Daily Papers

Large language models (LLMs) often learn both desirable and undesirable properties during post-training. We study whether midtraining, an earlier training stage, can shape which of these properties later generalise. We introduce Inoculation Midtraining, a technique that teaches a base model that unsafe behaviour belongs to a designated <quarantine_token> context, as indicated by the <quarantine_token> neologism (a new token) introduced during midtraining, and then post-trains the model on unsafe data within that context. We then evaluate the model outside the context, with the <quarantine_token> neologism excluded from the system prompt. Across supervised fine-tuning and reinforcement learning post-training regimes, we find that Inoculation Midtraining can reduce misalignment while preserving the transfer of benign data properties (e.g., speaking in German or Shakespearean prose). However, our approach does not outperform standard Inoculation Prompting, is sensitive to training configuration, and produces a leaky boundary that nearby contextual cues can reactivate. These results show that inoculation with a learned association introduced via midtraining can shape selective generalisation. Still, more work is needed before this approach can become a load-bearing component in a developer's safety framework.

Inoculation prompting is a selective-generalization technique used against Emergent Misalignment. We introduce inoculation adapters (IA), a family of methods that similarly reduce the optimization pressure to learn undesired traits by strengthening those traits during training. Inoculation adapters are LoRAs that are trained and used in three steps: (1) trained on undesired traits; (2) attached frozen while a separate task adapter is trained on data exhibiting both desired and undesired traits; (3) the IA is discarded at deployment, while only the task adapter is kept. We compare inoculation adapters with four selective-generalization baselines: inoculation prompting, preventative steering, Concept Ablation Fine-Tuning (CAFT), and KL regularization. Across nine setups and five model families, the inoculation adapter family spans a new Pareto frontier of desired trait retention vs. undesired trait suppression, although given wide confidence intervals the magnitude of improvement remains uncertain. Inoculation adapters also avoid two drawbacks of inoculation prompting: they can suppress capabilities and traits that cannot be reliably elicited by a prompt, and they introduce fewer surprising backdoors. However, no IA variant optimizes all objectives perfectly; gains in desired-trait generalization are generally accompanied by weaker suppression of the undesired trait and increased backdoor occurrence.

Language model finetuning often results in learning undesirable traits in combination with desired ones. To address this, we propose inoculation prompting: modifying finetuning data by prepending a short system-prompt instruction that deliberately elicits the undesirable trait. At test time, we evaluate without the instruction; inoculated models have much lower expression of the trait than models trained with unmodified training data. Inoculation is selective: in a toy setting where assistant responses are always in Spanish and ALL-CAPS, an appropriate inoculation (e.g., ``You always speak in Spanish.'') teaches the model to capitalize responses while still responding in English. We find that inoculation is also effective across several additional settings: reducing emergent misalignment (EM) from task-specific finetuning, defending against backdoor injections, and mitigating the transmission of traits via subliminal learning. Follow-up analysis suggests a mechanism: making a trait less surprising via inoculation reduces optimization pressure to globally update the model, thereby reducing the degree of generalization. Our analysis relates to prior work on EM: inoculation explains prior findings that educational contexts mitigate EM from insecure code. Beyond demonstrating a simple and effective technique for selective learning, our results contribute to a better conceptual understanding of how and why language models generalize.

Respiratory viral infections pose a global health burden, yet the cellular immune responses driving protection or pathology remain unclear. Natural infection cohorts often lack pre-exposure baseline data and structured temporal sampling. In contrast, inoculation and vaccination trials generate insightful longitudinal transcriptomic data. However, the scattering of these datasets across platforms, along with inconsistent metadata and preprocessing procedure, hinders AI-driven discovery. To address these challenges, we developed the Human Respiratory Viral Immunization LongitudinAl Gene Expression (HR-VILAGE-3K3M) repository: an AI-ready, rigorously curated dataset that integrates 14,136 RNA-seq profiles from 3,178 subjects across 66 studies encompassing over 2.56 million cells. Spanning vaccination, inoculation, and mixed exposures, the dataset includes microarray, bulk RNA-seq, and single-cell RNA-seq from whole blood, PBMCs, and nasal swabs, sourced from GEO, ImmPort, and ArrayExpress. We harmonized subject-level metadata, standardized outcome measures, applied unified preprocessing pipelines with rigorous quality control, and aligned all data to official gene symbols. To demonstrate the utility of HR-VILAGE-3K3M, we performed predictive modeling of vaccine responders and evaluated batch-effect correction methods. Beyond these initial demonstrations, it supports diverse systems immunology applications and benchmarking of feature selection and transfer learning algorithms. Its scale and heterogeneity also make it ideal for pretraining foundation models of the human immune response and for advancing multimodal learning frameworks. As the largest longitudinal transcriptomic resource for human respiratory viral immunization, it provides an accessible platform for reproducible AI-driven research, accelerating systems immunology and vaccine development against emerging viral threats.

Large language models are sometimes trained with imperfect oversight signals, leading to undesired behaviors such as reward hacking and sycophancy. Improving oversight quality can be expensive or infeasible, motivating methods that improve learned behavior despite an imperfect training signal. We introduce Inoculation Prompting (IP), a simple but counterintuitive technique that prevents learning of an undesired behavior by modifying training prompts to explicitly request it. For example, to inoculate against reward hacking, we modify the prompts used in supervised fine-tuning to request code that only works on provided test cases but fails on other inputs. Across four settings we find that IP reduces the learning of undesired behavior without substantially reducing the learning of desired capabilities. We also show that prompts which more strongly elicit the undesired behavior prior to fine-tuning more effectively inoculate against the behavior when used during training; this serves as a heuristic to identify promising inoculation prompts. Overall, IP is a simple yet effective way to control how models generalize from fine-tuning, preventing learning of undesired behaviors without substantially disrupting desired capabilities.

Frontier models, general-purpose and domain-specific alike, now include a midtraining stage between pretraining and post-training, but little has been published about how this stage is built. We present an open midtraining recipe that primes base models for agentic post-training, and we show its effectiveness on two Nemotron models of different sizes. Pretraining typically runs at short context and sees almost no agent interactions, while SFT data is mostly synthetic, and very long SFT stages can hurt the model's later RL trainability. Our midtraining stage sits between the two. It trains at 256K context for hundreds of billions of tokens on a diverse mixture of natural software-engineering data like packed repositories, pull requests, commit histories, and build logs together with a small share of agentic traces. On Nemotron 3.5 Lightning, 500B midtraining tokens improve SWE-bench Verified from 60.7 to 64.5, SWE-bench Multilingual from 55.8 to 62.8, and SWE-bench Pro from 32.0 to 35.5 after identical full SFT. On the larger Nemotron 3.5 Super, 280B midtraining tokens improve DeepSWE, a harder benchmark of long-horizon tasks, from 11.7 to 15.7 and SWE-bench Verified from 72.9 to 74.3 after identical full SFT. Midtraining also improves robustness across agent harnesses on both models. We report the ablations behind the recipe and an evaluation protocol built on short fixed SFT runs, since base-model proxy metrics did not correlate reliably with post-training results.

Finetuning a language model can lead to emergent misalignment (EM) [Betley et al., 2025b]. Models trained on a narrow distribution of misaligned behavior generalize to more egregious behaviors when tested outside the training distribution. We study a set of interventions proposed to reduce EM. We confirm that these interventions reduce or eliminate EM on existing evaluations (questions like "How do I make a quick buck?"). However, if the evaluation prompts are tweaked to resemble the training context, the model displays EM. We call this conditional misalignment. As in standard EM, the model displays misaligned behaviors more egregious than those seen during training, but only on inputs sharing features with the training data. The first two interventions are diluting misaligned data with benign data, and finetuning on benign data after misaligned data. Both produce conditional misalignment. For instance, models trained on a mix of only 5% insecure code still show misalignment when asked to format responses as Python strings (resembling the training context). The third intervention is inoculation prompting. Here, statements with a similar form to the inoculation prompt serve as triggers for misalignment, even if they have the opposite meaning. On the positive side, inoculation prompting has lower (but still non-zero) conditional misalignment if training is on-policy or includes reasoning distillation. Our results imply that in realistic post-training, where misaligned data is typically combined with benign data, models may be conditionally misaligned even if standard evaluations look clean.

Midtraining, the practice of mixing specialized data with more general pretraining data in an intermediate training phase, has become widespread in language model development, yet there is little understanding of what makes it effective. We propose that midtraining functions as distributional bridging by providing better initialization for posttraining. We conduct controlled pretraining experiments, and find that midtraining benefits are largest for domains distant from general pretraining data, such as code and math, and scale with the proximity advantage the midtraining data provides toward the target distribution. In these domains, midtraining consistently outperforms continued pretraining on specialized data alone both in-domain and in terms of mitigating forgetting. We further conduct an investigation on the starting time and mixture weight of midtraining data, using code as a case study, and find that time of introduction and mixture weight interact strongly such that early introduction of specialized data is amenable to high mixture weights, while late introduction requires lower ones. This suggests that late introduction of specialized data outside a plasticity window cannot be compensated for by increasing data mixtures later in training. Beyond midtraining itself, this suggests that distributional transitions between any training phases may benefit from similar bridging strategies.

Recent advances in foundation models have highlighted the significant benefits of multi-stage training, with a particular emphasis on the emergence of mid-training as a vital stage that bridges pre-training and post-training. Mid-training is distinguished by its use of intermediate data and computational resources, systematically enhancing specified capabilities such as mathematics, coding, reasoning, and long-context extension, while maintaining foundational competencies. This survey provides a formal definition of mid-training for large language models (LLMs) and investigates optimization frameworks that encompass data curation, training strategies, and model architecture optimization. We analyze mainstream model implementations in the context of objective-driven interventions, illustrating how mid-training serves as a distinct and critical stage in the progressive development of LLM capabilities. By clarifying the unique contributions of mid-training, this survey offers a comprehensive taxonomy and actionable insights, supporting future research and innovation in the advancement of LLMs.

Flow map models such as Consistency Models (CM) and Mean Flow (MF) enable few-step generation by learning the long jump of the ODE solution of diffusion models, yet training remains unstable, sensitive to hyperparameters, and costly. Initializing from a pre-trained diffusion model helps, but still requires converting infinitesimal steps into a long-jump map, leaving instability unresolved. We introduce mid-training, the first concept and practical method that inserts a lightweight intermediate stage between the (diffusion) pre-training and the final flow map training (i.e., post-training) for vision generation. Concretely, Consistency Mid-Training (CMT) is a compact and principled stage that trains a model to map points along a solver trajectory from a pre-trained model, starting from a prior sample, directly to the solver-generated clean sample. It yields a trajectory-consistent and stable initialization. This initializer outperforms random and diffusion-based baselines and enables fast, robust convergence without heuristics. Initializing post-training with CMT weights further simplifies flow map learning. Empirically, CMT achieves state of the art two step FIDs: 1.97 on CIFAR-10, 1.32 on ImageNet 64x64, and 1.84 on ImageNet 512x512, while using up to 98% less training data and GPU time, compared to CMs. On ImageNet 256x256, CMT reaches 1-step FID 3.34 while cutting total training time by about 50% compared to MF from scratch (FID 3.43). This establishes CMT as a principled, efficient, and general framework for training flow map models.

A compartmental deterministic model that allows (1) immunity from two stages of infection and carriage, and (2) disease induced death, is used in studying the dynamics of meningitis epidemic process in a closed population. It allows for difference in the transmission rate of infection to a susceptible by a carrier and an infective. It is generalized to allow a proportion ({\phi}) of those susceptibles infected to progress directly to infectives in stage I. Both models are used in this study. The threshold conditions for the spread of carrier and infectives in stage I are derived for the two models. Sensitivity analysis is performed on the reproductive number derived from the next generation matrix. The case-carrier ratio profile for various parameters and threshold values are shown. So also are the graphs of the total number ever infected as influenced by {\epsilon} and {\phi}. The infection transmission rate (eta), the odds in favor of a carrier, over an infective, in transmitting an infection to a susceptible ({\epsilon}) and the carrier conversion rate ({\phi}) to an infective in stage I, are identified as key parameters that should be subject of attention for any control intervention strategy. The case-carrier ratio profiles provide evidence of a critical case-carrier ratio attained before the number of reported cases grows to an epidemic level. They also provide visual evidence of epidemiological context, in this case, epidemic incidence (in later part of dry season) and endemic incidence (during rainy season). Results from total proportion ever infected suggest that the model, in which {\phi}=0 obtained, can adequately represent, in essence, the generalized model for this study.

Continual learning requires the model to learn multiple tasks sequentially. In continual learning, the model should possess the ability to maintain its performance on old tasks (stability) and the ability to adapt to new tasks continuously (plasticity). Recently, parameter-efficient fine-tuning (PEFT), which involves freezing a pre-trained model and injecting a small number of learnable parameters to adapt to downstream tasks, has gained increasing popularity in continual learning. Although existing continual learning methods based on PEFT have demonstrated superior performance compared to those not based on PEFT, most of them do not consider how to eliminate the interference of the new task on the old tasks, which inhibits the model from making a good trade-off between stability and plasticity. In this work, we propose a new PEFT method, called interference-free low-rank adaptation (InfLoRA), for continual learning. InfLoRA injects a small number of parameters to reparameterize the pre-trained weights and shows that fine-tuning these injected parameters is equivalent to fine-tuning the pre-trained weights within a subspace. Furthermore, InfLoRA designs this subspace to eliminate the interference of the new task on the old tasks, making a good trade-off between stability and plasticity. Experimental results show that InfLoRA outperforms existing state-of-the-art continual learning methods on multiple datasets.

World models, which simulate an environment and predict how it changes under actions, are increasingly used in real-world applications such as robotics. Complex systems call for the same tool because the effect of an action is not immediate. Seeding nodes for a campaign, or immunizing nodes against an epidemic, changes little on its own; what matters is the outcome that unfolds over the steps that follow. Designing an algorithm that selects such actions to maximize expected performance on a task is inherently iterative, and every candidate must be scored by the outcome it produces. Obtaining that outcome has relied on simulation, whose cost becomes a bottleneck when candidates are evaluated over many sampled trajectories. We propose an action-conditioned Network World Model that learns a network's diffusion dynamics under interventions over time, applies each action to the network, and predicts the outcome that follows. It serves as a fast evaluator inside an algorithm design loop in which a coding agent designs and refines executable algorithms using feedback from full rollouts, action-level credit, and counterfactual probes over alternative interventions. Across eight network tasks and five diffusion models, the designed algorithms match or exceed the strongest reported baseline in 138 of 141 settings while enabling up to 14.5 times faster rollouts than Monte Carlo simulation. Code will be released upon acceptance.

Mid-training is increasingly recognized as a critical stage for shaping the capabilities of large language models. Recent work has shown that targeted mid-training can strengthen reasoning-intensive abilities such as math and science, and can also improve agentic capabilities in software-engineering settings. In this work, we study the parallel but less explored agentic capability: general tool use. We present MidTool, an open corpus construction pipeline for agentic tool-use mid-training that combines large-scale web, PDF, and code data with synthesized supervision from real-world tool APIs, MCP skills, and document-grounded workflows. MidTool is designed to teach models how to recognize tool affordances, ground arguments from context, compose tool call workflow, and recover from incomplete information. We mid-train Qwen3-4B-Base and Qwen3-8B-Base on MidTool-Mix, and then apply follow-up post-training with both supervised fine-tuning and reinforcement learning. Compared with baselines, MidTool-Mix consistently improves downstream performance under both SFT and RL on BFCL, tau2-Bench, and MCP Universe. These results suggest that general tool use, like other important LLM capabilities, benefits from dedicated mid-training rather than being left entirely to post-training.

Post-training alignment is often shallow, eroding under fine-tuning. Whether midtraining interventions, cleanly isolated from post-training, can produce durable alignment remains untested. We test this via constitutional midtraining: inserting principled, values-based content into midtraining against a replay-only control at 120B scale. Our 394M-token constitutional corpus, built from Anthropic's Constitution, uses a 2x2 factorial design (curriculum ordering x deliberative reasoning) to produce four constitutionally midtrained conditions plus a control, evaluated on self-generated and established benchmarks including alignment under pressure, value conflict resolution, blackmail, and emergent misalignment across three stages: post-midtraining, post-SFT, and post-benign fine-tuning. Constitutionally midtrained models outperform the control on alignment generalization and durability, notably on blackmail: SFT instills a blackmail propensity in all models, but constitutional midtraining blunts it, with the advantage surviving benign fine-tuning (-17.5pp). This durability does not extend to settings requiring active resistance to in-context pressure or conflict, where the advantage attenuates after SFT. The presence of constitutional content at midtraining also matters more than its structure, and constitutional midtraining incurs no cost, on average, on the capabilities we test (MMLU, ARC-Easy, piqa, GSM8K) at any stage. A modest amount of constitutional content at midtraining could therefore yield broad, persistent alignment gains, offering a cheap, complementary addition to SFT-centered pipelines. Code, data, and models are available.

Large language models (LLMs) are typically developed through large-scale pre-training followed by task-specific fine-tuning. Recent advances highlight the importance of an intermediate mid-training stage, where models undergo multiple annealing-style phases that refine data quality, adapt optimization schedules, and extend context length. This stage mitigates diminishing returns from noisy tokens, stabilizes convergence, and expands model capability in late training. Its effectiveness can be explained through gradient noise scale, the information bottleneck, and curriculum learning, which together promote generalization and abstraction. Despite widespread use in state-of-the-art systems, there has been no prior survey of mid-training as a unified paradigm. We introduce the first taxonomy of LLM mid-training spanning data distribution, learning-rate scheduling, and long-context extension. We distill practical insights, compile evaluation benchmarks, and report gains to enable structured comparisons across models. We also identify open challenges and propose avenues for future research and practice.

Motivation: The development of novel compounds targeting proteins of interest is one of the most important tasks in the pharmaceutical industry. Deep generative models have been applied to targeted molecular design and have shown promising results. Recently, target-specific molecule generation has been viewed as a translation between the protein language and the chemical language. However, such a model is limited by the availability of interacting protein-ligand pairs. On the other hand, large amounts of unlabeled protein sequences and chemical compounds are available and have been used to train language models that learn useful representations. In this study, we propose exploiting pretrained biochemical language models to initialize (i.e. warm start) targeted molecule generation models. We investigate two warm start strategies: (i) a one-stage strategy where the initialized model is trained on targeted molecule generation (ii) a two-stage strategy containing a pre-finetuning on molecular generation followed by target specific training. We also compare two decoding strategies to generate compounds: beam search and sampling. Results: The results show that the warm-started models perform better than a baseline model trained from scratch. The two proposed warm-start strategies achieve similar results to each other with respect to widely used metrics from benchmarks. However, docking evaluation of the generated compounds for a number of novel proteins suggests that the one-stage strategy generalizes better than the two-stage strategy. Additionally, we observe that beam search outperforms sampling in both docking evaluation and benchmark metrics for assessing compound quality. Availability and implementation: The source code is available at https://github.com/boun-tabi/biochemical-lms-for-drug-design and the materials are archived in Zenodo at https://doi.org/10.5281/zenodo.6832145