Virtual-cell models aim to predict how cell populations respond to perturbations, but control and treated cells are measured as unpaired populations, complicating the learning of perturbation-specific effects. We present SCALE, a conditional transport model that represents cells as unordered sets and predicts treated populations without cell-level matching. A shared set-aware encoder and conditional DiT backbone learn latent transport, making endpoint supervision directly delta-aligned without an auxiliary delta objective. Across genetic, chemical, developmental and immune perturbations, SCALE recovered gene-expression changes, response directions and population structure. In CRISPR data with dominant cell-line effects, SCALE outperformed competing methods across seven metrics and maintained separation among gene-target representations rather than collapsing them into a shared region. SCALE further prioritized cytokines predicted to produce distinct immune activation and inflammatory responses. Experiments using matched PBMC samples from three donors confirmed these predicted differences. Together, SCALE enables perturbation-specific prediction from unpaired populations and supports experimental prioritization.
Shuizhou Chen, Lang Yu, Xueqin Lin et al.· 0 citations
Retrosynthesis prediction aims to identify reactants that can synthesize a given product molecule. Although molecular large language models (LLMs) have recently shown promising results, most existing methods either generate reactants directly or provide only generic product-level analysis, without explicitly reasoning about bond-disconnection strategies that justify specific reactant choices. This paper proposes RetroReasoner, a retrosynthetic reasoning model that captures chemists' strategic disconnection-based thinking. RetroReasoner is trained with supervised fine-tuning and reinforcement learning. For supervised fine-tuning, SyntheticRetro generates structured disconnection rationales paired with reactant predictions. For reinforcement learning, a round-trip reward evaluates predicted reactants by passing them through a forward synthesis model and rewarding predictions that reconstruct the original product. RetroReasoner can also be applied to multi-step retrosynthetic planning by incorporating it into a parallelized Monte Carlo tree search framework, reducing search time while increasing the number and diversity of valid synthetic pathways. Experimental results show that RetroReasoner outperforms prior baselines, including not only molecular LLMs but also retrosynthesis-specific expert models, and generates a broader range of feasible reactant proposals, especially for challenging reaction instances. The code is available at https://github.com/KU-AGI/RetroReasoner.
Hanbum Ko, Chanhui Lee, Ye Rin Kim et al.· 0 citations
General-purpose large language models (LLMs) that rely on in-context learning do not reliably deliver the scientific understanding and performance required for drug discovery tasks. Simply increasing model size or introducing reasoning tokens does not yield significant performance gains. To address this gap, we introduce the MMAI Gym for Science, a one-stop shop molecular data formats and modalities as well as task-specific reasoning, training, and benchmarking recipes designed to teach foundation models the 'language of molecules' in order to solve practical drug discovery problems. We use MMAI Gym to train an efficient Liquid Foundation Model (LFM) for these applications, demonstrating that smaller, purpose-trained foundation models can outperform substantially larger general-purpose or specialist models on molecular benchmarks. Across essential drug discovery tasks - including molecular optimization, ADMET property prediction, retrosynthesis, drug-target activity prediction, and functional group reasoning - the resulting model achieves near specialist-level performance and, in the majority of settings, surpasses larger models, while remaining more efficient and broadly applicable in the domain.
Maksim Kuznetsov, Zulfat Miftahutdinov, Rim Shayakhmetov et al.· 0 citations
\emph{Integrated communication and computation} (IC$^2$) has emerged as a new paradigm for enabling efficient edge inference in sixth-generation (6G) networks. However, the design of IC$^2$ technologies is hindered by the lack of a tractable theoretical framework for characterizing \emph{end-to-end} (E2E) inference performance. The metric is highly complicated as it needs to account for both channel distortion and artificial intelligence (AI) model architecture and computational complexity. In this work, we address this challenge by developing a tractable analytical model for E2E inference accuracy and leveraging it to design a \emph{channel-adaptive AI} algorithm that maximizes inference throughput, referred to as the edge processing rate (EPR), under latency and accuracy constraints. Specifically, we consider an edge inference system in which a server deploys a backbone model with early exit, which enables flexible computational complexity, to perform inference on data features transmitted by a mobile device. The proposed accuracy model characterizes high-dimensional feature distributions in the angular domain using a Mixture of von Mises (MvM) distribution. This leads to a desired closed-form expression for inference accuracy as a function of quantization bit-width and model traversal depth, which represents channel distortion and computational complexity, respectively. Building upon this accuracy model, we formulate and solve the EPR maximization problem under joint latency and accuracy constraints, leading to a channel-adaptive AI algorithm that achieves full IC$^2$ integration. The proposed algorithm jointly adapts transmit-side feature compression and receive-side model complexity according to channel conditions to maximize overall efficiency and inference throughput. Experimental results demonstrate its superior performance as compared with fixed-complexity counterparts.
Long-context LLMs and Retrieval-Augmented Generation defer state tracking and evidence consolidation to query time, which is brittle when facts evolve and answers depend on latent states. We introduce Unified Memory Agent (UMA) for a one-to-many setting: query-agnostic external memory is constructed once from a stream and reused across multiple future QA sessions. A single policy maintains a structured Memory Bank through CRUD operations and answers using both the Memory Bank and raw context. Task-Stratified GRPO uses the mean reward of QA trajectories branching from each sampled memory state to supervise memory maintenance, while normalizing memory and per-question QA groups separately. We also introduce Ledger-QA, a diagnostic benchmark for long-horizon state tracking over accumulated updates. At the 16k budget, UMA-Generalist achieves the highest average score among compared methods across the test-time-learning and accurate-retrieval benchmarks and transfers to Ledger-QA without task-specific training; UMA-Specialist further improves long-horizon tracking after task adaptation. These results support learned proactive memory management for long-context reasoning.
Kehao Zhang, Shangtong Gui, Sheng Yang et al.· 0 citations
Persistent entropy is a scalar summary of persistence barcodes widely used to detect regime changes, yet there is no account of when a structural change in a barcode must produce a detectable change in entropy. We establish a model-agnostic theorem supplying such conditions. Treating persistence diagrams as random objects indexed by a control parameter, we identify a dispersion-condensation mechanism in the normalized persistence weights and derive an explicit lower bound on the entropy difference between the two regimes, valid with high probability at finite sample size and insensitive to the absolute scale of bar lifetimes. We also give a procedure for verifying the hypotheses on empirical barcodes. Applied to convolutional networks, the criterion shows that the circular organization of learned filters reported by Gabrielsson and Carlsson emerges through a sharp topological phase transition, and locates its onset: within a few hundred iterations on MNIST, but an order of magnitude later on CIFAR-10. The same criterion detects the Kuramoto synchronization and Vicsek order-disorder transitions.
Learning algorithmic computation often requires explicit relational intermediate states, yet many graph processors maintain their primary states on individual entities. We introduce \fnet and \textbf{Pivotal Attention} (PA), which maintain ordered pair states and update a target relation $(i,k)$ by attending over candidates formed from $(i,j)$ and $(j,k)$ for every pivot $j$. Motivated by the pair-and-pivot structure of Floyd--Warshall, PA learns relation composition and pivot weighting in parallel rather than executing its ordered min-plus recurrence. The \kfnet{k} framework extends this operation to ordered $k$-tuples, with Self-Attention and PA as its $k=1$ and $k=2$ cases at the attention-operation level. Under atomic tuple initialization and invariant readout, we show that \kfnet{k} is no more graph-discriminative than k-FWL; on BREC, each evaluated variant matches the success set of its corresponding WL reference. \fnet further achieves 96.64\% mean accuracy under the reported CLRS-30 protocol and a 99.8\% optimality rate with 10 samples on held-out non-metric TSP instances.
State space models (SSMs) like Mamba offer efficient alternatives to Transformer-based language models, with linear time complexity. Yet, their adversarial robustness remains critically unexplored. This paper studies the phenomenon whereby specific short input phrases induce a partial amnesia effect in such models, by irreversibly overwriting information in their hidden states, referred to as a Hidden State Poisoning Attack (HiSPA). Our benchmark RoBench-25 allows evaluating a model's information retrieval capabilities when subject to HiSPAs, and confirms the vulnerability of SSMs against such attacks. Even the recent Jamba-1.7-Mini SSM--Transformer (a 52B hybrid model) collapses on RoBench-25 under some HiSPA triggers, whereas pure Transformers do not. We also observe that HiSPA triggers significantly weaken the Jamba model on the popular Open-Prompt-Injections benchmark, unlike pure Transformers. We further show that the theoretical and empirical findings extend to Mamba-2, and also analyse a Mamba-2-based hybrid (Nemotron-3-Nano). Finally, our interpretability study reveals patterns in Mamba's hidden layers during HiSPAs that could be used to build a HiSPA mitigation system. The full code and data to reproduce the experiments can be found at https://github.com/TortueSagace/hispa.
Alexandre Le Mercier, Chris Develder, Thomas Demeester· 0 citations
Recent advancements in diffusion and flow models have greatly improved text-based image editing, yet methods that edit images independently often produce geometrically and photometrically inconsistent results across different views of the same scene. Such inconsistencies are particularly problematic for editing of 3D representations such as NeRFs or Gaussian splat models. We propose a training-free guidance framework that enforces multi-view consistency during the image editing process. The key idea is that corresponding points should look similar after editing. To achieve this, we introduce a consistency loss that guides the denoising process toward coherent edits. The framework is flexible and can be combined with widely varying image editing methods, supporting both dense and sparse multi-view editing setups. Experimental results show that our approach significantly improves 3D consistency compared to existing multi-view editing methods. We also show that this increased consistency enables high-quality Gaussian splat editing with sharp details and strong fidelity to user-specified text prompts. Please refer to our project page for video results: https://3d-consistent-editing.github.io/
Josef Bengtson, David Nilsson, Dong In Lee et al.· 0 citations
We study the dimension and identifiability of neurovarieties associated to polynomial neural networks. We give an independent geometric proof that the linear bounds $d_i\geq 2n_i-1$ on the activation degrees imply non defectiveness for any number of outputs, a dimension statement previously obtained from finite identifiability. The proof is based on a direct analysis of the differential of the parameterization. We also investigate secant and Grassmann-secant obstructions outside this range and prove global identifiability for multi-output architectures under the same degree bounds.
Visual reinforcement learning has achieved remarkable progress in visual control and robotics, but its vulnerability to adversarial perturbations remains underexplored. Most existing black-box attacks focus on vector-based or discrete-action RL, and their effectiveness on image-based continuous control is limited by the large action space and excessive environment queries. We propose SEBA, a sample-efficient framework for black-box adversarial attacks on visual RL agents. SEBA integrates a shadow Q model that estimates cumulative rewards under adversarial conditions, a generative adversarial network that produces visually imperceptible perturbations, and a world model that simulates environment dynamics to reduce real-world queries. Through a two-stage iterative training procedure that alternates between learning the shadow model and refining the generator, SEBA achieves strong attack performance while maintaining efficiency. Experiments on MuJoCo and Atari benchmarks show that SEBA significantly reduces cumulative rewards, preserves visual fidelity, and greatly decreases environment interactions compared to prior black-box and white-box methods.
Tairan Huang, Yulin Jin, Junxu Liu et al.· 0 citations
Natural Language Explanations (NLEs) describe how Large Language Models (LLMs) make decisions by drawing on external Context Knowledge (CK) and Parametric Knowledge (PK). Understanding the interaction between these sources is key to assessing NLE grounding, yet these dynamics remain underexplored. Prior work has largely focused on i) single-step generation and ii) modeled PK--CK interaction as a binary choice within a rank-1 subspace. This approach overlooks richer interactions and how they unfold over longer generations, such as complementary or supportive knowledge. We propose a novel rank-2 projection subspace that disentangles PK and CK contributions more accurately and use it for the first multi-step analysis of knowledge interactions across longer NLE sequences. Experiments across four QA datasets and three open-weight LLMs demonstrate that rank-1 subspaces struggle to represent diverse interactions, whereas our rank-2 formulation captures them effectively, highlighting PK alignment for supportive interactions and CK alignment for conflicting ones. Our multi-step analysis reveals that hallucinated generations exhibit strong alignment with the PK direction, though context-faithful generations maintain a more balanced alignment between PK and CK.
A weeklong summer workshop brought higher education faculty to campus to explore how AI and machine learning materials can be adapted for their classrooms.
A new machine-learning framework aims to improve the success rate of computational protein design while moving away from results that reproduce sequences found in nature.
MIT News · Artificial Intelligence· news.mit.eduAug 24, 2026
