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Apr 23

Neuro-Symbolic Activation Discovery: Transferring Mathematical Structures from Physics to Ecology for Parameter-Efficient Neural Networks

Modern neural networks rely on generic activation functions (ReLU, GELU, SiLU) that ignore the mathematical structure inherent in scientific data. We propose Neuro-Symbolic Activation Discovery, a framework that uses Genetic Programming to extract interpretable mathematical formulas from data and inject them as custom activation functions. Our key contribution is the discovery of a Geometric Transfer phenomenon: activation functions learned from particle physics data successfully generalize to ecological classification, outperforming standard activations (ReLU, GELU, SiLU) in both accuracy and parameter efficiency. On the Forest Cover dataset, our Hybrid Transfer model achieves 82.4% accuracy with only 5,825 parameters, compared to 83.4% accuracy requiring 31,801 parameters for a conventional heavy network -- a 5.5x parameter reduction with only 1% accuracy loss. We introduce a Parameter Efficiency Score (E_{param} = AUC / log_{10}(Params)) and demonstrate that lightweight hybrid architectures consistently achieve 18-21% higher efficiency than over-parameterized baselines. Crucially, we establish boundary conditions: while Physics to Ecology transfer succeeds (both involve continuous Euclidean measurements), Physics to Text transfer fails (discrete word frequencies require different mathematical structures). Our work opens pathways toward domain-specific activation libraries for efficient scientific machine learning.

  • 1 authors
·
Jan 9

Refine Drugs, Don't Complete Them: Uniform-Source Discrete Flows for Fragment-Based Drug Discovery

We introduce InVirtuoGen, a discrete flow generative model for fragmented SMILES for de novo and fragment-constrained generation, and target-property/lead optimization of small molecules. The model learns to transform a uniform source over all possible tokens into the data distribution. Unlike masked models, its training loss accounts for predictions on all sequence positions at every denoising step, shifting the generation paradigm from completion to refinement, and decoupling the number of sampling steps from the sequence length. For de novo generation, InVirtuoGen achieves a stronger quality-diversity pareto frontier than prior fragment-based models and competitive performance on fragment-constrained tasks. For property and lead optimization, we propose a hybrid scheme that combines a genetic algorithm with a Proximal Property Optimization fine-tuning strategy adapted to discrete flows. Our approach sets a new state-of-the-art on the Practical Molecular Optimization benchmark, measured by top-10 AUC across tasks, and yields higher docking scores in lead optimization than previous baselines. InVirtuoGen thus establishes a versatile generative foundation for drug discovery, from early hit finding to multi-objective lead optimization. We further contribute to open science by releasing pretrained checkpoints and code, making our results fully reproduciblehttps://github.com/invirtuolabs/InVirtuoGen_results.

  • 4 authors
·
Sep 30, 2025

TITAN: T Cell Receptor Specificity Prediction with Bimodal Attention Networks

Motivation: The activity of the adaptive immune system is governed by T-cells and their specific T-cell receptors (TCR), which selectively recognize foreign antigens. Recent advances in experimental techniques have enabled sequencing of TCRs and their antigenic targets (epitopes), allowing to research the missing link between TCR sequence and epitope binding specificity. Scarcity of data and a large sequence space make this task challenging, and to date only models limited to a small set of epitopes have achieved good performance. Here, we establish a k-nearest-neighbor (K-NN) classifier as a strong baseline and then propose TITAN (Tcr epITope bimodal Attention Networks), a bimodal neural network that explicitly encodes both TCR sequences and epitopes to enable the independent study of generalization capabilities to unseen TCRs and/or epitopes. Results: By encoding epitopes at the atomic level with SMILES sequences, we leverage transfer learning and data augmentation to enrich the input data space and boost performance. TITAN achieves high performance in the prediction of specificity of unseen TCRs (ROC-AUC 0.87 in 10-fold CV) and surpasses the results of the current state-of-the-art (ImRex) by a large margin. Notably, our Levenshtein-distance-based K-NN classifier also exhibits competitive performance on unseen TCRs. While the generalization to unseen epitopes remains challenging, we report two major breakthroughs. First, by dissecting the attention heatmaps, we demonstrate that the sparsity of available epitope data favors an implicit treatment of epitopes as classes. This may be a general problem that limits unseen epitope performance for sufficiently complex models. Second, we show that TITAN nevertheless exhibits significantly improved performance on unseen epitopes and is capable of focusing attention on chemically meaningful molecular structures.

  • 3 authors
·
Apr 21, 2021

Rayleigh Quotient Graph Neural Networks for Graph-level Anomaly Detection

Graph-level anomaly detection has gained significant attention as it finds applications in various domains, such as cancer diagnosis and enzyme prediction. However, existing methods fail to capture the spectral properties of graph anomalies, resulting in unexplainable framework design and unsatisfying performance. In this paper, we re-investigate the spectral differences between anomalous and normal graphs. Our main observation shows a significant disparity in the accumulated spectral energy between these two classes. Moreover, we prove that the accumulated spectral energy of the graph signal can be represented by its Rayleigh Quotient, indicating that the Rayleigh Quotient is a driving factor behind the anomalous properties of graphs. Motivated by this, we propose Rayleigh Quotient Graph Neural Network (RQGNN), the first spectral GNN that explores the inherent spectral features of anomalous graphs for graph-level anomaly detection. Specifically, we introduce a novel framework with two components: the Rayleigh Quotient learning component (RQL) and Chebyshev Wavelet GNN with RQ-pooling (CWGNN-RQ). RQL explicitly captures the Rayleigh Quotient of graphs and CWGNN-RQ implicitly explores the spectral space of graphs. Extensive experiments on 10 real-world datasets show that RQGNN outperforms the best rival by 6.74% in Macro-F1 score and 1.44% in AUC, demonstrating the effectiveness of our framework. Our code is available at https://github.com/xydong127/RQGNN.

  • 3 authors
·
Oct 4, 2023

FireRedASR2S: A State-of-the-Art Industrial-Grade All-in-One Automatic Speech Recognition System

We present FireRedASR2S, a state-of-the-art industrial-grade all-in-one automatic speech recognition (ASR) system. It integrates four modules in a unified pipeline: ASR, Voice Activity Detection (VAD), Spoken Language Identification (LID), and Punctuation Prediction (Punc). All modules achieve SOTA performance on the evaluated benchmarks: FireRedASR2: An ASR module with two variants, FireRedASR2-LLM (8B+ parameters) and FireRedASR2-AED (1B+ parameters), supporting speech and singing transcription for Mandarin, Chinese dialects and accents, English, and code-switching. Compared to FireRedASR, FireRedASR2 delivers improved recognition accuracy and broader dialect and accent coverage. FireRedASR2-LLM achieves 2.89% average CER on 4 public Mandarin benchmarks and 11.55% on 19 public Chinese dialects and accents benchmarks, outperforming competitive baselines including Doubao-ASR, Qwen3-ASR, and Fun-ASR. FireRedVAD: An ultra-lightweight module (0.6M parameters) based on the Deep Feedforward Sequential Memory Network (DFSMN), supporting streaming VAD, non-streaming VAD, and multi-label VAD (mVAD). On the FLEURS-VAD-102 benchmark, it achieves 97.57% frame-level F1 and 99.60% AUC-ROC, outperforming Silero-VAD, TEN-VAD, FunASR-VAD, and WebRTC-VAD. FireRedLID: An Encoder-Decoder LID module supporting 100+ languages and 20+ Chinese dialects and accents. On FLEURS (82 languages), it achieves 97.18% utterance-level accuracy, outperforming Whisper and SpeechBrain. FireRedPunc: A BERT-style punctuation prediction module for Chinese and English. On multi-domain benchmarks, it achieves 78.90% average F1, outperforming FunASR-Punc (62.77%). To advance research in speech processing, we release model weights and code at https://github.com/FireRedTeam/FireRedASR2S.

  • 9 authors
·
Mar 11 2

When Self-Reference Fails to Close: Matrix-Level Dynamics in Large Language Models

We investigate how self-referential inputs alter the internal matrix dynamics of large language models. Measuring 106 scalar metrics across up to 7 analysis passes on four models from three architecture families -- Qwen3-VL-8B, Llama-3.2-11B, Llama-3.3-70B, and Gemma-2-9B -- over 300 prompts in a 14-level hierarchy at three temperatures (T in {0.0, 0.3, 0.7}), we find that self-reference alone is not destabilizing: grounded self-referential statements and meta-cognitive prompts are markedly more stable than paradoxical self-reference on key collapse-related metrics, and on several such metrics can be as stable as factual controls. Instability concentrates in prompts inducing non-closing truth recursion (NCTR) -- truth-value computations with no finite-depth resolution. NCTR prompts produce anomalously elevated attention effective rank -- indicating attention reorganization with global dispersion rather than simple concentration collapse -- and key metrics reach Cohen's d = 3.14 (attention effective rank) to 3.52 (variance kurtosis) vs. stable self-reference in the 70B model; 281/397 metric-model combinations differentiate NCTR from stable self-reference after FDR correction (q < 0.05), 198 with |d| > 0.8. Per-layer SVD confirms disruption at every sampled layer (d > +1.0 in all three models analyzed), ruling out aggregation artifacts. A classifier achieves AUC 0.81-0.90; 30 minimal pairs yield 42/387 significant combinations; 43/106 metrics replicate across all four models. We connect these observations to three classical matrix-semigroup problems and propose, as a conjecture, that NCTR forces finite-depth transformers toward dynamical regimes where these problems concentrate. NCTR prompts also produce elevated contradictory output (+34-56 percentage points vs. controls), suggesting practical relevance for understanding self-referential failure modes.

  • 1 authors
·
Apr 12

AWARE-NET: Adaptive Weighted Averaging for Robust Ensemble Network in Deepfake Detection

Deepfake detection has become increasingly important due to the rise of synthetic media, which poses significant risks to digital identity and cyber presence for security and trust. While multiple approaches have improved detection accuracy, challenges remain in achieving consistent performance across diverse datasets and manipulation types. In response, we propose a novel two-tier ensemble framework for deepfake detection based on deep learning that hierarchically combines multiple instances of three state-of-the-art architectures: Xception, Res2Net101, and EfficientNet-B7. Our framework employs a unique approach where each architecture is instantiated three times with different initializations to enhance model diversity, followed by a learnable weighting mechanism that dynamically combines their predictions. Unlike traditional fixed-weight ensembles, our first-tier averages predictions within each architecture family to reduce model variance, while the second tier learns optimal contribution weights through backpropagation, automatically adjusting each architecture's influence based on their detection reliability. Our experiments achieved state-of-the-art intra-dataset performance with AUC scores of 99.22% (FF++) and 100.00% (CelebDF-v2), and F1 scores of 98.06% (FF++) and 99.94% (CelebDF-v2) without augmentation. With augmentation, we achieve AUC scores of 99.47% (FF++) and 100.00% (CelebDF-v2), and F1 scores of 98.43% (FF++) and 99.95% (CelebDF-v2). The framework demonstrates robust cross-dataset generalization, achieving AUC scores of 88.20% and 72.52%, and F1 scores of 93.16% and 80.62% in cross-dataset evaluations.

  • 6 authors
·
May 1, 2025

Zero-Shot ECG Classification with Multimodal Learning and Test-time Clinical Knowledge Enhancement

Electrocardiograms (ECGs) are non-invasive diagnostic tools crucial for detecting cardiac arrhythmic diseases in clinical practice. While ECG Self-supervised Learning (eSSL) methods show promise in representation learning from unannotated ECG data, they often overlook the clinical knowledge that can be found in reports. This oversight and the requirement for annotated samples for downstream tasks limit eSSL's versatility. In this work, we address these issues with the Multimodal ECG Representation Learning (MERL}) framework. Through multimodal learning on ECG records and associated reports, MERL is capable of performing zero-shot ECG classification with text prompts, eliminating the need for training data in downstream tasks. At test time, we propose the Clinical Knowledge Enhanced Prompt Engineering (CKEPE) approach, which uses Large Language Models (LLMs) to exploit external expert-verified clinical knowledge databases, generating more descriptive prompts and reducing hallucinations in LLM-generated content to boost zero-shot classification. Based on MERL, we perform the first benchmark across six public ECG datasets, showing the superior performance of MERL compared against eSSL methods. Notably, MERL achieves an average AUC score of 75.2% in zero-shot classification (without training data), 3.2% higher than linear probed eSSL methods with 10\% annotated training data, averaged across all six datasets. Code and models are available at https://github.com/cheliu-computation/MERL

  • 6 authors
·
Mar 11, 2024

Detecting Intrinsic and Instrumental Self-Preservation in Autonomous Agents: The Unified Continuation-Interest Protocol

Autonomous agents, especially delegated systems with memory, persistent context, and multi-step planning, pose a measurement problem not present in stateless models: an agent that preserves continued operation as a terminal objective and one that does so merely instrumentally can produce observationally similar trajectories. External behavioral monitoring cannot reliably distinguish between them. We introduce the Unified Continuation-Interest Protocol (UCIP), a multi-criterion detection framework that moves this distinction from behavior to the latent structure of agent trajectories. UCIP encodes trajectories with a Quantum Boltzmann Machine (QBM), a classical algorithm based on the density-matrix formalism of quantum statistical mechanics, and measures the von Neumann entropy of the reduced density matrix induced by a bipartition of hidden units. We test whether agents with terminal continuation objectives (Type A) produce latent states with higher entanglement entropy than agents whose continuation is merely instrumental (Type B). Higher entanglement reflects stronger cross-partition statistical coupling. On gridworld agents with known ground-truth objectives, UCIP achieves 100% detection accuracy and 1.0 AUC-ROC on held-out non-adversarial evaluation under the frozen Phase I gate. The entanglement gap between Type A and Type B agents is Delta = 0.381 (p < 0.001, permutation test). Pearson r = 0.934 across an 11-point interpolation sweep indicates that, within this synthetic family, UCIP tracks graded changes in continuation weighting rather than merely a binary label. Among the tested models, only the QBM achieves positive Delta. All computations are classical; "quantum" refers only to the mathematical formalism. UCIP does not detect consciousness or subjective experience; it detects statistical structure in latent representations that correlates with known objectives.

Starlab Starlab
·
Mar 11 2

Can LLMs Outshine Conventional Recommenders? A Comparative Evaluation

In recent years, integrating large language models (LLMs) into recommender systems has created new opportunities for improving recommendation quality. However, a comprehensive benchmark is needed to thoroughly evaluate and compare the recommendation capabilities of LLMs with traditional recommender systems. In this paper, we introduce RecBench, which systematically investigates various item representation forms (including unique identifier, text, semantic embedding, and semantic identifier) and evaluates two primary recommendation tasks, i.e., click-through rate prediction (CTR) and sequential recommendation (SeqRec). Our extensive experiments cover up to 17 large models and are conducted across five diverse datasets from fashion, news, video, books, and music domains. Our findings indicate that LLM-based recommenders outperform conventional recommenders, achieving up to a 5% AUC improvement in the CTR scenario and up to a 170% NDCG@10 improvement in the SeqRec scenario. However, these substantial performance gains come at the expense of significantly reduced inference efficiency, rendering the LLM-as-RS paradigm impractical for real-time recommendation environments. We aim for our findings to inspire future research, including recommendation-specific model acceleration methods. We will release our code, data, configurations, and platform to enable other researchers to reproduce and build upon our experimental results.

  • 8 authors
·
Mar 7, 2025

SAMURAI: Adapting Segment Anything Model for Zero-Shot Visual Tracking with Motion-Aware Memory

The Segment Anything Model 2 (SAM 2) has demonstrated strong performance in object segmentation tasks but faces challenges in visual object tracking, particularly when managing crowded scenes with fast-moving or self-occluding objects. Furthermore, the fixed-window memory approach in the original model does not consider the quality of memories selected to condition the image features for the next frame, leading to error propagation in videos. This paper introduces SAMURAI, an enhanced adaptation of SAM 2 specifically designed for visual object tracking. By incorporating temporal motion cues with the proposed motion-aware memory selection mechanism, SAMURAI effectively predicts object motion and refines mask selection, achieving robust, accurate tracking without the need for retraining or fine-tuning. SAMURAI operates in real-time and demonstrates strong zero-shot performance across diverse benchmark datasets, showcasing its ability to generalize without fine-tuning. In evaluations, SAMURAI achieves significant improvements in success rate and precision over existing trackers, with a 7.1% AUC gain on LaSOT_{ext} and a 3.5% AO gain on GOT-10k. Moreover, it achieves competitive results compared to fully supervised methods on LaSOT, underscoring its robustness in complex tracking scenarios and its potential for real-world applications in dynamic environments. Code and results are available at https://github.com/yangchris11/samurai.

  • 5 authors
·
Nov 18, 2024 3

Towards Refining Developer Questions using LLM-Based Named Entity Recognition for Developer Chatroom Conversations

In software engineering chatrooms, communication is often hindered by imprecise questions that cannot be answered. Recognizing key entities can be essential for improving question clarity and facilitating better exchange. However, existing research using natural language processing techniques often overlooks these software-specific nuances. In this paper, we introduce Software-specific Named Entity Recognition, Intent Detection, and Resolution Classification (SENIR), a labeling approach that leverages a Large Language Model to annotate entities, intents, and resolution status in developer chatroom conversations. To offer quantitative guidance for improving question clarity and resolvability, we build a resolution prediction model that leverages SENIR's entity and intent labels along with additional predictive features. We evaluate SENIR on the DISCO dataset using a subset of annotated chatroom dialogues. SENIR achieves an 86% F-score for entity recognition, a 71% F-score for intent detection, and an 89% F-score for resolution status classification. Furthermore, our resolution prediction model, tested with various sampling strategies (random undersampling and oversampling with SMOTE) and evaluation methods (5-fold cross-validation, 10-fold cross-validation, and bootstrapping), demonstrates AUC values ranging from 0.7 to 0.8. Key factors influencing resolution include positive sentiment and entities such as Programming Language and User Variable across multiple intents, while diagnostic entities are more relevant in error-related questions. Moreover, resolution rates vary significantly by intent: questions about API Usage and API Change achieve higher resolution rates, whereas Discrepancy and Review have lower resolution rates. A Chi-Square analysis confirms the statistical significance of these differences.

  • 5 authors
·
Mar 1, 2025

MOOZY: A Patient-First Foundation Model for Computational Pathology

Computational pathology needs whole-slide image (WSI) foundation models that transfer across diverse clinical tasks, yet current approaches remain largely slide-centric, often depend on private data and expensive paired-report supervision, and do not explicitly model relationships among multiple slides from the same patient. We present MOOZY, a patient-first pathology foundation model in which the patient case, not the individual slide, is the core unit of representation. MOOZY explicitly models dependencies across all slides from the same patient via a case transformer during pretraining, combining multi-stage open self-supervision with scaled low-cost task supervision. In Stage 1, we pretrain a vision-only slide encoder on 77,134 public slide feature grids using masked self-distillation. In Stage 2, we align these representations with clinical semantics using a case transformer and multi-task supervision over 333 tasks from 56 public datasets, including 205 classification and 128 survival tasks across four endpoints. Across eight held-out tasks with five-fold frozen-feature probe evaluation, MOOZY achieves best or tied-best performance on most metrics and improves macro averages over TITAN by +7.37%, +5.50%, and +7.83% and over PRISM by +8.83%, +10.70%, and +9.78% for weighted F1, weighted ROC-AUC, and balanced accuracy, respectively. MOOZY is also parameter efficient with 85.77M parameters, 14x smaller than GigaPath. These results demonstrate that open, reproducible patient-level pretraining yields transferable embeddings, providing a practical path toward scalable patient-first histopathology foundation models.

LoMa: Local Feature Matching Revisited

Local feature matching has long been a fundamental component of 3D vision systems such as Structure-from-Motion (SfM), yet progress has lagged behind the rapid advances of modern data-driven approaches. The newer approaches, such as feed-forward reconstruction models, have benefited extensively from scaling dataset sizes, whereas local feature matching models are still only trained on a few mid-sized datasets. In this paper, we revisit local feature matching from a data-driven perspective. In our approach, which we call LoMa, we combine large and diverse data mixtures, modern training recipes, scaled model capacity, and scaled compute, resulting in remarkable gains in performance. Since current standard benchmarks mainly rely on collecting sparse views from successful 3D reconstructions, the evaluation of progress in feature matching has been limited to relatively easy image pairs. To address the resulting saturation of benchmarks, we collect 1000 highly challenging image pairs from internet data into a new dataset called HardMatch. Ground truth correspondences for HardMatch are obtained via manual annotation by the authors. In our extensive benchmarking suite, we find that LoMa makes outstanding progress across the board, outperforming the state-of-the-art method ALIKED+LightGlue by +18.6 mAA on HardMatch, +29.5 mAA on WxBS, +21.4 (1m, 10^circ) on InLoc, +24.2 AUC on RUBIK, and +12.4 mAA on IMC 2022. We release our code and models publicly at https://github.com/davnords/LoMa.

  • 9 authors
·
Apr 5