OpenRaiser/Intern-Atlas huggingface dataset:
Weight-sparse transformers have interpretable circuits
Venue: arXiv cs.LG 2025
Year: 2025

Finding human-understandable circuits in language models is a central goal of the field of mechanistic interpretability. We train models to have more understandable circuits by constraining most of their weights to be zeros, so that each neuron only has a few connections. To recover fine-grained circuits underlying each of several hand-crafted tasks, we prune the models to isolate the part responsible for the task. These circuits often contain neurons and residual channels that correspond to natural concepts, with a small number of straightforwardly interpretable connections between them. We study how these models scale and find that making weights sparser trades off capability for interpretability, and scaling model size improves the capability-interpretability frontier. However, scaling sparse models beyond tens of millions of nonzero parameters while preserving interpretability remains a challenge. In addition to training weight-sparse models de novo, we show preliminary results suggesting our method can also be adapted to explain existing dense models. Our work produces circuits that achieve an unprecedented level of human understandability and validates them with considerable rigor.
Ontology-Driven Model-to-Model Transformation of Workflow Specifications
Venue: arXiv cs.SE 2025
Year: 2025

Proprietary workflow modeling languages such as Smart Forms & Smart Flow hamper interoperability and reuse because they lock process knowledge into closed formats. To address this vendor lock-in and ease migration to open standards, we introduce an ontology-driven model-to-model pipeline that systematically translates domain-specific workflow definitions to Business Process Model and Notation (BPMN) 2.0. The pipeline comprises three phases: RML-based semantic lifting of JSON to RDF/OWL, ontology alignment and reasoning, and BPMN generation via the Camunda Model API. By externalizing mapping knowledge into ontologies and declarative rules rather than code, the approach supports reusability across vendor-specific formats and preserves semantic traceability between source definitions and target BPMN models. We instantiated the pipeline for Instituto Superior Técnico (IST)'s Smart Forms & Smart Flow and implemented a converter that produces standard-compliant BPMN diagrams. Evaluation on a corpus of 69 real-world workflows produced 92 BPMN diagrams with a 94.2% success rate. Failures (5.81%) stemmed from dynamic behaviors and time-based transitions not explicit in the static JSON. Interviews with support and development teams indicated that the resulting diagrams provide a top-down view that improves comprehension, diagnosis and onboarding by exposing implicit control flow and linking tasks and forms back to their sources. The pipeline is generalizable to other proprietary workflow languages by adapting the ontology and mappings, enabling interoperability and reducing vendor dependency while supporting continuous integration and long-term maintainability. The presented case study demonstrates that ontology-driven M2M transformation can systematically bridge domain-specific workflows and standard notations, offering quantifiable performance and qualitative benefits for stakeholders.
Rare Genomic Subtype Discovery from RNA-seq via Autoencoder Embeddings and Stability-Aware Clustering
Venue: arXiv cs.LG 2025
Year: 2025

Unsupervised learning on high-dimensional RNA-seq data can reveal molecular subtypes beyond standard labels. We combine an autoencoder-based representation with clustering and stability analysis to search for rare but reproducible genomic subtypes. On the UCI "Gene Expression Cancer RNA-Seq" dataset (801 samples, 20,531 genes; BRCA, COAD, KIRC, LUAD, PRAD), a pan-cancer analysis shows clusters aligning almost perfectly with tissue of origin (Cramer's V = 0.887), serving as a negative control. We therefore reframe the problem within KIRC (n = 146): we select the top 2,000 highly variable genes, standardize them, train a feed-forward autoencoder (128-dimensional latent space), and run k-means for k = 2-10. While global indices favor small k, scanning k with a pre-specified discovery rule (rare < 10 percent and stable with Jaccard >= 0.60 across 20 seeds after Hungarian alignment) yields a simple solution at k = 5 (silhouette = 0.129, DBI = 2.045) with a rare cluster C0 (6.85 percent of patients) that is highly stable (Jaccard = 0.787). Cluster-vs-rest differential expression (Welch's t-test, Benjamini-Hochberg FDR) identifies coherent markers. Overall, pan-cancer clustering is dominated by tissue of origin, whereas a stability-aware within-cancer approach reveals a rare, reproducible KIRC subtype.
Refine Thought: A Test-Time Inference Method for Embedding Model Reasoning
Venue: arXiv cs.CL 2025
Year: 2025

We propose RT (Refine Thought), a method that can enhance the semantic rea-soning ability of text embedding models. The method obtains the final semanticrepresentation by running multiple forward passes of the text embedding model.Experiments show that RT achieves significant improvements on semantic reason-ing tasks in BRIGHT and the person job matching benchmark PJBenchmark1, while maintaining consistent performance on general-purpose semantic under-standing tasks such as C-MTEB. Our results indicate that RT is effective becauseit further activates the semantic reasoning ability learned during pretraining bydecoder-only text embedding models(e.g., Qwen3-Embedding-8B). RT canbe seen as a test-time inference method.
Emotion Recognition in Multi-Speaker Conversations through Speaker Identification, Knowledge Distillation, and Hierarchical Fusion
Venue: arXiv cs.SD 2025
Year: 2025

Emotion recognition in multi-speaker conversations faces significant challenges due to speaker ambiguity and severe class imbalance. We propose a novel framework that addresses these issues through three key innovations: (1) a speaker identification module that leverages audio-visual synchronization to accurately identify the active speaker, (2) a knowledge distillation strategy that transfers superior textual emotion understanding to audio and visual modalities, and (3) hierarchical attention fusion with composite loss functions to handle class imbalance. Comprehensive evaluations on MELD and IEMOCAP datasets demonstrate superior performance, achieving 67.75% and 72.44% weighted F1 scores respectively, with particularly notable improvements on minority emotion classes.
Multi-Horizon Time Series Forecasting of non-parametric CDFs with Deep Lattice Networks
Venue: arXiv cs.LG 2025
Year: 2025

Probabilistic forecasting is not only a way to add more information to a prediction of the future, but it also builds on weaknesses in point prediction. Sudden changes in a time series can still be captured by a cumulative distribution function (CDF), while a point prediction is likely to miss it entirely. The modeling of CDFs within forecasts has historically been limited to parametric approaches, but due to recent advances, this no longer has to be the case. We aim to advance the fields of probabilistic forecasting and monotonic networks by connecting them and propose an approach that permits the forecasting of implicit, complete, and nonparametric CDFs. For this purpose, we propose an adaptation to deep lattice networks (DLN) for monotonically constrained simultaneous/implicit quantile regression in time series forecasting. Quantile regression usually produces quantile crossovers, which need to be prevented to achieve a legitimate CDF. By leveraging long short term memory units (LSTM) as the embedding layer, and spreading quantile inputs to all sub-lattices of a DLN with an extended output size, we can produce a multi-horizon forecast of an implicit CDF due to the monotonic constraintability of DLNs that prevent quantile crossovers. We compare and evaluate our approach's performance to relevant state of the art within the context of a highly relevant application of time series forecasting: Day-ahead, hourly forecasts of solar irradiance observations. Our experiments show that the adaptation of a DLN performs just as well or even better than an unconstrained approach. Further comparison of the adapted DLN against a scalable monotonic neural network shows that our approach performs better. With this adaptation of DLNs, we intend to create more interest and crossover investigations in techniques of monotonic neural networks and probabilistic forecasting.
MoETTA: Test-Time Adaptation Under Mixed Distribution Shifts with MoE-LayerNorm
Venue: arXiv cs.LG 2025
Year: 2025

Test-Time adaptation (TTA) has proven effective in mitigating performance drops under single-domain distribution shifts by updating model parameters during inference. However, real-world deployments often involve mixed distribution shifts, where test samples are affected by diverse and potentially conflicting domain factors, posing significant challenges even for SOTA TTA methods. A key limitation in existing approaches is their reliance on a unified adaptation path, which fails to account for the fact that optimal gradient directions can vary significantly across different domains. Moreover, current benchmarks focus only on synthetic or homogeneous shifts, failing to capture the complexity of real-world heterogeneous mixed distribution shifts. To address this, we propose MoETTA, a novel entropy-based TTA framework that integrates the Mixture-of-Experts (MoE) architecture. Rather than enforcing a single parameter update rule for all test samples, MoETTA introduces a set of structurally decoupled experts, enabling adaptation along diverse gradient directions. This design allows the model to better accommodate heterogeneous shifts through flexible and disentangled parameter updates. To simulate realistic deployment conditions, we introduce two new benchmarks: potpourri and potpourri+. While classical settings focus solely on synthetic corruptions, potpourri encompasses a broader range of domain shifts--including natural, artistic, and adversarial distortions--capturing more realistic deployment challenges. Additionally, potpourri+ further includes source-domain samples to evaluate robustness against catastrophic forgetting. Extensive experiments across three mixed distribution shifts settings show that MoETTA consistently outperforms strong baselines, establishing SOTA performance and highlighting the benefit of modeling multiple adaptation directions via expert-level diversity.
What happens when nanochat meets DiLoCo?
Venue: arXiv cs.DC 2025
Year: 2025

Although LLM training is typically centralized with high-bandwidth interconnects and large compute budgets, emerging methods target communication-constrained training in distributed environments. The model trade-offs introduced by this shift remain underexplored, and our goal is to study them. We use the open-source nanochat project, a compact 8K-line full-stack ChatGPT-like implementation containing tokenization, pretraining, fine-tuning, and serving, as a controlled baseline. We implement the DiLoCo algorithm as a lightweight wrapper over nanochat's training loop, performing multiple local steps per worker before synchronization with an outer optimizer, effectively reducing communication by orders of magnitude. This inner-outer training is compared against a standard data-parallel (DDP) setup. Because nanochat is small and inspectable, it enables controlled pipeline adaptations and allows direct comparison with the conventional centralized baseline. DiLoCo achieves stable convergence and competitive loss in pretraining but yields worse MMLU, GSM8K, and HumanEval scores after mid-training and SFT. We discover that using DiLoCo-pretrained weights and running mid- and post-training with DDP fails to recover performance, revealing irreversible representation drift from asynchronous updates that impairs downstream alignment. We provide this implementation as an official fork of nanochat on GitHub.
PROF: An LLM-based Reward Code Preference Optimization Framework for Offline Imitation Learning
Venue: arXiv cs.LG 2025
Year: 2025

Offline imitation learning (offline IL) enables training effective policies without requiring explicit reward annotations. Recent approaches attempt to estimate rewards for unlabeled datasets using a small set of expert demonstrations. However, these methods often assume that the similarity between a trajectory and an expert demonstration is positively correlated with the reward, which oversimplifies the underlying reward structure. We propose PROF, a novel framework that leverages large language models (LLMs) to generate and improve executable reward function codes from natural language descriptions and a single expert trajectory. We propose Reward Preference Ranking (RPR), a novel reward function quality assessment and ranking strategy without requiring environment interactions or RL training. RPR calculates the dominance scores of the reward functions, where higher scores indicate better alignment with expert preferences. By alternating between RPR and text-based gradient optimization, PROF fully automates the selection and refinement of optimal reward functions for downstream policy learning. Empirical results on D4RL demonstrate that PROF surpasses or matches recent strong baselines across numerous datasets and domains, highlighting the effectiveness of our approach.
Imagine in Space: Exploring the Frontier of Spatial Intelligence and Reasoning Efficiency in Vision Language Models
Venue: arXiv cs.AI 2025
Year: 2025

Large language models (LLMs) and vision language models (VLMs), such as DeepSeek R1,OpenAI o3, and Gemini 2.5 Pro, have demonstrated remarkable reasoning capabilities across logical inference, problem solving, and decision making. However, spatial reasoning:a fundamental component of human cognition that includes mental rotation, navigation, and spatial relationship comprehension remains a significant challenge for current advanced VLMs. We hypothesize that imagination, the internal simulation of spatial states, is the dominant reasoning mechanism within a spatial world model. To test this hypothesis and systematically probe current VLM spatial reasoning mechanisms, we introduce SpatiaLite, a fully synthetic benchmark that jointly measures spatial reasoning accuracy and reasoning efficiency. Comprehensive experiments reveal three key findings. First, advanced VLMs predominantly rely on linguistic representations for reasoning and imagination, resulting in significant deficiencies on visual centric tasks that demand perceptual spatial relations and 3D geometry transformations such as mental rotation or projection prediction. Second, advanced VLMs exhibit severe inefficiency in their current spatial reasoning mechanisms, with token usage growing rapidly as transformation complexity increases. Third, we propose an Imagery Driven Framework (IDF) for data synthesis and training, which can implicitly construct an internal world model that is critical for spatial reasoning in VLMs. Building on SpatiaLite, this work delineates the spatial reasoning limits and patterns of advanced VLMs, identifies key shortcomings, and informs future advances
Uncovering and Aligning Anomalous Attention Heads to Defend Against NLP Backdoor Attacks
Venue: arXiv cs.CR 2025
Year: 2025

Backdoor attacks pose a serious threat to the security of large language models (LLMs), causing them to exhibit anomalous behavior under specific trigger conditions. The design of backdoor triggers has evolved from fixed triggers to dynamic or implicit triggers. This increased flexibility in trigger design makes it challenging for defenders to identify their specific forms accurately. Most existing backdoor defense methods are limited to specific types of triggers or rely on an additional clean model for support. To address this issue, we propose a backdoor detection method based on attention similarity, enabling backdoor detection without prior knowledge of the trigger. Our study reveals that models subjected to backdoor attacks exhibit unusually high similarity among attention heads when exposed to triggers. Based on this observation, we propose an attention safety alignment approach combined with head-wise fine-tuning to rectify potentially contaminated attention heads, thereby effectively mitigating the impact of backdoor attacks. Extensive experimental results demonstrate that our method significantly reduces the success rate of backdoor attacks while preserving the model's performance on downstream tasks.
FusionFM: All-in-One Multi-Modal Image Fusion with Flow Matching
Venue: arXiv cs.CV 2025
Year: 2025

Current multi-modal image fusion methods typically rely on task-specific models, leading to high training costs and limited scalability. While generative methods provide a unified modeling perspective, they often suffer from slow inference due to the complex sampling trajectories from noise to image. To address this, we formulate image fusion as a direct probabilistic transport from source modalities to the fused image distribution, leveraging the flow matching paradigm to improve sampling efficiency and structural consistency. To mitigate the lack of high-quality fused images for supervision, we collect fusion results from multiple state-of-the-art models as priors, and employ a task-aware selection function to select the most reliable pseudo-labels for each task. We further introduce a Fusion Refiner module that employs a divide-and-conquer strategy to systematically identify, decompose, and enhance degraded components in selected pseudo-labels. For multi-task scenarios, we integrate elastic weight consolidation and experience replay mechanisms to preserve cross-task performance and enhance continual learning ability from both parameter stability and memory retention perspectives. Our approach achieves competitive performance across diverse fusion tasks, while significantly improving sampling efficiency and maintaining a lightweight model design. The code will be available at: https://github.com/Ist-Zhy/FusionFM.
Synergizing Multigrid Algorithms with Vision Transformer: A Novel Approach to Enhance the Seismic Foundation Model
Venue: arXiv cs.CV 2025
Year: 2025

Due to the emergency and homogenization of Artificial Intelligence (AI) technology development, transformer-based foundation models have revolutionized scientific applications, such as drug discovery, materials research, and astronomy. However, seismic data presents unique characteristics that require specialized processing techniques for pretraining foundation models in seismic contexts with high- and low-frequency features playing crucial roles. Existing vision transformers (ViTs) with sequential tokenization ignore the intrinsic pattern and fail to grasp both the high- and low-frequency seismic information efficiently and effectively. This work introduces a novel adaptive two-grid foundation model training strategy (ADATG) with Hilbert encoding specifically tailored for seismogram data, leveraging the hierarchical structures inherent in seismic data. Specifically, our approach employs spectrum decomposition to separate high- and low-frequency components and utilizes hierarchical Hilbert encoding to represent the data effectively. Moreover, observing the frequency principle observed in ViTs, we propose an adaptive training strategy that initially emphasizes coarse-level information and then progressively refines the model's focus on fine-level features. Our extensive experiments demonstrate the effectiveness and efficiency of our training methods. This research highlights the importance of data encoding and training strategies informed by the distinct characteristics of high- and low-frequency features in seismic images, ultimately contributing to the enhancement of visual seismic foundation models pretraining.
Do MPI Derived Datatypes Actually Help? A Single-Node Cross-Implementation Study on Shared-Memory Communication
Venue: arXiv cs.DC 2025
Year: 2025

MPI's derived datatypes (DDTs) promise easier, copy-free communication of non-contiguous data, yet their practical performance remains debated and is often reported only for a single MPI stack. We present a cross-implementation assessment using three 2D applications: a Jacobi CFD solver, Conway's Game of Life, and a lattice-based image reconstruction. Each application is written in two ways: (i) a BASIC version with manual packing and unpacking of non-contiguous regions and (ii) a DDT version using MPI_Type_vector and MPI_Type_create_subarray with correct true extent via MPI_Type_create_resized. For API parity, we benchmark identical communication semantics: non-blocking point-to-point (Irecv/Isend + Waitall), neighborhood collectives (MPI_Neighbor_alltoallw), and MPI-4 persistent operations (*_init). We run strong and weak scaling on 1-4 ranks, validate bitwise-identical halos, and evaluate four widely used MPI implementations: MPICH, Open MPI, Intel MPI, and MVAPICH2 on a single ARCHER2 node. Results are mixed. DDTs can be fastest, for example for the image reconstruction code on Intel MPI and MPICH, but can also be among the slowest on other stacks, such as Open MPI and MVAPICH2 for the same code. For the CFD solver, BASIC variants generally outperform DDTs across semantics, whereas for Game of Life the ranking flips depending on the MPI library. We also observe stack-specific anomalies, for example MPICH slowdowns with DDT neighborhood and persistent modes. Overall, no strategy dominates across programs, semantics, and MPI stacks; performance portability for DDTs is not guaranteed. We therefore recommend profiling both DDT-based and manual-packing designs under the intended MPI implementation and communication mode. Our study is limited to a single node and does not analyze memory overhead; multi-node and GPU-aware paths are left for future work.
Zipf-Gramming: Scaling Byte N-Grams Up to Production Sized Malware Corpora
Venue: arXiv cs.CR 2025
Year: 2025

A classifier using byte n-grams as features is the only approach we have found fast enough to meet requirements in size (sub 2 MB), speed (multiple GB/s), and latency (sub 10 ms) for deployment in numerous malware detection scenarios. However, we've consistently found that 6-8 grams achieve the best accuracy on our production deployments but have been unable to deploy regularly updated models due to the high cost of finding the top-k most frequent n-grams over terabytes of executable programs. Because the Zipfian distribution well models the distribution of n-grams, we exploit its properties to develop a new top-k n-gram extractor that is up to $35\times$ faster than the previous best alternative. Using our new Zipf-Gramming algorithm, we are able to scale up our production training set and obtain up to 30\% improvement in AUC at detecting new malware. We show theoretically and empirically that our approach will select the top-k items with little error and the interplay between theory and engineering required to achieve these results.