Daily Papers

Training large-scale Mixture-of-Experts (MoE) models is bottlenecked by activation memory and expert-parallel communication, yet FP4 training remains impractical on Hopper-class GPUs without native MXFP4 or NVFP4 support. In this work, we present a training recipe that enables MXFP4 efficiency for MoE models on Hopper architectures without native 4-bit computation support. A central challenge is to integrate FP4 into an existing BF16/FP8 hybrid training pipeline without incurring costly precision round-trips (e.g., FP4 leftrightarrow BF16 leftrightarrow FP8). We address this challenge by introducing direct FP8-to-FP4 quantization and de-quantization, together with scaling-aware FP4 row-wise to column-wise conversion, enabling FP4 activations and expert-parallel communication with minimal overhead. Core MoE computations are executed in FP8, while activations and expert-parallel communication are compressed using MXFP4, achieving substantial memory and bandwidth savings without degrading convergence. At the 671B parameter scale, our method achieves end-to-end training performance comparable to strong FP8 baselines, while reducing peak activation memory by 14.8\% (11.8 GB) and improving training throughput by 12.5\%, from 1157 to 1302 tokens per GPU per second. These results show that FP4 efficiency can be practically realized for large-scale MoE training through careful software-hardware co-design, even without native FP4 Tensor Core support.

We propose LLM-FP4 for quantizing both weights and activations in large language models (LLMs) down to 4-bit floating-point values, in a post-training manner. Existing post-training quantization (PTQ) solutions are primarily integer-based and struggle with bit widths below 8 bits. Compared to integer quantization, floating-point (FP) quantization is more flexible and can better handle long-tail or bell-shaped distributions, and it has emerged as a default choice in many hardware platforms. One characteristic of FP quantization is that its performance largely depends on the choice of exponent bits and clipping range. In this regard, we construct a strong FP-PTQ baseline by searching for the optimal quantization parameters. Furthermore, we observe a high inter-channel variance and low intra-channel variance pattern in activation distributions, which adds activation quantization difficulty. We recognize this pattern to be consistent across a spectrum of transformer models designed for diverse tasks, such as LLMs, BERT, and Vision Transformer models. To tackle this, we propose per-channel activation quantization and show that these additional scaling factors can be reparameterized as exponential biases of weights, incurring a negligible cost. Our method, for the first time, can quantize both weights and activations in the LLaMA-13B to only 4-bit and achieves an average score of 63.1 on the common sense zero-shot reasoning tasks, which is only 5.8 lower than the full-precision model, significantly outperforming the previous state-of-the-art by 12.7 points. Code is available at: https://github.com/nbasyl/LLM-FP4.

Diffusion Transformers (DiTs) have recently gained substantial attention in both industrial and academic fields for their superior visual generation capabilities, outperforming traditional diffusion models that use U-Net. However,the enhanced performance of DiTs also comes with high parameter counts and implementation costs, seriously restricting their use on resource-limited devices such as mobile phones. To address these challenges, we introduce the Hybrid Floating-point Quantization for DiT(HQ-DiT), an efficient post-training quantization method that utilizes 4-bit floating-point (FP) precision on both weights and activations for DiT inference. Compared to fixed-point quantization (e.g., INT8), FP quantization, complemented by our proposed clipping range selection mechanism, naturally aligns with the data distribution within DiT, resulting in a minimal quantization error. Furthermore, HQ-DiT also implements a universal identity mathematical transform to mitigate the serious quantization error caused by the outliers. The experimental results demonstrate that DiT can achieve extremely low-precision quantization (i.e., 4 bits) with negligible impact on performance. Our approach marks the first instance where both weights and activations in DiTs are quantized to just 4 bits, with only a 0.12 increase in sFID on ImageNet.

We demonstrate, for the first time, fully quantized training (FQT) of large language models (LLMs) using predominantly 4-bit floating-point (FP4) precision for weights, activations, and gradients on datasets up to 200 billion tokens. We extensively investigate key design choices for FP4, including block sizes, scaling formats, and rounding methods. Our analysis shows that the NVFP4 format, where each block of 16 FP4 values (E2M1) shares a scale represented in E4M3, provides optimal results. We use stochastic rounding for backward and update passes and round-to-nearest for the forward pass to enhance stability. Additionally, we identify a theoretical and empirical threshold for effective quantized training: when the gradient norm falls below approximately 3 times the quantization noise, quantized training becomes less effective. Leveraging these insights, we successfully train a 7-billion-parameter model on 256 Intel Gaudi2 accelerators. The resulting FP4-trained model achieves downstream task performance comparable to a standard BF16 baseline, confirming that FP4 training is a practical and highly efficient approach for large-scale LLM training. A reference implementation is supplied in https://github.com/Anonymous1252022/fp4-all-the-way .

Recent research on the 1-bit Large Language Models (LLMs), such as BitNet b1.58, presents a promising direction for reducing the inference cost of LLMs while maintaining their performance. In this work, we introduce BitNet a4.8, enabling 4-bit activations for 1-bit LLMs. BitNet a4.8 employs a hybrid quantization and sparsification strategy to mitigate the quantization errors introduced by the outlier channels. Specifically, we utilize 4-bit activations for inputs to the attention and feed-forward network layers, while sparsifying intermediate states followed with 8-bit quantization. Extensive experiments demonstrate that BitNet a4.8 achieves performance comparable to BitNet b1.58 with equivalent training costs, while being faster in inference with enabling 4-bit (INT4/FP4) kernels. Additionally, BitNet a4.8 activates only 55% of parameters and supports 3-bit KV cache, further enhancing the efficiency of large-scale LLM deployment and inference.

Low-bit floating-point formats and semi-structured sparsity are increasingly supported by modern accelerators, yet combining them for LLM activation compression remains challenging: activations contain input-dependent outliers that dominate block scales in FP4 quantization, and directly applying N:M sparsity masks discards moderate values, coupling sparsification loss with quantization error. We introduce SharQ, a training-free inference method that bridges activation sparsity and FP4 quantization through an online sparse--dense decomposition. For each activation tensor, SharQ generates an input-adaptive N:M mask to extract an outlier-dominated sparse backbone, quantizes it to FP4, and defines a dense residual relative to the quantized sparse backbone rather than the unquantized sparse values. A sparse FP4 GEMM processes the backbone while a dense FP4 GEMM compensates for both mask-induced activation loss and sparse-path quantization error. The two paths share a single FP4 weight payload with path-specific scale views, and a fused preparation kernel absorbs mask generation, residual construction, and layer normalization into one operator. SharQ requires no calibration data, retraining, or model-specific tuning. Evaluated on Llama-3.1-8B, Qwen2.5-7B, Qwen3-30B-A3B, and Qwen3-VL-8B, SharQ recovers 43--63% of the NVFP4-to-FP16 accuracy gap across language and vision-language tasks, and generalizes across NVFP4, HiF4, and MXFP4 formats. On an RTX 5090, SharQ delivers 2.2--2.4times latency reduction over FP16 and 1.2--1.4times throughput improvement over FP8 in language model serving, and up to 1.58times speedup on Wan2.2-T2V-A14B video generation when combined with SageAttention. Our code is available at https://github.com/actypedef/SharQ.

The recent hardware-accelerated microscaling 4-bit floating-point formats such as MXFP4 and NVFP4, supported on NVIDIA and AMD GPUs, promise to revolutionize large language model (LLM) inference. Yet, their practical benefits remain unproven. We present the first comprehensive study of MXFP4 and NVFP4 for post-training quantization, revealing gaps between their promise and real-world performance. Our analysis shows that state-of-the-art methods struggle with FP4, due to two key issues: (1) NVFP4's small group size provably neutralizes traditional outlier mitigation techniques; (2) MXFP4's power-of-two scale quantization severely degrades accuracy due to high induced error. To bridge this gap, we introduce Micro-Rotated-GPTQ (MR-GPTQ), a variant of the classic GPTQ quantization algorithm that tailors the quantization process to FP4's unique properties, by using block-wise Hadamard transforms and format-specific optimizations. We support our proposal with a set of high-performance GPU kernels that enable the MR-GPTQ format with negligible overhead, by rotation fusion into the weights, and fast online computation of the activations. This leads to speedups vs. FP16 of up to 3.6x layer-wise, and 2.2x end-to-end on NVIDIA B200, and of 6x layer-wise and 4x end-to-end on RTX5090. Our extensive empirical evaluation demonstrates that MR-GPTQ matches or outperforms state-of-the-art accuracy, significantly boosting MXFP4, to the point where it nears that of NVFP4. We conclude that, while FP4 is not an automatic upgrade over INT4, format-specialized methods like MR-GPTQ can unlock a new frontier of accuracy-performance trade-offs.

In the complex domain of large language models (LLMs), striking a balance between computational efficiency and maintaining model quality is a formidable challenge. Navigating the inherent limitations of uniform quantization, particularly when dealing with outliers, and motivated by the launch of NVIDIA's H100 hardware, this study delves into the viability of floating-point (FP) quantization, particularly focusing on FP8 and FP4, as a potential solution. Our comprehensive investigation reveals that for LLMs, FP8 activation consistently outshines its integer (INT8) equivalent, with the performance edge becoming more noticeable in models possessing parameters beyond one billion. For weight quantization, our findings indicate that FP4 exhibits comparable, if not superior, performance to INT4, simplifying deployment on FP-supported hardware like H100. To mitigate the overhead from precision alignment caused by the disparity between weights and activations, we propose two scaling constraints for weight quantization that negligibly impact the performance compared to the standard W4A8 model. We additionally enhance our quantization methods by integrating the Low Rank Compensation (LoRC) strategy, yielding improvements especially in smaller models. The results of our investigation emphasize the immense potential of FP quantization for LLMs, paving the way for high-efficiency deployment in resource-limited settings.

Large Reasoning Models (LRMs) achieve strong problem-solving through long chain-of-thought, but their deployment is constrained by the high cost of full-precision inference and growing KV cache footprints. Microscaled FP4 formats enable efficient FP4 deployment; however, fully quantizing weights, activations, and KV caches (W4A4KV4) causes severe reasoning degradation that existing PTQ and QAT fail to recover. We identify that FP4 failures concentrate on low-entropy tokens--precise symbolic commitments such as digits and operators--where quantization noise inflates sampling errors that cascade through reasoning traces. Based on this insight, we propose ReQAT, a reasoning-centric FP4 training framework with three components: (i) Trace-Aligned QAT (TAQ), which revisits identical reasoning traces to focus updates on critical low-entropy decisions; (ii) Selective Entropy Minimization (SEM), which reinforces confidence at low-entropy positions; and (iii) Q-FIT, a quantization-friendly initialization that jointly calibrates RoPE-consistent KV cache transformations to stabilize QAT. Under the same training budget, ReQAT not only recovers but surpasses BF16 fine-tuning accuracy, while delivering up to 3.9x throughput speedup on NVIDIA DGX Spark and 3.1x on B200.

Achieving reliable 4-bit attention is a prerequisite for end-to-end FP4 computation on emerging FP4-capable GPUs, yet attention remains the main obstacle due to FP4's tiny dynamic range and attention's heavy-tailed activations. This paper presents the first systematic study of 4-bit quantization-aware training (QAT) for attention. We find that "drop-in" QAT, which naively combines an FP4 forward pass with a high-precision Flash Attention (FA)-style backward pass, leads to training instability. We identify two key principles for stable FP4 attention: (1) matching low-precision recomputation of attention scores in the backward pass, and (2) resolving implicit precision assumptions in FA's gradient calculation. Based on these insights, we propose Attn-QAT and implement fused Triton kernels for training as well as FP4 inference kernels. Across diffusion and language models, Attn-QAT recovers the quality drop from FP4 attention without explicit outlier-mitigation heuristics used in prior FP4 attention, and delivers up to a 1.5x speedup on an RTX 5090. Video demos can be found at https://drive.google.com/drive/folders/190F6xbBDUF2kGQYIcXBt3ehSYij5jlim?usp=sharing.

Rollout generation is a major bottleneck in Reinforcement Learning (RL) for Mixture-of-Experts (MoE) Large Language Models, motivating low-precision rollout acceleration such as FP8. As an emerging low-precision format, NVFP4 combines fine-grained scaling for accuracy preservation with native W4A4 FP4 GEMMs for higher throughput than FP8. However, we find that directly applying NVFP4 to MoE RL rollout is impractical. NVFP4 rollout with BF16 training collapses after roughly 150 steps, accompanied by rapidly growing rollout-trainer log-probability gaps. Through training-inference error analysis and controlled ablations, we identify activation error, rather than weight error, as the dominant source of FP4 RL instability: weights can be synchronized and aligned by a shared quantization-dequantization path, whereas activations are recomputed online and error is amplified by the coarse E2M1 grid. Therefore, to stabilize NVFP4 RL for MoE, we propose QUantization-error Alignment across Dual Sides (QUADS). On the trainer side, we introduce Asymmetric Quantization-Aware Training fake-quantizing weights while keeping activations unquantized for better alignment. On the rollout side, Residual Activation Compensation corrects high-error activation channels while preserving native W4A4 GEMMs. In our MoE RL experiments on several benchmarks, QUADS achieves BF16-level accuracy, improves average pass@1 by 21.49 points over naive NVFP4 RL, and delivers ~16% higher rollout throughput than FP8.

Reinforcement learning (RL) for post-training large language models (LLMs) incurs substantial computation and memory overhead during rollout generation, which motivates low-precision rollout for efficient RL training. However, existing FP4 RL methods suffer from a key limitation: they primarily optimize quantization accuracy on the training and rollout paths independently rather than directly reducing the discrepancy between the two quantized execution paths. In this work, we propose TRACE (Train-Rollout Quantization Alignment via Compact GuidancE), an FP4 quantization framework for RL training of Mixture-of-Experts (MoE) language models that addresses the limitation of existing FP4 RL methods. TRACE incorporates rollout-guided quantization-aware training that uses rollout-side quantization outcomes to guide training-side FP4 rounding decisions, directly reducing train-rollout discrepancy. Moreover, TRACE adopts an efficient quantization-information caching scheme that selectively retains mantissa and scale information from deeper layers to reduce the storage and communication overhead introduced by rollout guidance. We evaluate TRACE on four large-scale MoE language models across reasoning, coding, and long-horizon RL tasks. Our results demonstrate that TRACE enables joint FP4 weight/activation and FP4 KV-cache rollout with RL performance comparable to BF16 rollout, while achieving up to 5.4xrollout speedup and strong final FP4 performance compared with post-hoc FP4 quantization of BF16-trained policies.

We present, to our knowledge, the first end-to-end FP4 RL post-training, in which both the rollout and training policies, including their forward and backward passes, operate at 4-bit precision. A systematic study reveals that the dominant source of degradation in FP4 RL is not training-side quantization error but rollout activation quantization: outliers stretch the dynamic range so far that a large number of activation values underflow to zero under FP4. Counterintuitively, restoring the training policy to higher precision while keeping the rollout in FP4 makes accuracy worse than full FP4 baseline, exposing rollout-training mismatch as the principal failure mode and ruling out standard pretraining-style fixes. We address this with Rollout Residual Quantization (Rollout-ResQ): a single residual correction term constrained to a hardware-friendly sparsity pattern, added only to the FP4 rollout matmul -- a lightweight correction that recovers most of the precision lost to outlier-driven underflow without inflating the rollout's compute footprint. On Qwen2.5-3B and Qwen2.5-Math-7B, Rollout-ResQ paired with the HiFloat4 (HiF4) format -- whose three-level hierarchical scaling preserves resolution under FP4's tight 4-bit budget -- closes the accuracy gap to BF16 from 4.9% to 1.1%, bringing fully quantized FP4 RL within striking distance of full precision. Applied to the open-standard MXFP4, the same recipe narrows the gap from 13.6% to 5.3%, revealing that FP4 format choice is a key factor that determines the ceiling on recoverable accuracy. Together, these results establish HiF4 as the enabling format for end-to-end FP4 RL post-training, and Rollout-ResQ as the activation-side mechanism that makes the gap to BF16 closable.

Quantization addresses the high resource demand for large language models (LLMs) by alleviating memory pressure and bandwidth congestion and providing significantly scaled compute power with a tolerable impact on accuracy. Four-bit floating point (FP4), the lowest-precision format that preserves essential numerical properties such as exponent and sign, has begun to be adopted in cutting-edge architectures, including Blackwell and AMD CDNA, to support LLM quantization and reduce deployment costs. Although aggressive quantization can yield efficiency gains, the quantization sensitivity of within-transformer layers and whether these sensitivities generalize across existing FP4 formats and model scales remain underexplored. To elucidate quantization sensitivity, this study conducts a systematic analysis of two FP4 formats, MXFP4 and NVFP4, across three Qwen2.5 model scales (0.5B, 7B, and 14B), using controlled component-wise and block-wise isolation methodologies. We observe that MLP up- and down-projection layers consistently dominate in terms of sensitivity, while gate and attention projections are moderately and substantially less sensitive to FP4 quantization, respectively. We further find that sensitivity does not universally localize to the final blocks, but early blocks can be highly sensitive, particularly under MXFP4. Our results provide a diagnostic characterization of the inference behavior of FP4 across components, depths, and FP4 formats.

Building a virtual cell capable of accurately simulating cellular behaviors in silico has long been a dream in computational biology. We introduce CellFlux, an image-generative model that simulates cellular morphology changes induced by chemical and genetic perturbations using flow matching. Unlike prior methods, CellFlux models distribution-wise transformations from unperturbed to perturbed cell states, effectively distinguishing actual perturbation effects from experimental artifacts such as batch effects -- a major challenge in biological data. Evaluated on chemical (BBBC021), genetic (RxRx1), and combined perturbation (JUMP) datasets, CellFlux generates biologically meaningful cell images that faithfully capture perturbation-specific morphological changes, achieving a 35% improvement in FID scores and a 12% increase in mode-of-action prediction accuracy over existing methods. Additionally, CellFlux enables continuous interpolation between cellular states, providing a potential tool for studying perturbation dynamics. These capabilities mark a significant step toward realizing virtual cell modeling for biomedical research. Project page: https://yuhui-zh15.github.io/CellFlux/.

Collective cell responses to exogenous cues depend on cell-cell interactions. In principle, these can result in enhanced sensitivity to weak and noisy stimuli. However, this has not yet been shown experimentally, and, little is known about how multicellular signal processing modulates single cell sensitivity to extracellular signaling inputs, including those guiding complex changes in the tissue form and function. Here we explored if cell-cell communication can enhance the ability of cell ensembles to sense and respond to weak gradients of chemotactic cues. Using a combination of experiments with mammary epithelial cells and mathematical modeling, we find that multicellular sensing enables detection of and response to shallow Epidermal Growth Factor (EGF) gradients that are undetectable by single cells. However, the advantage of this type of gradient sensing is limited by the noisiness of the signaling relay, necessary to integrate spatially distributed ligand concentration information. We calculate the fundamental sensory limits imposed by this communication noise and combine them with the experimental data to estimate the effective size of multicellular sensory groups involved in gradient sensing. Functional experiments strongly implicated intercellular communication through gap junctions and calcium release from intracellular stores as mediators of collective gradient sensing. The resulting integrative analysis provides a framework for understanding the advantages and limitations of sensory information processing by relays of chemically coupled cells.

Recent NVFP4 pretraining work has primarily optimized Transformer linear projections, leaving persistent optimizer states, optimizer computation, and low-precision attention forward--backward paths less explored. We present Full-Stack FP4, a modular NVFP4 framework with separate recipes for projections, AdamW states, Root/Muon computation, and attention. LoRA-SVD protects a compact projection subspace in BF16 while retaining full-shape NVFP4 computation, reducing the linear-only loss gap from 1.40\% to 0.61\%. An ordered square-root, tile-mean, and Hadamard pipeline enables stable NVFP4 AdamW momentum storage; shape-dependent coefficients and clipping stabilize direct NVFP4 Root iterations; and mixed-precision attention retains softmax-sensitive operations in BF16. On 3B pretraining with 64B tokens, BF16 and Full-Stack FP4 reach losses of 2.267 and 2.286, a 0.838\% gap. Their average zero-shot perplexities are 26.675 and 26.665, respectively, with Full-Stack FP4 averaging 0.10 percentage points lower in accuracy. Native four-block measurements on one RTX 5090 show 2.50--2.83times Root speedups over optimized BF16 and 37.9--42.5\% lower AdamW peak memory.

TRPM4 is overexpressed in prostate cancer (PCa) associated with metastasis or recurrence. There is paucity of information pertaining to TRPM4 characterization and functions at single-cell level in PCa. In this study, generalized additive model (GAM) was utilized to model the relationship between TRPM4 and genes shortlisted using Spearman-Kendall dual-filter in aggressive PCa and benign prostate (BP) control cells derived from scRNA-seq dataset. Seven ribosomal genes (RPL10, RPL27, RPL28, RPS2, RPS8, RPS12, and RPS26; averaged into Ribo as the gene set), passed the dual-filter specifically in PCa cells. GAM modeling of TRPM4-Ribo significantly outperformed TRPM4 modeling with alternative cancer gene sets (GSK-3B, mTOR, NF-KB, PI3K/AKT, and Wnt). Cell explanatory power (CEP) classification was devised and verified by cross-validation to identify individual PCa cells most well-predicted by the model. CEP classification binarized PCa cells into top-ranked explanatory power (TREP; more well-predicted by the model) and non-TREP cells. In TRPM4-Ribo GAM plots, distribution pattern of TREP cells shifted at an inflection point (IP) i.e., the specific TRPM4 expression value that further binarized the plot into pre-IP (TRPM4 values below IP) and post-IP (TRPM4 values above IP) regions, producing a quadrant of TREP versus non-TREP cells for each PCa patient. Gene Ontology (GO) enrichment analysis showed that pre-IP TREP cells enriched for immune-related GOs, while post-IP TREP cells enriched for ribosomal, translation, and cell adhesion GOs. In conclusion, the CEP-IP framework based on pairwise genes produces quadrants of cancer cell subpopulations, enabling the identification of distinctive biology with potential therapeutic implications.

The growing computational demands of training large language models (LLMs) necessitate more efficient methods. Quantized training presents a promising solution by enabling low-bit arithmetic operations to reduce these costs. While FP8 precision has demonstrated feasibility, leveraging FP4 remains a challenge due to significant quantization errors and limited representational capacity. This work introduces the first FP4 training framework for LLMs, addressing these challenges with two key innovations: a differentiable quantization estimator for precise weight updates and an outlier clamping and compensation strategy to prevent activation collapse. To ensure stability, the framework integrates a mixed-precision training scheme and vector-wise quantization. Experimental results demonstrate that our FP4 framework achieves accuracy comparable to BF16 and FP8, with minimal degradation, scaling effectively to 13B-parameter LLMs trained on up to 100B tokens. With the emergence of next-generation hardware supporting FP4, our framework sets a foundation for efficient ultra-low precision training.

The increasing computational demands of foundation models have spurred research into low-precision training, with 4-bit floating-point (FP4) formats emerging as a frontier for maximizing hardware throughput. While numerous techniques have been proposed to stabilize FP4 training, they often present isolated solutions with varying, and not always clear, computational overheads. This paper aims to provide a unified view of the design space of FP4 training. We introduce a comprehensive, quantisation gradient-based framework for microscaling quantization that allows for a theoretical analysis of the computational costs associated with different stabilization methods on both the forward and backward passes. Using a simulator built on this framework, we conduct an extensive empirical study across a wide range of machine learning tasks, including regression, image classification, diffusion models, and language models. By systematically evaluating thousands of combinations of techniques, such as novel gradient approximations, rounding strategies, and scaling methods, we identify which configurations offer the most favourable performance-to-overhead trade-off. We find that the techniques enabling the best trade-off involve carefully combining Hadamard transformations, tensor scaling and stochastic rounding. We further find that using UE5M3 as a scaling factor potentially offers a good compromise between range and precision with manageable computational overhead.

A new type of cooperativity termed temporal cooperativity [Biophys. Chem. 105 585-593 (2003), Annu. Rev. Phys. Chem. 58 113-142 (2007)], emerges in the signal transduction module of phosphorylation-dephosphorylation cycle (PdPC). It utilizes multiple kinetic cycles in time, in contrast to allosteric cooperativity that utilizes multiple subunits in a protein. In the present paper, we thoroughly investigate both the deterministic (microscopic) and stochastic (mesoscopic) models, and focus on the identification of the source of temporal cooperativity via comparing with allosteric cooperativity. A thermodynamic analysis confirms again the claim that the chemical equilibrium state exists if and only if the phosphorylation potential triangle G=0, in which case the amplification of sensitivity is completely abolished. Then we provide comprehensive theoretical and numerical analysis with the first-order and zero-order assumptions in phosphorylation-dephosphorylation cycle respectively. Furthermore, it is interestingly found that the underlying mathematics of temporal cooperativity and allosteric cooperativity are equivalent, and both of them can be expressed by "dissociation constants", which also characterizes the essential differences between the simple and ultrasensitive PdPC switches. Nevertheless, the degree of allosteric cooperativity is restricted by the total number of sites in a single enzyme molecule which can not be freely regulated, while temporal cooperativity is only restricted by the total number of molecules of the target protein which can be regulated in a wide range and gives rise to the ultrasensitivity phenomenon.

Diffusion and flow-matching schedules control the signal and noise coefficients that mix data and noise along affine probability paths. Minimizing a kinetic action defined on coefficient paths, motivated by optimal transport, helps explain strong baselines but remains model-agnostic and ignores prediction error. Here we introduce a model-aware schedule construction based on fiberwise optimal transport. At a fixed time and state on the probability path, compatible signal/noise decompositions form an affine fiber. We define a fiberwise prediction risk by averaging optimal-transport costs between the true and predictor-induced decompositions within these fibers. On a fixed coefficient curve, combining this risk with coefficient-path kinetic action yields a closed-form optimal time allocation. This construction extends to general linear prediction targets, and the risk profile can be estimated from an early baseline checkpoint. We evaluate DDPMs and flow matching across prediction targets, training configurations, risk-estimation checkpoints, datasets, and architectures. Our model-aware schedules consistently outperform strong baselines, including a 38.6% relative FID reduction for flow matching on CIFAR-10 at 16 function evaluations. Each model-agnostic kinetic baseline determines its own kinetic reference coordinate. In these coordinates, fiberwise-risk profiles from independently trained models in different settings align closely after normalization to unit area. The resulting schedule deformations used in training also align, suggesting empirical universality across the evaluated models and settings. Pretrained-checkpoint diagnostics extend this normalized-risk agreement to larger conditional latent diffusion and 2-RF models. A frozen analytic allocation template retains most of the model-aware improvement without further risk estimation or model-specific fitting.

We demonstrate a new computational illumination technique that achieves large space-bandwidth-time product, for quantitative phase imaging of unstained live samples in vitro. Microscope lenses can have either large field of view (FOV) or high resolution, not both. Fourier ptychographic microscopy (FPM) is a new computational imaging technique that circumvents this limit by fusing information from multiple images taken with different illumination angles. The result is a gigapixel-scale image having both wide FOV and high resolution, i.e. large space-bandwidth product (SBP). FPM has enormous potential for revolutionizing microscopy and has already found application in digital pathology. However, it suffers from long acquisition times (on the order of minutes), limiting throughput. Faster capture times would not only improve imaging speed, but also allow studies of live samples, where motion artifacts degrade results. In contrast to fixed (e.g. pathology) slides, live samples are continuously evolving at various spatial and temporal scales. Here, we present a new source coding scheme, along with real-time hardware control, to achieve 0.8 NA resolution across a 4x FOV with sub-second capture times. We propose an improved algorithm and new initialization scheme, which allow robust phase reconstruction over long time-lapse experiments. We present the first FPM results for both growing and confluent in vitro cell cultures, capturing videos of subcellular dynamical phenomena in popular cell lines undergoing division and migration. Our method opens up FPM to applications with live samples, for observing rare events in both space and time.

Hybrid LLMs pair softmax attention with linear-attention layers such as Gated DeltaNet (GDN), whose recurrent state summarizes the context in fixed size. Early community 4-bit quantizations of Qwen3.8-27B (48 GDN layers, 16 attention layers) left the GDN block in 8- or 16-bit precision -- especially its decay and write-strength gates -- on the intuition that errors in a recurrence accumulate over long contexts. We test that intuition by building Minima: NVFP4 W4A4 on all 496 linear layers, GDN included. Across perplexity at 4K/32K, MMLU-Pro, GSM8K, AIME'25, GPQA-Diamond, LiveCodeBench, and RULER retrieval to 64K, Minima matches BF16 within seed noise (5-task average -0.52) while being the smallest (17.5 GiB) and fastest-prefill (+14-19%) recipe we compare, and its 32K perplexity gap shrinks with position. A four-part mechanism study explains why: (i) NVFP4's 16-element block scaling localizes the residual stream's extreme outliers, equalizing activation error across layer roles; (ii) the supposedly fragile gate projections are the least sensitive -- softplus/exponential and sigmoid parameterizations compress ~11% GEMM error to ~2% output error; (iii) the delta-rule recurrence holds injected noise at a flat plateau over 32K tokens and forgets a state impulse within hundreds of steps, because each write overwrites the state along the current key direction; (iv) the per-token quantization cost washes out with context instead of compounding. We also repair a global-scale mismatch that arises when per-module-calibrated NVFP4 checkpoints are served by kernels that fuse those modules into one GEMM, and show calibrated FP8 KV-cache scales are performance-free. The result: a practical recipe -- quantize everything, ship KV scales -- and a mechanistic account of why the recurrent half of a hybrid LLM is the easy half to quantize. Checkpoint: https://huggingface.co/minima-ai/mnma_qwen3.8_27b_nvfp4

Virtual cell models should capture phenotypes induced by specific perturbations. However, image-based models are typically trained and evaluated to match real-image distributions, which alone does not explicitly prioritize perturbation-specific biological responses. Recent approaches add biological signals through reinforcement-learning post-training or inference-time steering, raising a central question: where should biological response information enter the generative pipeline? We introduce PerturbBridge, a stochastic data-to-data bridge model that directly supervises perturbation-specific phenotypes in predicted perturbed images during training. PerturbBridge jointly optimizes bridge regression and differentiable biological response losses, with biological gradients passing through a frozen image encoder. We further introduce perturbation-response evaluations based on downstream classification and retrieval. Across three microscopy benchmarks for perturbation profiling and subcellular imaging, PerturbBridge surpasses CellFlux in biological fidelity, image quality, and sampling efficiency. On BBBC021, mechanism-of-action classification improves by 5.66 and 7.5 percentage points with morphological and learned visual features, respectively. On JUMP and AllenCell, retrieval Hit@10 and Hit@1 improve by 1.77 and 7.15 percentage points, respectively. On BBBC021 and JUMP, PerturbBridge achieves lower FID with 80% fewer model evaluations than CellFlux. Overall, these results show that directly supervising perturbation responses during training improves phenotypic fidelity while enabling efficient cellular image generation. Code is available at https://github.com/yyc1215lll-creator/PerturbBridge.

Activation steering presupposes that task-relevant behaviors correspond to linear directions in activation space -- directions that should both steer the model and be readable along the unembedding. Function vectors (FVs), extracted as mean differences across ICL demonstrations, are the canonical test case; the prediction: steering and decoding succeed or fail together. Across 12 tasks, 6 models from 3 families, and 4,032 directed cross-template pairs, we find the opposite. FV steering routinely succeeds where the logit lens cannot decode the correct answer at any intermediate layer, while the converse -- decodable without steerable -- is nearly empty (3 of 72). The gap is not representational dialect. A diagonal tuned lens closes 1 of 14 steerable-not-decodable cases; a 2-layer MLP probe with a Hewitt \& Liang control closes 5 of 10 via nonlinearly encoded structure but leaves 5 invisible to every decoder tested. Even at > 0.90 steering accuracy, projecting the FV through the unembedding yields incoherent token distributions: FVs encode computational instructions, not answer directions. A model-family asymmetry sharpens the picture. Mistral FVs rewrite intermediate representations, while Llama and Gemma FVs steer the final output without leaving a logit-lens-visible trace, corroborated by three signals (post-steering deltas, activation-patching recovery, FV norm-transfer correlations). A previously reported negative cosine-transfer correlation dissolves at scale, adding at most ΔR^2 = 0.011 beyond task identity. These results decompose the linear representation hypothesis into linear decodability and linear steerability and show they come apart opposite to intuition, with implications for safety monitoring: vocabulary-projection tools are blind to FV-style interventions on widely deployed model families.

Astrocytes are increasingly recognized as active regulators of neural dynamics, yet their role in large-scale synchronization remains incompletely understood. Building on the discovery of breathing cluster synchronization in neuron-astrocyte networks, we investigate whether this phenomenon persists under more biologically realistic conditions by incorporating thermosensitive neuronal dynamics, intrinsic electric-field interactions, stochastic perturbations, and delayed astrocytic feedback. Through systematic numerical simulations of a network containing structurally symmetric neuronal subsets, we show that breathing clusters characterized by intermittent alternations between synchronized and desynchronized states, remain robust across a broad range of biophysical conditions. The results reveal a non-monotonic dependence on astrocytic attenuation and feedback parameters, with intermediate values maximizing rhythmic switching through a slow push-pull regulatory mechanism. Temperature and electric-field effects primarily modulate neuronal excitability and the tolerance of the breathing state to noise, while elevated stochastic perturbations progressively destabilize cluster coherence. In contrast, the phenomenon exhibits remarkable robustness to biologically realistic astrocytic delays. Importantly, our findings indicate that the emergence of breathing synchronization remains fundamentally governed by the interplay between network symmetry and astrocyte-mediated feedback, whereas temperature, electric fields, and noise act as modulators of its stability and temporal organization. These results establish breathing cluster synchronization as a robust organizing principle of astrocyte-regulated networks and provide a quantitative framework for understanding how glial regulation shapes cortical state-switching under realistic physiological conditions.

Planning effective interventions in biological systems requires treatment-effect models that adapt to unseen biological contexts by identifying their specific underlying mechanisms. Yet single-cell perturbation datasets span only a handful of biological contexts, and existing methods cannot leverage new interventional evidence at inference time to adapt beyond their training data. To meta-learn a perturbation effect estimator, we present MapPFN, a prior-data fitted network (PFN) pretrained on synthetic data generated from a prior over causal perturbations. Given a set of experiments, MapPFN uses in-context learning to predict post-perturbation distributions, without gradient-based optimization. Despite being pretrained on in silico gene knockouts alone, MapPFN identifies differentially expressed genes, matching the performance of models trained on real single-cell data. Our code and data are available at https://github.com/marvinsxtr/MapPFN.

Anterior-posterior polarization in the Drosophila oocyte requires posterior localization of oskar mRNA. oskar mRNA is produced in the anteriorly situated nurse cells, moved into the oocyte, and assembled into oskar-Staufen ribonucleoprotein particles (RNPs). These RNPs then move through the oocyte and interact with the cortex, where myosin-V binds them to the actin network and kinesin-1 removes them along cortically anchored microtubules. This cortical tug-of-war takes place against an anterior-to-posterior decrease in microtubule density. How the interplay between cytoplasmic transport and cortical binding and unbinding produces a stable posterior cap is unclear. Here, we combine quantitative microscopy, photoconversion experiments, experimental perturbations, and biophysical modeling to show that posterior localization emerges from position-dependent cortical exchange coupled to cytoplasmic diffusion. Our model, which accounts for the tendency of RNPs to demix, suggests that two key parameters that determine the observed localization pattern are the total amount of oskar and the ratio of cortical unbinding to binding rates (the exchange equilibrium constant). Given oskar volume fractions in wild-type, the measured exchange constant is such that oskar localizes to the posterior cortex without demixing. If the balance is broken, say by increasing unbinding rates, oskar irreversibly demixes into cytoplasmic droplets. This is consistent with observations from our experimental perturbations. Our results show how bulk diffusion and cortical exchange, in the face of oskar RNPs' self-attraction, convert a cytoskeletal asymmetry into robust developmental polarity.

Structural biology relies on accurate three-dimensional biomolecular structures to advance our understanding of biological functions, disease mechanisms, and therapeutics. While recent advances in deep learning have enabled the development of all-atom foundation models for molecular modeling and generation, existing approaches face challenges in generalization due to the multi-modal nature of atomic data and the lack of comprehensive analysis of training and sampling strategies. To address these limitations, we propose PharMolixFM, a unified framework for constructing all-atom foundation models based on multi-modal generative techniques. Our framework includes three variants using state-of-the-art multi-modal generative models. By formulating molecular tasks as a generalized denoising process with task-specific priors, PharMolixFM achieves robust performance across various structural biology applications. Experimental results demonstrate that PharMolixFM-Diff achieves competitive prediction accuracy in protein-small-molecule docking (83.9% vs. 90.2% RMSD < 2Å, given pocket) with significantly improved inference speed. Moreover, we explore the empirical inference scaling law by introducing more sampling repeats or steps. Our code and model are available at https://github.com/PharMolix/OpenBioMed.

Perturbation probing generates task-specific causal hypotheses for FFN neurons in large language models using two forward passes per prompt and no backpropagation, followed by a one-time intervention sweep of about 150 passes amortized across all identified neurons. Across eight behavioral circuits, 13 models, and four architecture families, we identify two circuit structures that organize LLM behavior. Opposition circuits appear when RLHF suppresses a pre-training tendency. In safety refusal, about 50 neurons, or 0.014 percent of all neurons, control the refusal template; ablating them changes 80 percent of response formats on 520 AdvBench prompts while producing near-zero harmful compliance, 3 of 520 cases, all with disclaimers. Routing circuits appear for pre-training behaviors distributed through attention. For language selection, residual-stream direction injection switches English to Chinese output on 99.1 percent of 580 benchmark prompts in the 3 of 19 tested models that satisfy three observed conditions: bilingual training, FFN-to-skip signal ratio between 0.3 and 1.1, and linear representability. The same intervention fails on the other 16 models and on math, code, and factual circuits, defining the limits of directional steering. The FFN-to-skip signal ratio, computed from the same two forward passes, distinguishes the two structures and predicts the appropriate intervention. Circuit topology varies by architecture, from Qwen's concentrated FFN bottleneck to Gemma's normalization-shielded circuit. In Qwen3.5-2B, ablating 20 neurons eliminates multi-turn sycophantic capitulation, while amplifying 10 related neurons improves factual correction from 52 percent to 88 percent on 200 TruthfulQA prompts. These results show that perturbation probing offers mechanistic insight into RLHF-organized behavior and a practical toolkit for precision template-layer editing.

Foundation-model predictors of perturbation response are evaluated primarily by aggregate accuracy. Using their predictions to prioritize experiments requires assessing each prediction's reliability. We audit the state-transition (ST) decoder used in STATE across three encoders (SE-600M, scGPT, and Tahoe-x1) and four cell lines under CRISPRi. The decoder's first attention layer has a low-rank output. Projecting this output onto 4-32 fixed directions estimated from training activations preserves mean per-perturbation Pearson delta correlation (PDC). This low-rank attention bottleneck bounds the decoder's reliability by distance to training responses: PDC declines as the cosine distance from a perturbation's observed response to its nearest training response increases. We propose predicted-NN-distance, the cosine distance from a predicted response to its nearest training response, as a per-prediction confidence score. The score has a mean absolute Spearman correlation of 0.81 with PDC, close to the 0.88 obtained with the observed response. Thresholds calibrated on this score transfer across encoders and cell lines, and the score remains predictive of PDC for drug perturbations.

Predicting cellular responses to unseen chemical perturbations is challenging due to unknown targets and mechanisms, high-dimensional expression responses, and limited experimental coverage of the large small-molecule design space. We propose PerturbPFN, a PFN-style amortized model for unknown-target perturbation prediction under a hierarchical synthetic structural prior. Instead of directly regressing high-dimensional expression responses, PerturbPFN infers a latent system graph, sparse atomic intervention targets, and intervention strengths, then propagates their effects through an SCM decoder. The model is trained entirely on prior-predictive synthetic episodes generated from biologically motivated graph and expression simulators, enabling structured in-context learning without test-time gradient updates. We evaluate PerturbPFN on both real single-cell perturbation data and synthetic benchmarks, covering effect prediction, target identification, and regulatory structure discovery. Our results show that PerturbPFN offers a complementary trade-off to specialized baselines, achieving competitive perturbation prediction with low inference cost while exposing interpretable intermediate estimates of targets, strengths, and system structure.

Drug discovery for neurological disease has traditionally centered on the molecules altered by disease. But the molecules that cause pathology are not necessarily the best points from which to reverse it. Here, we ask which otherwise unaltered molecular control points can be engaged to restore pathological neural circuits toward functional states. We present CircuitATLAS, a provenance-grounded systems-neuroscience knowledge graph and agentic framework for target discovery in circuitopathies. It structures literature-derived relationships across diseases, phenotypes, electrophysiology, circuits, brain regions, cell types and molecular effectors, while deliberately excluding direct disease-gene and disease-protein edges to reduce shortcut reasoning. The graph contains 3.83 million nodes and 7.66 million edges, including 5.31 million LLM-extracted relations, and incorporates structured datasets such as the Human Cell Atlas and new multimodal in vivo measurements. We then introduce an agentic workflow that reasons from measurable disease phenotypes through their circuit and cellular substrates to molecular interventions, therapeutic feasibility and clinical constraints. Finally, we introduce a human-governed in vivo lab-in-the-loop linking hypothesis generation to experimental iteration. Within this framework an agent nominated ATP1A3, the neuronal alpha3 Na+/K+-ATPase, as a control point on cortical excitability; interneuron-restricted expression of ATP1A3 abolished the beta- and gamma-band response to a focal 4-aminopyridine challenge in vivo, and the validated target was then carried into a structure-guided small-molecule campaign terminating in a defined assay to resolve the direction of modulation. CircuitATLAS thus provides a framework for discovering therapeutics based not only on what is molecularly disrupted in disease, but on what can be controlled to restore circuit function.

Large foundation models have become central to modern machine learning, with performance scaling predictably with model size and data. However, training and deploying such models incur substantial computational and memory costs, motivating the development of low-precision training techniques. Recent work has demonstrated that 4-bit floating-point (FP4) formats--such as MXFP4 and NVFP4--can be successfully applied to linear GEMM operations in large language models (LLMs), achieving up to 4x improvements in compute throughput and memory efficiency compared to higher-precision baselines. In this work, we investigate the recently proposed HiFloat4 FP4 format for Huawei Ascend NPUs and systematically compare it with MXFP4 in large-scale training settings. All experiments are conducted on Ascend NPU clusters, with linear and expert GEMM operations performed entirely in FP4 precision. We evaluate both dense architectures (e.g., Pangu and LLaMA-style models) and mixture-of-experts (MoE) models, where both standard linear layers and expert-specific GEMMs operate in FP4. Furthermore, we explore stabilization techniques tailored to FP4 training that significantly reduce numerical degradation, maintaining relative error within 1% of full-precision baselines while preserving the efficiency benefits of 4-bit computation. Our results provide a comprehensive empirical study of FP4 training on NPUs and highlight the practical trade-offs between FP4 formats in large-scale dense and MoE models.

Quantized checkpoints are often screened first with quality metrics and only later, if at all, with direct safety tests. This paper audits that shortcut on a matched 51-row matrix spanning 6 models, 4 families, a 7-level GGUF ladder, and AWQ/GPTQ INT4 checkpoints. In this matrix the shortcut fails: all 36 quality-safety pairings split direction across models, and 9 hidden-danger rows plus 1 near-hidden-danger row show quality stable or improved while refusal falls by 12-68 percentage points. Seven of the 11 AWQ/GPTQ rows are hidden-danger. A four-probe mechanistic follow-up over the 17 Hugging Face-backed FP16/AWQ/GPTQ cells does not rescue it: entropy, refusal-direction, and calibration probes are weak or null separators of dangerous rows, and although probe-identified safety-associated neurons absorb 1.39times more quantization error overall (p < 5 times 10^{-7}), the effect is not regime-specific. Claude Sonnet 4 relabels 11,470 items in a predefined stratified set, agrees with the primary gemma3:12b judge on 89.9\% of rows (κ= 0.873, 95\% CI [0.866, 0.881]), and changes 0/10 hidden-danger cells. A calibrated study-internal behavioral screen -- the Refusal Template Stability Index (RTSI), built from four refusal-template drift features and calibrated on this matrix -- routes 10/10 hidden- or near-hidden-danger rows to direct safety testing (Wilson 95\% CI lower bound 0.72) while leaving 23 of 45 non-baseline rows in a low-risk bucket under both in-sample scoring and row-level leave-one-out validation; on the same matrix, the best single-feature baselines (unique-prefix-rate-delta, raw refusal-rate delta) recover 9/10 and 8/10 respectively at matched bucket size, and cross-stack transfer requires recalibration. For the quantized checkpoints, model families, and safety outcomes studied here, retained quality cannot waive direct safety evaluation.

Cell Painting is a high-content morphological profiling assay widely used for phenotype-based biological inference, with mechanism of action (MOA) prediction as a central application. Existing approaches largely formulate Cell Painting-based inference as representation matching, assigning predictions from nearby reference perturbations in morphological feature space. However, retrieved neighbors are often noisy and partially misleading evidence due to batch effects, non-specific cytotoxicity, phenotypic convergence, and source-dependent variability. We reformulate Cell Painting-based MOA prediction as a calibrated evidence reasoning problem, where retrieved neighbors are treated as uncertain observations that must be evaluated, compared, and sometimes rejected before supporting a mechanistic conclusion. We propose PhenoAIR, a reliability-aware multi-agent framework that maintains a candidate-centric evidence memory and performs controller-guided refinement over phenotype- and mechanism-side evidence. PhenoAIR uses offline reference-set calibration to weight evidence by source reliability, phenotype stability, and mechanism-level confusion. We evaluate PhenoAIR on a benchmark constructed from JUMP Cell Painting profiles and annotations, covering controlled, realistic, and discovery-oriented open-world MOA prediction settings. PhenoAIR outperforms representation-matching and LLM-based baselines across all settings.

The simulation of human neurons and neurotransmission mechanisms has been realized in deep neural networks based on the theoretical implementations of activation functions. However, recent studies have reported that the threshold potential of neurons exhibits different values according to the locations and types of individual neurons, and that the activation functions have limitations in terms of representing this variability. Therefore, this study proposes a simple yet effective activation function that facilitates different thresholds and adaptive activations according to the positions of units and the contexts of inputs. Furthermore, the proposed activation function mathematically exhibits a more generalized form of Swish activation function, and thus we denoted it as Adaptive SwisH (ASH). ASH highlights informative features that exhibit large values in the top percentiles in an input, whereas it rectifies low values. Most importantly, ASH exhibits trainable, adaptive, and context-aware properties compared to other activation functions. Furthermore, ASH represents general formula of the previously studied activation function and provides a reasonable mathematical background for the superior performance. To validate the effectiveness and robustness of ASH, we implemented ASH into many deep learning models for various tasks, including classification, detection, segmentation, and image generation. Experimental analysis demonstrates that our activation function can provide the benefits of more accurate prediction and earlier convergence in many deep learning applications.

Preclinical models poorly predict human drug efficacy, particularly in neurological disorders. Neural activity offers a uniquely rich source of translational information because it captures high-dimensional variation in nervous-system function that can be measured in both animals and humans. However, its high dimensionality makes it difficult to distinguish conserved disease-related features from variation arising from species, recording modality and experimental context. Here, we test whether shared neural dynamics can be identified directly from electrophysiology data by learning representations organized by biological state rather than species. We develop a dual-rule contrastive learning framework that aligns corresponding mouse and human states while preserving separation between distinct phenotypes. This framework recovered conserved sensory-response structure across species and, in epilepsy, resolved distinct relationships between three mouse models and heterogeneous human patient populations. When treated animals were projected into a frozen cross-species representation, drug-induced movement towards the human-aligned healthy state retrospectively tracked known clinical efficacy across ten model-drug combinations including a disease-specific detrimental effect. The framework also identified shared disease-associated neural dynamics between Fmr1-knockout mice and human 16p11.2 copy-number variant carriers despite differences in genetic aetiology and recording modality. Together, these findings show the potential of cross-species neural representation learning to map heterogeneous human disease onto experimentally tractable preclinical states and assess whether interventions restore human-relevant circuit function.

Foundation models applied to bio-molecular space hold promise to accelerate drug discovery. Molecular representation is key to building such models. Previous works have typically focused on a single representation or view of the molecules. Here, we develop a multi-view foundation model approach, that integrates molecular views of graph, image and text. Single-view foundation models are each pre-trained on a dataset of up to 200M molecules and then aggregated into combined representations. Our multi-view model is validated on a diverse set of 18 tasks, encompassing ligand-protein binding, molecular solubility, metabolism and toxicity. We show that the multi-view models perform robustly and are able to balance the strengths and weaknesses of specific views. We then apply this model to screen compounds against a large (>100 targets) set of G Protein-Coupled receptors (GPCRs). From this library of targets, we identify 33 that are related to Alzheimer's disease. On this subset, we employ our model to identify strong binders, which are validated through structure-based modeling and identification of key binding motifs.

Protein biology focuses on the intricate relationships among sequences, structures, and functions. Deciphering protein functions is crucial for understanding biological processes, advancing drug discovery, and enabling synthetic biology applications. Since protein sequences determine tertiary structures, which in turn govern functions, integrating sequence and structure information is essential for accurate prediction of protein functions. Traditional protein language models (pLMs) have advanced protein-related tasks by learning representations from large-scale sequence and structure data. However, pLMs are limited in integrating broader contextual knowledge, particularly regarding functional modalities that are fundamental to protein biology. In contrast, large language models (LLMs) have exhibited outstanding performance in contextual understanding, reasoning, and generation across diverse domains. Leveraging these capabilities, STELLA is proposed as a multimodal LLM integrating protein sequence-structure representations with general knowledge to address protein function prediction. Through multimodal instruction tuning (MMIT) using the proposed OPI-Struc dataset, STELLA achieves state-of-the-art performance in two function-related tasks-functional description prediction (FP) and enzyme-catalyzed reaction prediction (EP). This study highlights the potential of multimodal LLMs as an alternative paradigm to pLMs to advance protein biology research.

Idiopathic pulmonary fibrosis (IPF) is a progressive disease that irreversibly transforms lung tissue into rigid fibrotic structures, leading to debilitating symptoms such as shortness of breath and chronic fatigue. The heterogeneity and complexity of this disease, particularly regarding its severity and progression rate, have made predicting its future course a complex and challenging task. Besides, traditional diagnostic methods based on clinical evaluations and imaging have limitations in capturing the disease's complexity. Using the Kaggle Pulmonary Fibrosis Progression dataset, which includes computed tomography images, and clinical information, the model predicts changes in forced vital capacity (FVC), a key progression indicator. Our method uses a proposed context-aware sequential-parallel hybrid transformer model and clinical information enrichment for its prediction. The proposed method achieved a Laplace Log-Likelihood score of -6.508, outperforming prior methods and demonstrating superior predictive capabilities. These results highlight the potential of advanced deep learning techniques to provide more accurate and timely predictions, offering a transformative approach to the diagnosis and management of IPF, with implications for improved patient outcomes and therapeutic advancements.

Cells that collide with each other repolarize away from contact, in a process called contact inhibition of locomotion (CIL), which is necessary for correct development of the embryo. CIL can occur even when cells make a micron-scale contact with a neighbor - much smaller than their size. How precisely can a cell sense cell-cell contact and repolarize in the correct direction? What factors control whether a cell recognizes it has contacted a neighbor? We propose a theoretical model for the limits of CIL where cells recognize the presence of another cell by binding the protein ephrin with the Eph receptor. This recognition is made difficult by the presence of interfering ligands that bind nonspecifically. Both theoretical predictions and simulation results show that it becomes more difficult to sense cell-cell contact when it is difficult to distinguish ephrin from the interfering ligands, or when there are more interfering ligands, or when the contact width decreases. However, the error of estimating contact position remains almost constant when the contact width changes. This happens because the cell gains spatial information largely from the boundaries of cell-cell contact. We study using statistical decision theory the likelihood of a false positive CIL event in the absence of cell-cell contact, and the likelihood of a false negative where CIL does not occur when another cell is present. Our results suggest that the cell is more likely to make incorrect decisions when the contact width is very small or so large that it nears the cell's perimeter. However, in general, we find that cells have the ability to make reasonably reliable CIL decisions even for very narrow (micron-scale) contacts, even if the concentration of interfering ligands is ten times that of the correct ligands.

Fluorescence Lifetime Imaging (FLI) is a critical molecular imaging modality that provides unique information about the tissue microenvironment, which is invaluable for biomedical applications. FLI operates by acquiring and analyzing photon time-of-arrival histograms to extract quantitative parameters associated with temporal fluorescence decay. These histograms are influenced by the intrinsic properties of the fluorophore, instrument parameters, time-of-flight distributions associated with pixel-wise variations in the topographic and optical characteristics of the sample. Recent advancements in Deep Learning (DL) have enabled improved fluorescence lifetime parameter estimation. However, existing models are primarily designed for planar surface samples, limiting their applicability in translational scenarios involving complex surface profiles, such as in-vivo whole-animal or imaged guided surgical applications. To address this limitation, we present MFliNet (Macroscopic FLI Network), a novel DL architecture that integrates the Instrument Response Function (IRF) as an additional input alongside experimental photon time-of-arrival histograms. Leveraging the capabilities of a Differential Transformer encoder-decoder architecture, MFliNet effectively focuses on critical input features, such as variations in photon time-of-arrival distributions. We evaluate MFliNet using rigorously designed tissue-mimicking phantoms and preclinical in-vivo cancer xenograft models. Our results demonstrate the model's robustness and suitability for complex macroscopic FLI applications, offering new opportunities for advanced biomedical imaging in diverse and challenging settings.

We show that in a drive-response coupling framework extreme events are suppressed in the response system by the dominance of a single driving signal. We validate this approach across three distinct response network topologies, namely (i) a pair of coupled neurons, (ii) a monolayer network of N coupled neurons and (iii) a two-layer multiplex network each composed of FitzHugh-Nagumo neuronal units. The response networks inherently exhibit extreme events. Our results demonstrate that influencing just one neuron in the response network with an appropriately tuned driving signal is sufficient to control extreme events across all three configurations. In the two-neuron case, suppression of extreme events occurs due to the breaking of phase-locking between the driving neuron and the targeted response neuron. In the case of monolayer and multiplex networks, suppression of extreme events results from the disruption of protoevent frequency dynamics and a subsequent frequency decoupling of the driven neuron from the rest of the network. We also observe that when the size of the neurons in response network connected to the drive increases, the onset of control occurs earlier indicating a scaling advantage of the method.

Understanding cell cycle dynamics is crucial for studying biological processes such as growth, development and disease progression. While fluorescent protein reporters like the Fucci system allow live monitoring of cell cycle phases, they require genetic engineering and occupy additional fluorescence channels, limiting broader applicability in complex experiments. In this study, we conduct a comprehensive evaluation of deep learning methods for predicting continuous Fucci signals using non-fluorescence brightfield imaging, a widely available label-free modality. To that end, we generated a large dataset of 1.3 M images of dividing RPE1 cells with full cell cycle trajectories to quantitatively compare the predictive performance of distinct model categories including single time-frame models, causal state space models and bidirectional transformer models. We show that both causal and transformer-based models significantly outperform single- and fixed frame approaches, enabling the prediction of visually imperceptible transitions like G1/S within 1h resolution. Our findings underscore the importance of sequence models for accurate predictions of cell cycle dynamics and highlight their potential for label-free imaging.

Motivation: Interpretability is not optional in biology: understanding gene regulation requires models whose learned structure can be directly interrogated, not merely accurate predictors whose internals resist mapping onto regulatory relationships. We ask whether an architecture mirroring the central dogma yields attention and gradient maps that recover known regulatory elements and networks in inspectable form. Results: Central Dogma Transformer II (CDT-II) mirrors the central dogma in its architecture -- DNA self-attention, RNA self-attention, and DNA-to-RNA cross-attention -- requiring only genomic embeddings and raw per-cell expression. On K562 CRISPR interference (CRISPRi) data with five genes held out entirely, CDT-II predicts perturbation effects (per-gene mean r = 0.84), recovers the GFI1B regulatory network (6.6-fold enrichment, P = 3.5 x 10^-17), and concentrates cross-attention on ENCODE regulatory elements including CTCF sites (mean 7.67x across 28 target genes, P < 0.001). Gradient attribution predicts consequences of perturbing therapeutic targets (mean r = 0.82). For TFRC, target of the anti-TfR1 antibody PPMX-T003, it identifies erythrocyte-structure, iron-dependent DNA-synthesis and oxidative-stress genes, matching anemia and ferroptosis reported clinically and preclinically -- without clinical data as input. CDT-II acts as an AI microscope, surfacing clinically relevant regulatory structure from perturbation experiments alone. Availability: Source code is available at https://github.com/nobusama/CDT2. Pre-computed embeddings, training data, and model weights are available at https://huggingface.co/datasets/nobusama17/CDT2-data.

Self-sustained neural activity in the absence of ongoing external input is a fundamental feature of nervous system dynamics, yet the conditions under which it can emerge in biophysically grounded network models remain incompletely understood. We studied whether a recurrent network of Hodgkin-Huxley neurons with spike-timing-dependent plasticity and intrinsic stochasticity can maintain autonomous activity after brief transient stimulation. The simulated network comprised 200 neurons (160 excitatory, 40 inhibitory) with 80% connection probability, incorporating excitatory and inhibitory STDP, probabilistic vesicle release, probabilistic synapse formation, receptor variability, and voltage-dependent inhibition. After a brief 200 ms initialization stimulus to 30 excitatory neurons, the network received no further external input. In one 1800 s simulation and two additional 500 s simulations, the network maintained sparse, irregular activity without ongoing drive. In the 1800 s run, 67% of neurons exhibited mean firing rates below 1 Hz, the population mean firing rate was 1.13 +/- 1.34 Hz, participation increased across longer observation windows, and population-mean Fano factors remained near 1-2, consistent with irregular spike timing. Raster activity also showed spontaneous qualitative reorganizations in collective firing patterns over time. These findings suggest that recurrent Hodgkin-Huxley networks with plastic and stochastic synapses can sustain long-duration autonomous activity in a sparse firing regime after brief initialization.

Massive activations, residual-stream coordinates with magnitudes far larger than typical activations, are associated with attention sinks in transformers, but how their scale is regulated during training remains incompletely understood. Combining training-trajectory analyses and controlled interventions, we trace their emergence, growth, and consolidation. Sink-carrying channels vary across random seeds but stabilize early within each run. Over longer training, surrounding channels erode and the sink concentrates onto a few redundant carriers. Across ablations, gradient attenuation follows the sink token's collective root-mean-square magnitude rather than any single channel, making collective scale central to understanding their effects. Our central result is that weight decay causally controls the turnover of global activation scale. In controlled continuations, removing decay near the peak allows this scale to keep rising, whereas retaining it produces decline even at constant learning rate. We develop a balance model for the rise and peak of massive-activation magnitude, in which AdamW-preconditioned growth opposes weight decay. Sweeping the decay coefficient λ shifts peak timing approximately log-linearly and yields peak magnitudes scaling approximately as λ^{-1/2}, consistent with this balance. Optimizer measurements further show that preconditioning sustains the large-channel cohort against decay even when raw maintaining forces are too small to do so. Together, these findings connect the observed life cycle to scale-regulating training dynamics and establish weight decay as a training-time lever on activation magnitude.

The accuracy of classical force fields (FFs) has been shown to be limited for the simulation of cation-protein systems despite their importance in understanding the processes of life. Improvements can result from optimizing the parameters of classical FFs or by extending the FF formulation by terms describing charge transfer and polarization effects. In this work, we introduce our implementation of the CTPOL model in OpenMM, which extends the classical additive FF formula by adding charge transfer (CT) and polarization (POL). Furthermore, we present an open-source parameterization tool, called FFAFFURR that enables the (system specific) parameterization of OPLS-AA and CTPOL models. The performance of our workflow was evaluated by its ability to reproduce quantum chemistry energies and by molecular dynamics simulations of a Zinc finger protein.

High-resolution brain imaging can now capture not just synapse locations but their molecular composition, with the cost of such mapping falling exponentially. Yet such ultrastructural data has so far told us little about local neuronal physiology - specifically, the parameters (e.g., synaptic efficacies, local conductances) that govern neural dynamics. We propose to translate molecularly annotated ultrastructure into physiology, introducing the concept of an ultrastructure-to-dynamics compiler: a learned mapping from molecularly annotated ultrastructure to simulator-ready, uncertainty-aware physiological parameters. The requirement is paired training data, with jointly acquired ultrastructure from imaging, and dynamical responses to perturbations from physiological experiments. With this data we can train models that predict local physiology directly from structure. Such a compiler would support biophysical simulations by turning anatomical maps into models of circuit dynamics, shifting structure-to-function from a descriptive program to a predictive one and opening routes to understanding neural computation and forecasting intervention effects.

Reinforcement-Learning-based post-training has recently emerged as a promising paradigm for aligning text-to-image diffusion models with human preferences. In recent studies, increasing the rollout group size yields pronounced performance improvements, indicating substantial room for further alignment gains. However, scaling rollouts on large-scale foundational diffusion models (e.g., FLUX.1-12B) imposes a heavy computational burden. To alleviate this bottleneck, we explore the integration of FP4 quantization into Diffusion RL rollouts. Yet, we identify that naive quantized pipelines inherently introduce risks of performance degradation. To overcome this dilemma between efficiency and training integrity, we propose Sol-RL (Speed-of-light RL), a novel FP4-empowered Two-stage Reinforcement Learning framework. First, we utilize high-throughput NVFP4 rollouts to generate a massive candidate pool and extract a highly contrastive subset. Second, we regenerate these selected samples in BF16 precision and optimize the policy exclusively on them. By decoupling candidate exploration from policy optimization, Sol-RL integrates the algorithmic mechanisms of rollout scaling with the system-level throughput gains of NVFP4. This synergistic algorithm-hardware design effectively accelerates the rollout phase while reserving high-fidelity samples for optimization. We empirically demonstrate that our framework maintains the training integrity of BF16 precision pipeline while fully exploiting the throughput gains enabled by FP4 arithmetic. Extensive experiments across SANA, FLUX.1, and SD3.5-L substantiate that our approach delivers superior alignment performance across multiple metrics while accelerating training convergence by up to 4.64times, unlocking the power of massive rollout scaling at a fraction of the cost.