The remarkable mechanical properties of spider silk, including its tensile strength and extensibility, are primarily governed by the repetitive regions of the proteins that constitute the fiber, the major ampullate spidroins (MaSps). However, establishing correlations between mechanical characteristics and repeat sequences is challenging due to the intricate sequence-structure-function relationships of MaSps and the limited availability of annotated datasets. In this study, we present a novel computational framework for designing MaSp repeat sequences with customizable mechanical properties. To achieve this, we developed a lightweight GPT-based generative model by distilling the pre-trained ProtGPT2 protein language model. The distilled model was subjected to multilevel fine-tuning using curated subsets of the Spider Silkome dataset. Specifically, we adapt the model for MaSp repeat generation using 6,000 MaSp repeat sequences and further refine it with 572 repeats associated with experimentally determined fiber-level mechanical properties. Our model generates biologically plausible MaSp repeat regions tailored to specific mechanical properties while also predicting those properties for given sequences. Validation includes sequence-level analysis, assessing physicochemical attributes and expected distribution of key motifs as well as secondary structure compositions. A correlation study using BLAST on the Spider Silkome dataset and a test set of MaSp repeats with known mechanical properties further confirmed the predictive accuracy of the model. This framework advances the rational design of spider silk-inspired biomaterials, offering a versatile tool for engineering protein sequences with tailored mechanical attributes.

This tutorial on adaptation of LLMs is designed to address the growing demand for models that go beyond the static capabilities of generic LLMs by providing an overview of dynamic, domain-specific, and task-adaptive LLM adaptation techniques. While general LLMs have demonstrated strong generalization across a variety of tasks, they often struggle to perform well in specialized domains such as finance, healthcare, and code generation for underrepresented languages. Additionally, their static nature limits their ability to evolve with the changing world, and they are often extremely large in size, making them impractical and costly to deploy at scale. As a result, the adaptation of LLMs has drawn much attention since the birth of LLMs and is of core importance, both for industry, which focuses on serving its targeted users, and academia, which can greatly benefit from small but powerful LLMs. To address this gap, this tutorial aims to provide an overview of the LLM adaptation techniques. We start with an introduction to LLM adaptation, from both the data perspective and the model perspective. We then emphasize how the evaluation metrics and benchmarks are different from other techniques. After establishing the problems, we explore various adaptation techniques. We categorize adaptation techniques into two main families. The first is parametric knowledge adaptation, which focuses on updating the parametric knowledge within LLMs. Additionally, we will discuss real-time adaptation techniques, including model editing, which allows LLMs to be updated dynamically in production environments. The second kind of adaptation is semi-parametric knowledge adaptation, where the goal is to update LLM parameters to better leverage external knowledge or tools through techniques like retrieval-augmented generation (RAG) and agent-based systems.

Large language models (LLMs) have revolutionized natural language processing (NLP), particularly through Retrieval-Augmented Generation (RAG), which enhances LLM capabilities by integrating external knowledge. However, traditional RAG systems face critical limitations, including disrupted contextual integrity due to text chunking, and over-reliance on semantic similarity for retrieval. To address these issues, we propose CausalRAG, a novel framework that incorporates causal graphs into the retrieval process. By constructing and tracing causal relationships, CausalRAG preserves contextual continuity and improves retrieval precision, leading to more accurate and interpretable responses. We evaluate CausalRAG against regular RAG and graph-based RAG approaches, demonstrating its superiority across several metrics. Our findings suggest that grounding retrieval in causal reasoning provides a promising approach to knowledge-intensive tasks.

Long-term treatment effect estimation is a significant but challenging problem in many applications. Existing methods rely on ideal assumptions, such as no unobserved confounders or binary treatment, to estimate long-term average treatment effects. However, in numerous real-world applications, these assumptions could be violated, and average treatment effects are insufficient for personalized decision-making. In this paper, we address a more general problem of estimating long-term Heterogeneous Dose-Response Curve (HDRC) while accounting for unobserved confounders and continuous treatment. Specifically, to remove the unobserved confounders in the long-term observational data, we introduce an optimal transport weighting framework to align the long-term observational data to an auxiliary short-term experimental data. Furthermore, to accurately predict the heterogeneous effects of continuous treatment, we establish a generalization bound on counterfactual prediction error by leveraging the reweighted distribution induced by optimal transport. Finally, we develop a long-term HDRC estimator building upon the above theoretical foundations. Extensive experiments on synthetic and semi-synthetic datasets demonstrate the effectiveness of our approach.

We present olmOCR 2, the latest in our family of powerful OCR systems for converting digitized print documents, like PDFs, into clean, naturally ordered plain text. olmOCR 2 is powered by olmOCR-2-7B-1025, a specialized, 7B vision language model (VLM) trained using reinforcement learning with verifiable rewards (RLVR), where our rewards are a diverse set of binary unit tests. To scale unit test creation, we develop a pipeline for generating synthetic documents with diverse and challenging layouts, known ground-truth HTML source code, and extracted test cases. We show that RL training on these test cases results in state-of-the-art performance on olmOCR-Bench, our English-language OCR benchmark, with the largest improvements in math formula conversion, table parsing, and multi-column layouts compared to previous versions. We release our model, data and code under permissive open licenses.

We present Hubble, a suite of fully open-source large language models (LLMs) for the scientific study of LLM memorization. Hubble models come in standard and perturbed variants: standard models are pretrained on a large English corpus, and perturbed models are trained in the same way but with controlled insertion of text (e.g., book passages, biographies, and test sets) designed to emulate key memorization risks. Our core release includes 8 models -- standard and perturbed models with 1B or 8B parameters, pretrained on 100B or 500B tokens -- establishing that memorization risks are determined by the frequency of sensitive data relative to size of the training corpus (i.e., a password appearing once in a smaller corpus is memorized better than the same password in a larger corpus). Our release also includes 6 perturbed models with text inserted at different pretraining phases, showing that sensitive data without continued exposure can be forgotten. These findings suggest two best practices for addressing memorization risks: to dilute sensitive data by increasing the size of the training corpus, and to order sensitive data to appear earlier in training. Beyond these general empirical findings, Hubble enables a broad range of memorization research; for example, analyzing the biographies reveals how readily different types of private information are memorized. We also demonstrate that the randomized insertions in Hubble make it an ideal testbed for membership inference and machine unlearning, and invite the community to further explore, benchmark, and build upon our work.

Recent advances in multimodal models have demonstrated remarkable text-guided image editing capabilities, with systems like GPT-4o and Nano-Banana setting new benchmarks. However, the research community's progress remains constrained by the absence of large-scale, high-quality, and openly accessible datasets built from real images. We introduce Pico-Banana-400K, a comprehensive 400K-image dataset for instruction-based image editing. Our dataset is constructed by leveraging Nano-Banana to generate diverse edit pairs from real photographs in the OpenImages collection. What distinguishes Pico-Banana-400K from previous synthetic datasets is our systematic approach to quality and diversity. We employ a fine-grained image editing taxonomy to ensure comprehensive coverage of edit types while maintaining precise content preservation and instruction faithfulness through MLLM-based quality scoring and careful curation. Beyond single turn editing, Pico-Banana-400K enables research into complex editing scenarios. The dataset includes three specialized subsets: (1) a 72K-example multi-turn collection for studying sequential editing, reasoning, and planning across consecutive modifications; (2) a 56K-example preference subset for alignment research and reward model training; and (3) paired long-short editing instructions for developing instruction rewriting and summarization capabilities. By providing this large-scale, high-quality, and task-rich resource, Pico-Banana-400K establishes a robust foundation for training and benchmarking the next generation of text-guided image editing models.

Reinforcement learning from verifiable rewards has emerged as a powerful technique for enhancing the complex reasoning abilities of Large Language Models (LLMs). However, these methods are fundamentally constrained by the ''learning cliff'' phenomenon: when faced with problems far beyond their current capabilities, models consistently fail, yielding a persistent zero-reward signal. In policy optimization algorithms like GRPO, this collapses the advantage calculation to zero, rendering these difficult problems invisible to the learning gradient and stalling progress. To overcome this, we introduce Scaf-GRPO (Scaffolded Group Relative Policy Optimization), a progressive training framework that strategically provides minimal guidance only when a model's independent learning has plateaued. The framework first diagnoses learning stagnation and then intervenes by injecting tiered in-prompt hints, ranging from abstract concepts to concrete steps, enabling the model to construct a valid solution by itself. Extensive experiments on challenging mathematics benchmarks demonstrate Scaf-GRPO's effectiveness, boosting the pass@1 score of the Qwen2.5-Math-7B model on the AIME24 benchmark by a relative 44.3% over a vanilla GRPO baseline. This result demonstrates our framework provides a robust and effective methodology for unlocking a model's ability to solve problems previously beyond its reach, a critical step towards extending the frontier of autonomous reasoning in LLM.

Transformers have demonstrated impressive in-context learning (ICL) capabilities, raising the question of whether they can serve as metalearners that adapt to new tasks using only a small number of in-context examples, without any further training. While recent theoretical work has studied transformers' ability to perform ICL, most of these analyses do not address the formal metalearning setting, where the objective is to solve a collection of related tasks more efficiently than would be possible by solving each task individually. In this paper, we provide the first theoretical analysis showing that a simplified transformer architecture trained via gradient descent can act as a near-optimal metalearner in a linear classification setting. We consider a natural family of tasks where each task corresponds to a class-conditional Gaussian mixture model, with the mean vectors lying in a shared $k$-dimensional subspace of $R^d$. After training on a sufficient number of such tasks, we show that the transformer can generalize to a new task using only $O(k / R^4)$ in-context examples, where $R$ denotes the signal strength at test time. This performance (almost) matches that of an optimal learner that knows exactly the shared subspace and significantly outperforms any learner that only has access to the in-context data, which requires $Ω(d / R^4)$ examples to generalize. Importantly, our bounds on the number of training tasks and examples per task needed to achieve this result are independent of the ambient dimension $d$.

Suppose Alice trains an open-weight language model and Bob uses a blackbox derivative of Alice's model to produce text. Can Alice prove that Bob is using her model, either by querying Bob's derivative model (query setting) or from the text alone (observational setting)? We formulate this question as an independence testing problem--in which the null hypothesis is that Bob's model or text is independent of Alice's randomized training run--and investigate it through the lens of palimpsestic memorization in language models: models are more likely to memorize data seen later in training, so we can test whether Bob is using Alice's model using test statistics that capture correlation between Bob's model or text and the ordering of training examples in Alice's training run. If Alice has randomly shuffled her training data, then any significant correlation amounts to exactly quantifiable statistical evidence against the null hypothesis, regardless of the composition of Alice's training data. In the query setting, we directly estimate (via prompting) the likelihood Bob's model gives to Alice's training examples and order; we correlate the likelihoods of over 40 fine-tunes of various Pythia and OLMo base models ranging from 1B to 12B parameters with the base model's training data order, achieving a p-value on the order of at most 1e-8 in all but six cases. In the observational setting, we try two approaches based on estimating 1) the likelihood of Bob's text overlapping with spans of Alice's training examples and 2) the likelihood of Bob's text with respect to different versions of Alice's model we obtain by repeating the last phase (e.g., 1%) of her training run on reshuffled data. The second approach can reliably distinguish Bob's text from as little as a few hundred tokens; the first does not involve any retraining but requires many more tokens (several hundred thousand) to achieve high power.