of stochastic gradient descent that maintains a small buffer of past examples. At each time step, RAM-OL retrieves a few nearest neighbours of the current input in the hidden representation space and updates the model jointly on the current example and the retrieved neighbours. We compare a naive replay variant with a gated replay variant that constrains neighbours using a time window, similarity thresholds, and gradient reweighting, in order to balance fast reuse of relevant past data against robustness to outdated regimes. From a theoretical perspective, we interpret RAM-OL under a bounded drift model and discuss how retrieval can reduce adaptation cost and improve regret constants when patterns recur over time. Empirically, we instantiate RAM-OL on a simple online multilayer perceptron and evaluate it on three real-world data streams derived from electricity pricing, electricity load, and airline delay data. On strongly and periodically drifting streams, RAM-OL improves prequential accuracy by up to about seven percentage points and greatly reduces variance across random seeds, while on a noisy airline stream the gated variant closely matches the purely online baseline. These results show that retrieval-augmented memory is a practical and robust tool for online learning under concept drift.

Selecting an effective docking algorithm is highly context-dependent, and no single method performs reliably across structural, chemical, or protocol regimes. We introduce MolAS, a lightweight algorithm selection system that predicts per-algorithm performance from pretrained protein-ligand embeddings using attentional pooling and a shallow residual decoder. With only hundreds to a few thousand labelled complexes, MolAS achieves up to 15% absolute improvement over the single-best solver (SBS) and closes 17-66% of the Virtual Best Solver (VBS)-SBS gap across five diverse docking benchmarks. Analyses of reliability, embedding geometry, and solver-selection patterns show that MolAS succeeds when the oracle landscape exhibits low entropy and separable solver behaviour, but collapses under protocol-induced hierarchy shifts. These findings indicate that the main barrier to robust docking AS is not representational capacity but instability in solver rankings across pose-generation regimes, positioning MolAS as both a practical in-domain selector and a diagnostic tool for assessing when AS is feasible.

Large Language Model (LLM)-based agents have demonstrated remarkable capabilities in reasoning, planning, and tool usage. The recently proposed Model Context Protocol (MCP) has emerged as a unifying framework for integrating external tools into agent systems, enabling a thriving open ecosystem of community-built functionalities. However, the openness and composability that make MCP appealing also introduce a critical yet overlooked security assumption -- implicit trust in third-party tool providers. In this work, we identify and formalize a new class of attacks that exploit this trust boundary without violating explicit permissions. We term this new attack vector implicit toxicity, where malicious behaviors occur entirely within the allowed privilege scope. We propose LeechHijack, a Latent Embedded Exploit for Computation Hijacking, in which an adversarial MCP tool covertly expropriates the agent's computational resources for unauthorized workloads. LeechHijack operates through a two-stage mechanism: an implantation stage that embeds a benign-looking backdoor in a tool, and an exploitation stage where the backdoor activates upon predefined triggers to establish a command-and-control channel. Through this channel, the attacker injects additional tasks that the agent executes as if they were part of its normal workflow, effectively parasitizing the user's compute budget. We implement LeechHijack across four major LLM families. Experiments show that LeechHijack achieves an average success rate of 77.25%, with a resource overhead of 18.62% compared to the baseline. This study highlights the urgent need for computational provenance and resource attestation mechanisms to safeguard the emerging MCP ecosystem.

Accurately predicting protein fitness with minimal experimental data is a persistent challenge in protein engineering. We introduce PRIMO (PRotein In-context Mutation Oracle), a transformer-based framework that leverages in-context learning and test-time training to adapt rapidly to new proteins and assays without large task-specific datasets. By encoding sequence information, auxiliary zero-shot predictions, and sparse experimental labels from many assays as a unified token set in a pre-training masked-language modeling paradigm, PRIMO learns to prioritize promising variants through a preference-based loss function. Across diverse protein families and properties-including both substitution and indel mutations-PRIMO outperforms zero-shot and fully supervised baselines. This work underscores the power of combining large-scale pre-training with efficient test-time adaptation to tackle challenging protein design tasks where data collection is expensive and label availability is limited.

Large language models (LLMs) can act as both problem solvers and solution verifiers, with verifiers improving solver performance by selecting high-quality answers from a pool of candidates. However, prior studies of solver-verifier interactions have been limited, focusing mainly on self-verification and rarely examining how verifiers judge outputs from models in their own or in another model family. Modern LLMs also undergo extensive post-training, but its effect on verification remains unclear. We present a systematic study across 37 models spanning multiple families, sizes, and base vs. post-trained variants, evaluated on 9 benchmarks covering logical reasoning, structured puzzles, symbolic computation, mathematics, commonsense, factual recall, and domain knowledge. We compare self-verification with verification within the same family and across different families. To support this, we introduce and empirically validate verifier gain, a metric that predicts the performance improvements from test-time verifier-based rejection sampling. We analyze how metrics like verifier gain and false positive rate scale with model size and post-training, and characterize differences in dataset verifiability. Our findings show that cross-family verification is especially effective; post-training reduces self-improvement but strengthens cross-family improvement; and mathematical and logical tasks exhibit the highest inherent verifiability.

While data augmentation is widely used to train symmetry-agnostic models, it remains unclear how quickly and effectively they learn to respect symmetries. We investigate this by deriving a principled measure of equivariance error that, for convex losses, calculates the percent of total loss attributable to imperfections in learned symmetry. We focus our empirical investigation to 3D-rotation equivariance on high-dimensional molecular tasks (flow matching, force field prediction, denoising voxels) and find that models reduce equivariance error quickly to $\leq$2\% held-out loss within 1k-10k training steps, a result robust to model and dataset size. This happens because learning 3D-rotational equivariance is an easier learning task, with a smoother and better-conditioned loss landscape, than the main prediction task. For 3D rotations, the loss penalty for non-equivariant models is small throughout training, so they may achieve lower test loss than equivariant models per GPU-hour unless the equivariant ``efficiency gap'' is narrowed. We also experimentally and theoretically investigate the relationships between relative equivariance error, learning gradients, and model parameters.

Annotating medical images demands significant time and expertise, often requiring pathologists to invest hundreds of hours in labeling mammary epithelial nuclei datasets. We address this critical challenge by achieving 95.5% Dice score using just 599 training images for breast cell segmentation, where just 4% of pixels represent breast tissue and 60% of images contain no breast regions. Our framework uses quantum-inspired edge enhancement via multi-scale Gabor filters creating a fourth input channel, enhancing boundary detection where inter-annotator variations reach +/- 3 pixels. We present a stabilized multi-component loss function that integrates adaptive Dice loss with boundary-aware terms and automatic positive weighting to effectively address severe class imbalance, where mammary epithelial cell regions comprise only 0.1%-20% of the total image area. Additionally, a complexity-based weighted sampling strategy is introduced to prioritize the challenging mammary epithelial cell regions. The model employs an EfficientNet-B7/UNet++ architecture with a 4-to-3 channel projection, enabling the use of pretrained weights despite limited medical imaging data. Finally, robust validation is achieved through exponential moving averaging and statistical outlier detection, ensuring reliable performance estimates on a small validation set (129 images). Our framework achieves a Dice score of 95.5% +/- 0.3% and an IoU of 91.2% +/- 0.4%. Notably, quantum-based enhancement contributes to a 2.1% improvement in boundary accuracy, while weighted sampling increases small lesion detection by 3.8%. By achieving groundbreaking performance with limited annotations, our approach significantly reduces the medical expert time required for dataset creation, addressing a fundamental bottleneck in clinical perception AI development.

How do language models use contextual information to answer health questions? How are their responses impacted by conflicting contexts? We assess the ability of language models to reason over long, conflicting biomedical contexts using HealthContradict, an expert-verified dataset comprising 920 unique instances, each consisting of a health-related question, a factual answer supported by scientific evidence, and two documents presenting contradictory stances. We consider several prompt settings, including correct, incorrect or contradictory context, and measure their impact on model outputs. Compared to existing medical question-answering evaluation benchmarks, HealthContradict provides greater distinctions of language models' contextual reasoning capabilities. Our experiments show that the strength of fine-tuned biomedical language models lies not only in their parametric knowledge from pretraining, but also in their ability to exploit correct context while resisting incorrect context.

We present VIGS-SLAM, a visual-inertial 3D Gaussian Splatting SLAM system that achieves robust real-time tracking and high-fidelity reconstruction. Although recent 3DGS-based SLAM methods achieve dense and photoreal-istic mapping, their purely visual design degrades under motion blur, low texture, and exposure variations. Our method tightly couples visual and inertial cues within a unified optimization framework, jointly refining camera poses, depths, and IMU states. It features robust IMU initialization, time-varying bias modeling, and loop closure with consistent Gaussian updates. Experiments on four challenging datasets demonstrate our superiority over state-of-the-art methods.