The rapid evolution of Large Language Models (LLMs) has driven the need for increasingly sophisticated inference pipelines and hardware platforms. Modern LLM serving extends beyond traditional prefill-decode workflows, incorporating multi-stage processes such as Retrieval Augmented Generation (RAG), key-value (KV) cache retrieval, dynamic model routing, and multi step reasoning. These stages exhibit diverse computational demands, requiring distributed systems that integrate GPUs, ASICs, CPUs, and memory-centric architectures. However, existing simulators lack the fidelity to model these heterogeneous, multi-engine workflows, limiting their ability to inform architectural decisions. To address this gap, we introduce HERMES, a Heterogeneous Multi-stage LLM inference Execution Simulator. HERMES models diverse request stages; including RAG, KV retrieval, reasoning, prefill, and decode across complex hardware hierarchies. HERMES supports heterogeneous clients executing multiple models concurrently unlike prior frameworks while incorporating advanced batching strategies and multi-level memory hierarchies. By integrating real hardware traces with analytical modeling, HERMES captures critical trade-offs such as memory bandwidth contention, inter-cluster communication latency, and batching efficiency in hybrid CPU-accelerator deployments. Through case studies, we explore the impact of reasoning stages on end-to-end latency, optimal batching strategies for hybrid pipelines, and the architectural implications of remote KV cache retrieval. HERMES empowers system designers to navigate the evolving landscape of LLM inference, providing actionable insights into optimizing hardware-software co-design for next-generation AI workloads.

Continual Learning with Pre-trained Models holds great promise for efficient adaptation across sequential tasks. However, most existing approaches freeze PTMs and rely on auxiliary modules like prompts or adapters, limiting model plasticity and leading to suboptimal generalization when facing significant distribution shifts. While full fine-tuning can improve adaptability, it risks disrupting crucial pre-trained knowledge. In this paper, we propose Mutual Information-guided Sparse Tuning (MIST), a plug-and-play method that selectively updates a small subset of PTM parameters, less than 5%, based on sensitivity to mutual information objectives. MIST enables effective task-specific adaptation while preserving generalization. To further reduce interference, we introduce strong sparsity regularization by randomly dropping gradients during tuning, resulting in fewer than 0.5% of parameters being updated per step. Applied before standard freeze-based methods, MIST consistently boosts performance across diverse continual learning benchmarks. Experiments show that integrating our method into multiple baselines yields significant performance gains. Our code is available at https://github.com/zhwhu/MIST.

Various parallelism, such as data, tensor, and pipeline parallelism, along with memory optimizations like activation checkpointing, redundancy elimination, and offloading, have been proposed to accelerate distributed training for Large Language Models. To find the best combination of these techniques, automatic distributed training systems are proposed. However, existing systems only tune a subset of optimizations, due to the lack of overlap awareness, inability to navigate the vast search space, and ignoring the inter-microbatch imbalance, leading to sub-optimal performance. To address these shortcomings, we propose Mist, a memory, overlap, and imbalance-aware automatic distributed training system that comprehensively co-optimizes all memory footprint reduction techniques alongside parallelism. Mist is based on three key ideas: (1) fine-grained overlap-centric scheduling, orchestrating optimizations in an overlapped manner, (2) symbolic-based performance analysis that predicts runtime and memory usage using symbolic expressions for fast tuning, and (3) imbalance-aware hierarchical tuning, decoupling the process into an inter-stage imbalance and overlap aware Mixed Integer Linear Programming problem and an intra-stage Dual-Objective Constrained Optimization problem, and connecting them through Pareto frontier sampling. Our evaluation results show that Mist achieves an average of 1.28$\times$ (up to 1.73$\times$) and 1.27$\times$ (up to 2.04$\times$) speedup compared to state-of-the-art manual system Megatron-LM and state-of-the-art automatic system Aceso, respectively.

Motivation: A major challenge in metabolomics is annotation: assigning molecular structures to mass spectral fragmentation patterns. Despite recent advances in molecule-to-spectra and in spectra-to-molecular fingerprint prediction (FP), annotation rates remain low. Results: We introduce in this paper a novel paradigm (JESTR) for annotation. Unlike prior approaches that explicitly construct molecular fingerprints or spectra, JESTR leverages the insight that molecules and their corresponding spectra are views of the same data and effectively embeds their representations in a joint space. Candidate structures are ranked based on cosine similarity between the embeddings of query spectrum and each candidate. We evaluate JESTR against mol-to-spec and spec-to-FP annotation tools on three datasets. On average, for rank@[1-5], JESTR outperforms other tools by 23.6%-71.6%. We further demonstrate the strong value of regularization with candidate molecules during training, boosting rank@1 performance by 11.4% and enhancing the model's ability to discern between target and candidate molecules. Through JESTR, we offer a novel promising avenue towards accurate annotation, therefore unlocking valuable insights into the metabolome.

Medical imaging segmentation is a highly active area of research, with deep learning-based methods achieving state-of-the-art results in several benchmarks. However, the lack of standardized tools for training, testing, and evaluating new methods makes the comparison of methods difficult. To address this, we introduce the Medical Imaging Segmentation Toolkit (MIST), a simple, modular, and end-to-end medical imaging segmentation framework designed to facilitate consistent training, testing, and evaluation of deep learning-based medical imaging segmentation methods. MIST standardizes data analysis, preprocessing, and evaluation pipelines, accommodating multiple architectures and loss functions. This standardization ensures reproducible and fair comparisons across different methods. We detail MIST's data format requirements, pipelines, and auxiliary features and demonstrate its efficacy using the BraTS Adult Glioma Post-Treatment Challenge dataset. Our results highlight MIST's ability to produce accurate segmentation masks and its scalability across multiple GPUs, showcasing its potential as a powerful tool for future medical imaging research and development.

State-of-the-art performance in QA tasks is currently achieved by systems employing Large Language Models (LLMs), however these models tend to hallucinate information in their responses. One approach focuses on enhancing the generation process by incorporating attribution from the given input to the output. However, the challenge of identifying appropriate attributions and verifying their accuracy against a source is a complex task that requires significant improvements in assessing such systems. We introduce an attribution-oriented Chain-of-Thought reasoning method to enhance the accuracy of attributions. This approach focuses the reasoning process on generating an attribution-centric output. Evaluations on two context-enhanced question-answering datasets using GPT-4 demonstrate improved accuracy and correctness of attributions. In addition, the combination of our method with finetuning enhances the response and attribution accuracy of two smaller LLMs, showing their potential to outperform GPT-4 in some cases.

Domain generalization is a critical challenge for machine learning systems. Prior domain generalization methods focus on extracting domain-invariant features across several stationary domains to enable generalization to new domains. However, in non-stationary tasks where new domains evolve in an underlying continuous structure, such as time, merely extracting the invariant features is insufficient for generalization to the evolving new domains. Nevertheless, it is non-trivial to learn both evolving and invariant features within a single model due to their conflicts. To bridge this gap, we build causal models to characterize the distribution shifts concerning the two patterns, and propose to learn both dynamic and invariant features via a new framework called Mutual Information-Based Sequential Autoencoders (MISTS). MISTS adopts information theoretic constraints onto sequential autoencoders to disentangle the dynamic and invariant features, and leverage a domain adaptive classifier to make predictions based on both evolving and invariant information. Our experimental results on both synthetic and real-world datasets demonstrate that MISTS succeeds in capturing both evolving and invariant information, and present promising results in evolving domain generalization tasks.

Recently, many studies utilized adversarial examples (AEs) to raise the cost of malicious image editing and copyright violation powered by latent diffusion models (LDMs). Despite their successes, a few have studied the surrogate model they used to generate AEs. In this paper, from the perspective of adversarial transferability, we investigate how the surrogate model's property influences the performance of AEs for LDMs. Specifically, we view the time-step sampling in the Monte-Carlo-based (MC-based) adversarial attack as selecting surrogate models. We find that the smoothness of surrogate models at different time steps differs, and we substantially improve the performance of the MC-based AEs by selecting smoother surrogate models. In the light of the theoretical framework on adversarial transferability in image classification, we also conduct a theoretical analysis to explain why smooth surrogate models can also boost AEs for LDMs.

In Member Inference (MI) attacks, the adversary try to determine whether an instance is used to train a machine learning (ML) model. MI attacks are a major privacy concern when using private data to train ML models. Most MI attacks in the literature take advantage of the fact that ML models are trained to fit the training data well, and thus have very low loss on training instances. Most defenses against MI attacks therefore try to make the model fit the training data less well. Doing so, however, generally results in lower accuracy. We observe that training instances have different degrees of vulnerability to MI attacks. Most instances will have low loss even when not included in training. For these instances, the model can fit them well without concerns of MI attacks. An effective defense only needs to (possibly implicitly) identify instances that are vulnerable to MI attacks and avoids overfitting them. A major challenge is how to achieve such an effect in an efficient training process. Leveraging two distinct recent advancements in representation learning: counterfactually-invariant representations and subspace learning methods, we introduce a novel Membership-Invariant Subspace Training (MIST) method to defend against MI attacks. MIST avoids overfitting the vulnerable instances without significant impact on other instances. We have conducted extensive experimental studies, comparing MIST with various other state-of-the-art (SOTA) MI defenses against several SOTA MI attacks. We find that MIST outperforms other defenses while resulting in minimal reduction in testing accuracy.

Large-scale medical imaging datasets have accelerated development of artificial intelligence tools for clinical decision support. However, the large size of these datasets is a bottleneck for users with limited storage and bandwidth. Many users may not even require such large datasets as AI models are often trained on lower resolution images. If users could directly download at their desired resolution, storage and bandwidth requirements would significantly decrease. However, it is impossible to anticipate every users' requirements and impractical to store the data at multiple resolutions. What if we could store images at a single resolution but send them at different ones? We propose MIST, an open-source framework to operationalize progressive resolution for streaming medical images at multiple resolutions from a single high-resolution copy. We demonstrate that MIST can dramatically reduce imaging infrastructure inefficiencies for hosting and streaming medical images by >90%, while maintaining diagnostic quality for deep learning applications.