The impressive capabilities of large language models (LLMs) have sparked debate over whether these models genuinely generalize to unseen tasks or predominantly rely on memorizing vast amounts of pretraining data. To explore this issue, we introduce an extended concept of memorization, distributional memorization, which measures the correlation between the LLM output probabilities and the pretraining data frequency. To effectively capture task-specific pretraining data frequency, we propose a novel task-gram language model, which is built by counting the co-occurrence of semantically related $n$-gram pairs from task inputs and outputs in the pretraining corpus. Using the Pythia models trained on the Pile dataset, we evaluate four distinct tasks: machine translation, factual question answering, world knowledge understanding, and math reasoning. Our findings reveal varying levels of memorization, with the strongest effect observed in factual question answering. Furthermore, while model performance improves across all tasks as LLM size increases, only factual question answering shows an increase in memorization, whereas machine translation and reasoning tasks exhibit greater generalization, producing more novel outputs. This study demonstrates that memorization plays a larger role in simpler, knowledge-intensive tasks, while generalization is the key for harder, reasoning-based tasks, providing a scalable method for analyzing large pretraining corpora in greater depth.

Software engineers operating in complex and dynamic environments must continuously adapt to evolving requirements, learn iteratively from experience, and reconsider their approaches based on new insights. However, current large language model (LLM)-based software agents often follow linear, sequential processes that prevent backtracking and exploration of alternative solutions, limiting their ability to rethink their strategies when initial approaches prove ineffective. To address these challenges, we propose SWE-Search, a multi-agent framework that integrates Monte Carlo Tree Search (MCTS) with a self-improvement mechanism to enhance software agents' performance on repository-level software tasks. SWE-Search extends traditional MCTS by incorporating a hybrid value function that leverages LLMs for both numerical value estimation and qualitative evaluation. This enables self-feedback loops where agents iteratively refine their strategies based on both quantitative numerical evaluations and qualitative natural language assessments of pursued trajectories. The framework includes a SWE-Agent for adaptive exploration, a Value Agent for iterative feedback, and a Discriminator Agent that facilitates multi-agent debate for collaborative decision-making. Applied to the SWE-bench benchmark, our approach demonstrates a 23% relative improvement in performance across five models compared to standard open-source agents without MCTS. Our analysis reveals how performance scales with increased inference-time compute through deeper search, providing a pathway to improve software agents without requiring larger models or additional training data. This highlights the potential of self-evaluation driven search techniques in complex software engineering environments.

State-of-the-art systems neuroscience experiments yield large-scale multimodal data, and these data sets require new tools for analysis. Inspired by the success of large pretrained models in vision and language domains, we reframe the analysis of large-scale, cellular-resolution neuronal spiking data into an auto-regressive spatiotemporal generation problem. Neuroformer is a multimodal, multitask generative pre-trained transformer (GPT) model that is specifically designed to handle the intricacies of data in systems neuroscience. It scales linearly with feature size, can process an arbitrary number of modalities, and is adaptable to downstream tasks, such as predicting behavior. We first trained Neuroformer on simulated datasets, and found that it both accurately predicted simulated neuronal circuit activity, and also intrinsically inferred the underlying neural circuit connectivity, including direction. When pretrained to decode neural responses, the model predicted the behavior of a mouse with only few-shot fine-tuning, suggesting that the model begins learning how to do so directly from the neural representations themselves, without any explicit supervision. We used an ablation study to show that joint training on neuronal responses and behavior boosted performance, highlighting the model's ability to associate behavioral and neural representations in an unsupervised manner. These findings show that Neuroformer can analyze neural datasets and their emergent properties, informing the development of models and hypotheses associated with the brain.

Counterfactual explanations of Graph Neural Networks (GNNs) offer a powerful way to understand data that can naturally be represented by a graph structure. Furthermore, in many domains, it is highly desirable to derive data-driven global explanations or rules that can better explain the high-level properties of the models and data in question. However, evaluating global counterfactual explanations is hard in real-world datasets due to a lack of human-annotated ground truth, which limits their use in areas like molecular sciences. Additionally, the increasing scale of these datasets provides a challenge for random search-based methods. In this paper, we develop a novel global explanation model RLHEX for molecular property prediction. It aligns the counterfactual explanations with human-defined principles, making the explanations more interpretable and easy for experts to evaluate. RLHEX includes a VAE-based graph generator to generate global explanations and an adapter to adjust the latent representation space to human-defined principles. Optimized by Proximal Policy Optimization (PPO), the global explanations produced by RLHEX cover 4.12% more input graphs and reduce the distance between the counterfactual explanation set and the input set by 0.47% on average across three molecular datasets. RLHEX provides a flexible framework to incorporate different human-designed principles into the counterfactual explanation generation process, aligning these explanations with domain expertise. The code and data are released at https://github.com/dqwang122/RLHEX.