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Mar 5

Energy Efficient Protein Language Models: Leveraging Small Language Models with LoRA for Controllable Protein Generation

Large language models (LLMs) have demonstrated significant success in natural language processing (NLP) tasks and have shown promising results in other domains such as protein sequence generation. However, there remain salient differences between LLMs used for NLP, which effectively handle multiple tasks and are available in small sizes, and protein language models that are often specialized for specific tasks and only exist in larger sizes. In this work, we introduce two small protein language models, based on Llama-3-8B and Phi-3-mini, that are capable of both uncontrollable and controllable protein generation. For the uncontrollable generation task, our best model achieves an average pLDDT score of 69.75, demonstrating robust performance in generating viable protein structures. For the controllable generation task, in which the model generates proteins according to properties specified in the prompt, we achieve a remarkable average TM-Score of 0.84, indicating high structural similarity to target proteins. We chose 10 properties, including six classes of enzymes, to extend the capabilities of prior protein language models. Our approach utilizes the Low-Rank Adaptor (LoRA) technique, reducing trainable parameters to just 4% of the original model size, lowering computational requirements. By using a subset of the UniRef50 dataset and small models, we reduced the overall training time by 70% without compromising performance. Notably, Phi-3-mini reduced trainable parameters by 60%, decreasing training cost by 30% compared to Llama 3. Consequently, Phi-3 achieved a comparable TM-Score of 0.81, demonstrating that smaller models can match the performance of larger ones, like Llama 3. We also demonstrate the deployment of our models on the energy efficient ET-SoC-1 chip, significantly improving the TPS/W by a factor of 3.

  • 2 authors
·
Nov 8, 2024 2

Transition Path Sampling with Improved Off-Policy Training of Diffusion Path Samplers

Understanding transition pathways between two meta-stable states of a molecular system is crucial to advance drug discovery and material design. However, unbiased molecular dynamics (MD) simulations are computationally infeasible because of the high energy barriers that separate these states. Although recent machine learning techniques are proposed to sample rare events, they are often limited to simple systems and rely on collective variables (CVs) derived from costly domain expertise. In this paper, we introduce a novel approach that trains diffusion path samplers (DPS) to address the transition path sampling (TPS) problem without requiring CVs. We reformulate the problem as an amortized sampling from the transition path distribution by minimizing the log-variance divergence between the path distribution induced by DPS and the transition path distribution. Based on the log-variance divergence, we propose learnable control variates to reduce the variance of gradient estimators and the off-policy training objective with replay buffers and simulated annealing techniques to improve sample efficiency and diversity. We also propose a scale-based equivariant parameterization of the bias forces to ensure scalability for large systems. We extensively evaluate our approach, termed TPS-DPS, on a synthetic system, small peptide, and challenging fast-folding proteins, demonstrating that it produces more realistic and diverse transition pathways than existing baselines.

  • 5 authors
·
May 30, 2024

RecRecNet: Rectangling Rectified Wide-Angle Images by Thin-Plate Spline Model and DoF-based Curriculum Learning

The wide-angle lens shows appealing applications in VR technologies, but it introduces severe radial distortion into its captured image. To recover the realistic scene, previous works devote to rectifying the content of the wide-angle image. However, such a rectification solution inevitably distorts the image boundary, which potentially changes related geometric distributions and misleads the current vision perception models. In this work, we explore constructing a win-win representation on both content and boundary by contributing a new learning model, i.e., Rectangling Rectification Network (RecRecNet). In particular, we propose a thin-plate spline (TPS) module to formulate the non-linear and non-rigid transformation for rectangling images. By learning the control points on the rectified image, our model can flexibly warp the source structure to the target domain and achieves an end-to-end unsupervised deformation. To relieve the complexity of structure approximation, we then inspire our RecRecNet to learn the gradual deformation rules with a DoF (Degree of Freedom)-based curriculum learning. By increasing the DoF in each curriculum stage, namely, from similarity transformation (4-DoF) to homography transformation (8-DoF), the network is capable of investigating more detailed deformations, offering fast convergence on the final rectangling task. Experiments show the superiority of our solution over the compared methods on both quantitative and qualitative evaluations. The code and dataset will be made available.

  • 5 authors
·
Jan 4, 2023

LongCat-Flash Technical Report

We introduce LongCat-Flash, a 560-billion-parameter Mixture-of-Experts (MoE) language model designed for both computational efficiency and advanced agentic capabilities. Stemming from the need for scalable efficiency, LongCat-Flash adopts two novel designs: (a) Zero-computation Experts, which enables dynamic computational budget allocation and activates 18.6B-31.3B (27B on average) per token depending on contextual demands, optimizing resource usage. (b) Shortcut-connected MoE, which enlarges the computation-communication overlap window, demonstrating notable gains in inference efficiency and throughput compared to models of a comparable scale. We develop a comprehensive scaling framework for large models that combines hyperparameter transfer, model-growth initialization, a multi-pronged stability suite, and deterministic computation to achieve stable and reproducible training. Notably, leveraging the synergy among scalable architectural design and infrastructure efforts, we complete model training on more than 20 trillion tokens within 30 days, while achieving over 100 tokens per second (TPS) for inference at a cost of \$0.70 per million output tokens. To cultivate LongCat-Flash towards agentic intelligence, we conduct a large-scale pre-training on optimized mixtures, followed by targeted mid- and post-training on reasoning, code, and instructions, with further augmentation from synthetic data and tool use tasks. Comprehensive evaluations demonstrate that, as a non-thinking foundation model, LongCat-Flash delivers highly competitive performance among other leading models, with exceptional strengths in agentic tasks. The model checkpoint of LongCat-Flash is open-sourced to foster community research. LongCat Chat: https://longcat.ai Hugging Face: https://huggingface.co/meituan-longcat GitHub: https://github.com/meituan-longcat

meituan-longcat LongCat
·
Sep 1, 2025

LLaDA2.1: Speeding Up Text Diffusion via Token Editing

While LLaDA2.0 showcased the scaling potential of 100B-level block-diffusion models and their inherent parallelization, the delicate equilibrium between decoding speed and generation quality has remained an elusive frontier. Today, we unveil LLaDA2.1, a paradigm shift designed to transcend this trade-off. By seamlessly weaving Token-to-Token (T2T) editing into the conventional Mask-to-Token (M2T) scheme, we introduce a joint, configurable threshold-decoding scheme. This structural innovation gives rise to two distinct personas: the Speedy Mode (S Mode), which audaciously lowers the M2T threshold to bypass traditional constraints while relying on T2T to refine the output; and the Quality Mode (Q Mode), which leans into conservative thresholds to secure superior benchmark performances with manageable efficiency degrade. Furthering this evolution, underpinned by an expansive context window, we implement the first large-scale Reinforcement Learning (RL) framework specifically tailored for dLLMs, anchored by specialized techniques for stable gradient estimation. This alignment not only sharpens reasoning precision but also elevates instruction-following fidelity, bridging the chasm between diffusion dynamics and complex human intent. We culminate this work by releasing LLaDA2.1-Mini (16B) and LLaDA2.1-Flash (100B). Across 33 rigorous benchmarks, LLaDA2.1 delivers strong task performance and lightning-fast decoding speed. Despite its 100B volume, on coding tasks it attains an astounding 892 TPS on HumanEval+, 801 TPS on BigCodeBench, and 663 TPS on LiveCodeBench.

inclusionAI inclusionAI
·
Feb 9 4

Decompose-and-Formalise: Recursively Verifiable Natural Language Inference

Recent work has shown that integrating large language models (LLMs) with theorem provers (TPs) in neuro-symbolic pipelines helps with entailment verification and proof-guided refinement of explanations for natural language inference (NLI). However, scaling such refinement to naturalistic NLI remains difficult: long, syntactically rich inputs and deep multi-step arguments amplify autoformalisation errors, where a single local mismatch can invalidate the proof. Moreover, current methods often handle failures via costly global regeneration due to the difficulty of localising the responsible span or step from prover diagnostics. Aiming to address these problems, we propose a decompose-and-formalise framework that (i) decomposes premise-hypothesis pairs into an entailment tree of atomic steps, (ii) verifies the tree bottom-up to isolate failures to specific nodes, and (iii) performs local diagnostic-guided refinement instead of regenerating the whole explanation. Moreover, to improve faithfulness of autoformalisation, we introduce θ-substitution in an event-based logical form to enforce consistent argument-role bindings. Across a range of reasoning tasks using five LLM backbones, our method achieves the highest explanation verification rates, improving over the state-of-the-art by 26.2%, 21.7%, 21.6% and 48.9%, while reducing refinement iterations and runtime and preserving strong NLI accuracy.

  • 4 authors
·
Jan 27

HAMburger: Accelerating LLM Inference via Token Smashing

The growing demand for efficient Large Language Model (LLM) inference requires a holistic optimization on algorithms, systems, and hardware. However, very few works have fundamentally changed the generation pattern: each token needs one forward pass and one KV cache. This can be sub-optimal because we found that LLMs are extremely capable of self-identifying the exact dose of information that a single KV cache can store, and many tokens can be generated confidently without global context. Based on this insight, we introduce HAMburger, a Hierarchically Auto-regressive Model that redefines resource allocation in LLMs by moving beyond uniform computation and storage per token during inference. Stacking a compositional embedder and a micro-step decoder in between a base LLM, HAMburger smashes multiple tokens into a single KV and generates several tokens per step. Additionally, HAMburger functions as a speculative decoding framework where it can blindly trust self-drafted tokens. As a result, HAMburger shifts the growth of KV cache and forward FLOPs from linear to sub-linear with respect to output length, and adjusts its inference speed based on query perplexity and output structure. Extensive evaluations show that HAMburger reduces the KV cache computation by up to 2times and achieves up to 2times TPS, while maintaining quality in both short- and long-context tasks. Our method explores an extremely challenging inference regime that requires both computation- and memory-efficiency with a hardware-agnostic design.

  • 2 authors
·
May 26, 2025