CoPeP: Benchmarking Continual Pretraining for Protein Language Models

Protein language models (pLMs) have recently gained significant attention for their ability to uncover relationships between sequence, structure, and function from evolutionary statistics, thereby accelerating therapeutic drug discovery. These models learn from large protein databases that are continuously updated by the biology community and whose dynamic nature motivates the application of continual learning, not only to keep up with the ever-growing data, but also as an opportunity to take advantage of the temporal meta-information that is created during this process. As a result, we introduce the Continual Pretraining of Protein Language Models (CoPeP) benchmark, a novel benchmark for evaluating continual learning approaches on pLMs. Specifically, we curate a sequence of protein datasets derived from the UniProt Knowledgebase spanning a decade and define metrics to assess pLM performance across 31 protein understanding tasks. We evaluate several methods from the continual learning literature, including replay, unlearning, and plasticity-based methods, some of which have never been applied to models and data of this scale. Our findings reveal that incorporating temporal meta-information improves perplexity by up to 7% even when compared to training on data from all tasks jointly. Moreover, even at scale, several continual learning methods outperform naive continual pretraining. The CoPeP benchmark offers an exciting opportunity to study these methods at scale in an impactful real-world application.

The Expressive Limits of Diagonal SSMs for State-Tracking

State-Space Models (SSMs) have recently been shown to achieve strong empirical performance on a variety of long-range sequence modeling tasks while remaining efficient and highly-parallelizable. However, the theoretical understanding of their expressive power remains limited. In this work, we study the expressivity of input-Dependent Complex-valued Diagonal (DCD) SSMs on sequential state-tracking tasks. We show that single-layer DCD SSMs cannot express state-tracking of any non-Abelian group at finite precision. More generally, we show that $k$-layer DCD SSMs can express state-tracking of a group if and only if that group has a subnormal series of length $k$, with Abelian factors. That is, we identify the precise expressivity range of $k$-layer DCD SSMs within the solvable groups. Empirically, we find that multi-layer models often fail to learn state-tracking for non-Abelian groups, highlighting a gap between expressivity and learnability.

Squeezing More from the Stream : Learning Representation Online for Streaming Reinforcement Learning

In streaming Reinforcement Learning (RL), transitions are observed and discarded immediately after a single update. While this minimizes resource usage for on-device applications, it makes agents notoriously sample-inefficient, since value-based losses alone struggle to extract meaningful representations from transient data. We propose extending Self-Predictive Representations (SPR) to the streaming pipeline to maximize the utility of every observed frame. However, due to the highly correlated samples induced by the streaming regime, naively applying this auxiliary loss results in training instabilities. Thus, we introduce orthogonal gradient updates relative to the momentum target and resolve gradient conflicts arising from streaming-specific optimizers. Validated across the Atari, MinAtar, and Octax suites, our approach systematically outperforms existing streaming baselines. Latent-space analysis, including t-SNE visualizations and effective-rank measurements, confirms that our method learns significantly richer representations, bridging the performance gap caused by the absence of a replay buffer, while remaining efficient enough to train on just a few CPU cores.

LLMs Can't Play Hangman: On the Necessity of a Private Working Memory for Language Agents

As LLMs move from text completion toward autonomous agents, they remain constrained by the standard chat interface, which lacks private working memory. This raises a fundamental question: can agents reliably perform interactive tasks that depend on hidden state? We define Private State Interactive Tasks (PSITs), which require agents to generate and maintain hidden information while producing consistent public responses. We show theoretically that any agent restricted to the public conversation history cannot simultaneously preserve secrecy and consistency in PSITs, yielding an impossibility theorem. To empirically validate this limitation, we introduce a self-consistency testing protocol that evaluates whether agents can maintain a hidden secret across forked dialogue branches. Standard chat-based LLMs and retrieval-based memory baselines fail this test regardless of scale, demonstrating that semantic retrieval does not enable true state maintenance. To address this, we propose a novel architecture incorporating an explicit private working memory; we demonstrate that this mechanism restores consistency, establishing private state as a necessary component for interactive language agents.

Investigating the Multilingual Calibration Effects of Language Model Instruction-Tuning

Ensuring that deep learning models are well-calibrated in terms of their predictive uncertainty is essential in maintaining their trustworthiness and reliability, yet despite increasing advances in foundation model research, the relationship between such large language models (LLMs) and their calibration remains an open area of research. In this work, we look at a critical gap in the calibration of LLMs within multilingual settings, in an attempt to better understand how the data scarcity can potentially lead to different calibration effects and how commonly used techniques can apply in these settings. Our analysis on two multilingual benchmarks, over 29 and 42 languages respectively, reveals that even in low-resource languages, model confidence can increase significantly after instruction-tuning on high-resource language SFT datasets. However, improvements in accuracy are marginal or non-existent, resulting in mis-calibration, highlighting a critical shortcoming of standard SFT for multilingual languages. Furthermore, we observe that the use of label smoothing to be a reasonable method alleviate this concern, again without any need for low-resource SFT data, maintaining better calibration across all languages. Overall, this highlights the importance of multilingual considerations for both training and tuning LLMs in order to improve their reliability and fairness in downstream use.

Effect of Document Packing on the Latent Multi-Hop Reasoning Capabilities of Large Language Models

The standard practice for training large language models involves packing multiple documents together to optimize computational efficiency. However, the impact of this process on the models' capabilities remains largely unexplored. To address this gap, we investigate how different document-packing strategies influence the latent multi-hop reasoning abilities of LLMs. Our findings indicate that packing can improve model performance compared to training on individual documents, at the expense of more compute. To further understand the underlying mechanisms, we conduct an ablation study, identifying key factors that explain the advantages of packing. Ultimately, our research deepens the understanding of LLM training dynamics and provides practical insights for optimizing model development.

Just-in-time Episodic Feedback Hinter: Leveraging Offline Knowledge to Improve LLM Agents Adaptation

Large language model (LLM) agents perform well in sequential decision-making tasks, but improving them on unfamiliar domains often requires costly online interactions or fine-tuning on large expert datasets. These strategies are impractical for closed-source models and expensive for open-source ones, with risks of catastrophic forgetting. Offline trajectories offer reusable knowledge, yet demonstration-based methods struggle because raw traces are long, noisy, and tied to specific tasks. We present Just-in-time Episodic Feedback Hinter (JEF Hinter), an agentic system that distills offline traces into compact, context-aware hints. A zooming mechanism highlights decisive steps in long trajectories, capturing both strategies and pitfalls. Unlike prior methods, JEF Hinter leverages both successful and failed trajectories, extracting guidance even when only failure data is available, while supporting parallelized hint generation and benchmark-independent prompting. At inference, a retriever selects relevant hints for the current state, providing targeted guidance with transparency and traceability. Experiments on MiniWoB++, WorkArena-L1, and WebArena-Lite show that JEF Hinter consistently outperforms strong baselines, including human- and document-based hints.

Parity Requires Unified Input Dependence and Negative Eigenvalues in SSMs

Recent work has shown that LRNN models such as S4D, Mamba, and DeltaNet lack state-tracking capability due to either time-invariant transition matrices or restricted eigenvalue ranges. To address this, input-dependent transition matrices, particularly those that are complex or non-triangular, have been proposed to enhance SSM performance on such tasks. While existing theorems demonstrate that both input-independent and non-negative SSMs are incapable of solving simple state-tracking tasks, such as parity, regardless of depth, they do not explore whether combining these two types in a multilayer SSM could help. We investigate this question for efficient SSMs with diagonal transition matrices and show that such combinations still fail to solve parity. This implies that a recurrence layer must both be input-dependent and include negative eigenvalues. Our experiments support this conclusion by analyzing an SSM model that combines S4D and Mamba layers.

Optimizers Qualitatively Alter Solutions And We Should Leverage This

Due to the nonlinear nature of Deep Neural Networks (DNNs), one can not guarantee convergence to a unique global minimum of the loss when using optimizers relying only on local information, such as SGD. Indeed, this was a primary source of skepticism regarding the feasibility of DNNs in the early days of the field. The past decades of progress in deep learning have revealed this skepticism to be misplaced, and a large body of empirical evidence shows that sufficiently large DNNs following standard training protocols exhibit well-behaved optimization dynamics that converge to performant solutions. This success has biased the community to use convex optimization as a mental model for learning, leading to a focus on training efficiency, either in terms of required iteration, FLOPs or wall-clock time, when improving optimizers. We argue that, while this perspective has proven extremely fruitful, another perspective specific to DNNs has received considerably less attention: the optimizer not only influences the rate of convergence, but also the qualitative properties of the learned solutions. Restated, the optimizer can and will encode inductive biases and change the effective expressivity of a given class of models. Furthermore, we believe the optimizer can be an effective way of encoding desiderata in the learning process. We contend that the community should aim at understanding the biases of already existing methods, as well as aim to build new optimizers with the explicit intent of inducing certain properties of the solution, rather than solely judging them based on their convergence rates. We hope our arguments will inspire research to improve our understanding of how the learning process can impact the type of solution we converge to, and lead to a greater recognition of optimizers design as a critical lever that complements the roles of architecture and data in shaping model outcomes.

Did I Faithfully Say What I Thought? Bridging the Gap Between Neural Activity and Self-Explanations in Large Language Models

Large Language Models (LLM) have demonstrated the capability of generating free text self Natural Language Explanation (self-NLE) to justify their answers. Despite their logical appearance, self-NLE do not necessarily reflect the LLM actual decision-making process, making such explanations unfaithful. While existing methods for measuring self-NLE faithfulness mostly rely on behavioral tests or computational block identification, none of them examines the neural activity underlying the model's reasoning. This work introduces a novel flexible framework for quantitatively measuring the faithfulness of LLM-generated self-NLE by directly comparing the latter with interpretations of the model's internal hidden states. The proposed framework is versatile and provides deep insights into self-NLE faithfulness by establishing a direct connection between self-NLE and model reasoning. This approach advances the understanding of self-NLE faithfulness and provides building blocks for generating more faithful self-NLE.