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Apr 16

Beyond Simple Concatenation: Fairly Assessing PLM Architectures for Multi-Chain Protein-Protein Interactions Prediction

Protein-protein interactions (PPIs) are fundamental to numerous cellular processes, and their characterization is vital for understanding disease mechanisms and guiding drug discovery. While protein language models (PLMs) have demonstrated remarkable success in predicting protein structure and function, their application to sequence-based PPI binding affinity prediction remains relatively underexplored. This gap is often attributed to the scarcity of high-quality, rigorously refined datasets and the reliance on simple strategies for concatenating protein representations. In this work, we address these limitations. First, we introduce a meticulously curated version of the PPB-Affinity dataset of a total of 8,207 unique protein-protein interaction entries, by resolving annotation inconsistencies and duplicate entries for multi-chain protein interactions. This dataset incorporates a stringent, less than or equal to 30%, sequence identity threshold to ensure robust splitting into training, validation, and test sets, minimizing data leakage. Second, we propose and systematically evaluate four architectures for adapting PLMs to PPI binding affinity prediction: embeddings concatenation (EC), sequences concatenation (SC), hierarchical pooling (HP), and pooled attention addition (PAD). These architectures were assessed using two training methods: full fine-tuning and a lightweight approach employing ConvBERT heads over frozen PLM features. Our comprehensive experiments across multiple leading PLMs (ProtT5, ESM2, Ankh, Ankh2, and ESM3) demonstrated that the HP and PAD architectures consistently outperform conventional concatenation methods, achieving up to 12% increase in terms of Spearman correlation. These results highlight the necessity of sophisticated architectural designs to fully exploit the capabilities of PLMs for nuanced PPI binding affinity prediction.

  • 8 authors
·
May 26, 2025 2

Extending Sequence Length is Not All You Need: Effective Integration of Multimodal Signals for Gene Expression Prediction

Gene expression prediction, which predicts mRNA expression levels from DNA sequences, presents significant challenges. Previous works often focus on extending input sequence length to locate distal enhancers, which may influence target genes from hundreds of kilobases away. Our work first reveals that for current models, long sequence modeling can decrease performance. Even carefully designed algorithms only mitigate the performance degradation caused by long sequences. Instead, we find that proximal multimodal epigenomic signals near target genes prove more essential. Hence we focus on how to better integrate these signals, which has been overlooked. We find that different signal types serve distinct biological roles, with some directly marking active regulatory elements while others reflect background chromatin patterns that may introduce confounding effects. Simple concatenation may lead models to develop spurious associations with these background patterns. To address this challenge, we propose Prism, a framework that learns multiple combinations of high-dimensional epigenomic features to represent distinct background chromatin states and uses backdoor adjustment to mitigate confounding effects. Our experimental results demonstrate that proper modeling of multimodal epigenomic signals achieves state-of-the-art performance using only short sequences for gene expression prediction.

  • 6 authors
·
Feb 24

Two Views, One Truth: Spectral and Self-Supervised Features Fusion for Robust Speech Deepfake Detection

Recent advances in synthetic speech have made audio deepfakes increasingly realistic, posing significant security risks. Existing detection methods that rely on a single modality, either raw waveform embeddings or spectral based features, are vulnerable to non spoof disturbances and often overfit to known forgery algorithms, resulting in poor generalization to unseen attacks. To address these shortcomings, we investigate hybrid fusion frameworks that integrate self supervised learning (SSL) based representations with handcrafted spectral descriptors (MFCC , LFCC, CQCC). By aligning and combining complementary information across modalities, these fusion approaches capture subtle artifacts that single feature approaches typically overlook. We explore several fusion strategies, including simple concatenation, cross attention, mutual cross attention, and a learnable gating mechanism, to optimally blend SSL features with fine grained spectral cues. We evaluate our approach on four challenging public benchmarks and report generalization performance. All fusion variants consistently outperform an SSL only baseline, with the cross attention strategy achieving the best generalization with a 38% relative reduction in equal error rate (EER). These results confirm that joint modeling of waveform and spectral views produces robust, domain agnostic representations for audio deepfake detection.

  • 6 authors
·
Jul 27, 2025

VDT: General-purpose Video Diffusion Transformers via Mask Modeling

This work introduces Video Diffusion Transformer (VDT), which pioneers the use of transformers in diffusion-based video generation. It features transformer blocks with modularized temporal and spatial attention modules to leverage the rich spatial-temporal representation inherited in transformers. We also propose a unified spatial-temporal mask modeling mechanism, seamlessly integrated with the model, to cater to diverse video generation scenarios. VDT offers several appealing benefits. 1) It excels at capturing temporal dependencies to produce temporally consistent video frames and even simulate the physics and dynamics of 3D objects over time. 2) It facilitates flexible conditioning information, \eg, simple concatenation in the token space, effectively unifying different token lengths and modalities. 3) Pairing with our proposed spatial-temporal mask modeling mechanism, it becomes a general-purpose video diffuser for harnessing a range of tasks, including unconditional generation, video prediction, interpolation, animation, and completion, etc. Extensive experiments on these tasks spanning various scenarios, including autonomous driving, natural weather, human action, and physics-based simulation, demonstrate the effectiveness of VDT. Additionally, we present comprehensive studies on how \model handles conditioning information with the mask modeling mechanism, which we believe will benefit future research and advance the field. Project page: https:VDT-2023.github.io

  • 7 authors
·
May 22, 2023

Coherent and Multi-modality Image Inpainting via Latent Space Optimization

With the advancements in denoising diffusion probabilistic models (DDPMs), image inpainting has significantly evolved from merely filling information based on nearby regions to generating content conditioned on various prompts such as text, exemplar images, and sketches. However, existing methods, such as model fine-tuning and simple concatenation of latent vectors, often result in generation failures due to overfitting and inconsistency between the inpainted region and the background. In this paper, we argue that the current large diffusion models are sufficiently powerful to generate realistic images without further tuning. Hence, we introduce PILOT (inPainting vIa Latent OpTimization), an optimization approach grounded on a novel semantic centralization and background preservation loss. Our method searches latent spaces capable of generating inpainted regions that exhibit high fidelity to user-provided prompts while maintaining coherence with the background. Furthermore, we propose a strategy to balance optimization expense and image quality, significantly enhancing generation efficiency. Our method seamlessly integrates with any pre-trained model, including ControlNet and DreamBooth, making it suitable for deployment in multi-modal editing tools. Our qualitative and quantitative evaluations demonstrate that PILOT outperforms existing approaches by generating more coherent, diverse, and faithful inpainted regions in response to provided prompts.

  • 7 authors
·
Jul 10, 2024

Atomic-to-Compositional Generalization for Mobile Agents with A New Benchmark and Scheduling System

Autonomous agents powered by multimodal large language models have been developed to facilitate task execution on mobile devices. However, prior work has predominantly focused on atomic tasks -- such as shot-chain execution tasks and single-screen grounding tasks -- while overlooking the generalization to compositional tasks, which are indispensable for real-world applications. This work introduces UI-NEXUS, a comprehensive benchmark designed to evaluate mobile agents on three categories of compositional operations: Simple Concatenation, Context Transition, and Deep Dive. UI-NEXUS supports interactive evaluation in 20 fully controllable local utility app environments, as well as 30 online Chinese and English service apps. It comprises 100 interactive task templates with an average optimal step count of 14.05. Experimental results across a range of mobile agents with agentic workflow or agent-as-a-model show that UI-NEXUS presents significant challenges. Specifically, existing agents generally struggle to balance performance and efficiency, exhibiting representative failure modes such as under-execution, over-execution, and attention drift, causing visible atomic-to-compositional generalization gap. Inspired by these findings, we propose AGENT-NEXUS, a lightweight and efficient scheduling system to tackle compositional mobile tasks. AGENT-NEXUS extrapolates the abilities of existing mobile agents by dynamically decomposing long-horizon tasks to a series of self-contained atomic subtasks. AGENT-NEXUS achieves 24% to 40% task success rate improvement for existing mobile agents on compositional operation tasks within the UI-NEXUS benchmark without significantly sacrificing inference overhead. The demo video, dataset, and code are available on the project page at https://ui-nexus.github.io.

  • 6 authors
·
Jun 10, 2025

Bridging the gap: A comparative exploration of Speech-LLM and end-to-end architecture for multilingual conversational ASR

The INTERSPEECH 2025 Challenge on Multilingual Conversational Speech Language Models (MLC-SLM) promotes multilingual conversational ASR with large language models (LLMs). Our previous SHNU-mASR system adopted a competitive parallel-speech-encoder architecture that integrated Whisper and mHuBERT with an LLM. However, it faced two challenges: simple feature concatenation may not fully exploit complementary information, and the performance gap between LLM-based ASR and end-to-end(E2E) encoder-decoder ASR remained unexplored. In this work, we present an enhanced LLM-based ASR framework that combines fine-tuned Whisper and mHuBERT encoders with an LLM to enrich speech representations. We first evaluate E2E Whisper models with LoRA and full fine-tuning on the MLC-SLM ASR task, and then propose cross-attention-based fusion mechanisms for the parallel-speech-encoder. On the official evaluation set of the MLC-SLM Challenge, our system achieves a CER/WER of 10.69%, ranking on par with the top-ranked Track 1 systems, even though it uses only 1,500 hours of baseline training data compared with their large-scale training sets. Nonetheless, we find that our final LLM-based ASR still does not match the performance of a fine-tuned E2E Whisper model, providing valuable empirical guidance for future Speech-LLM design. Our code is publicly available at https://github.com/1535176727/MLC-SLM.

  • 4 authors
·
Jan 4

Vision Matters: Simple Visual Perturbations Can Boost Multimodal Math Reasoning

Despite the rapid progress of multimodal large language models (MLLMs), they have largely overlooked the importance of visual processing. In a simple yet revealing experiment, we interestingly find that language-only models, when provided with image captions, can achieve comparable or even better performance than MLLMs that consume raw visual inputs. This suggests that current MLLMs may generate accurate visual descriptions but fail to effectively integrate them during reasoning. Motivated by this, we propose a simple visual perturbation framework that enhances perceptual robustness without requiring algorithmic modifications or additional training data. Our approach introduces three targeted perturbations: distractor concatenation, dominance-preserving mixup, and random rotation, that can be easily integrated into existing post-training pipelines including SFT, DPO, and GRPO. Through extensive experiments across multiple datasets, we demonstrate consistent improvements in mathematical reasoning performance, with gains comparable to those achieved through algorithmic changes. Additionally, we achieve competitive performance among open-source 7B RL-tuned models by training Qwen2.5-VL-7B with visual perturbation. Through comprehensive ablation studies, we analyze the effectiveness of different perturbation strategies, revealing that each perturbation type contributes uniquely to different aspects of visual reasoning. Our findings highlight the critical role of visual perturbation in multimodal mathematical reasoning: better reasoning begins with better seeing. Our code is available at https://github.com/YutingLi0606/Vision-Matters.

  • 7 authors
·
Jun 11, 2025 2

CatVTON: Concatenation Is All You Need for Virtual Try-On with Diffusion Models

Virtual try-on methods based on diffusion models achieve realistic try-on effects but often replicate the backbone network as a ReferenceNet or use additional image encoders to process condition inputs, leading to high training and inference costs. In this work, we rethink the necessity of ReferenceNet and image encoders and innovate the interaction between garment and person by proposing CatVTON, a simple and efficient virtual try-on diffusion model. CatVTON facilitates the seamless transfer of in-shop or worn garments of any category to target persons by simply concatenating them in spatial dimensions as inputs. The efficiency of our model is demonstrated in three aspects: (1) Lightweight network: Only the original diffusion modules are used, without additional network modules. The text encoder and cross-attentions for text injection in the backbone are removed, reducing the parameters by 167.02M. (2) Parameter-efficient training: We identified the try-on relevant modules through experiments and achieved high-quality try-on effects by training only 49.57M parameters, approximately 5.51 percent of the backbone network's parameters. (3) Simplified inference: CatVTON eliminates all unnecessary conditions and preprocessing steps, including pose estimation, human parsing, and text input, requiring only a garment reference, target person image, and mask for the virtual try-on process. Extensive experiments demonstrate that CatVTON achieves superior qualitative and quantitative results with fewer prerequisites and trainable parameters than baseline methods. Furthermore, CatVTON shows good generalization in in-the-wild scenarios despite using open-source datasets with only 73K samples.

  • 8 authors
·
Jul 21, 2024

Bit Cipher -- A Simple yet Powerful Word Representation System that Integrates Efficiently with Language Models

While Large Language Models (LLMs) become ever more dominant, classic pre-trained word embeddings sustain their relevance through computational efficiency and nuanced linguistic interpretation. Drawing from recent studies demonstrating that the convergence of GloVe and word2vec optimizations all tend towards log-co-occurrence matrix variants, we construct a novel word representation system called Bit-cipher that eliminates the need of backpropagation while leveraging contextual information and hyper-efficient dimensionality reduction techniques based on unigram frequency, providing strong interpretability, alongside efficiency. We use the bit-cipher algorithm to train word vectors via a two-step process that critically relies on a hyperparameter -- bits -- that controls the vector dimension. While the first step trains the bit-cipher, the second utilizes it under two different aggregation modes -- summation or concatenation -- to produce contextually rich representations from word co-occurrences. We extend our investigation into bit-cipher's efficacy, performing probing experiments on part-of-speech (POS) tagging and named entity recognition (NER) to assess its competitiveness with classic embeddings like word2vec and GloVe. Additionally, we explore its applicability in LM training and fine-tuning. By replacing embedding layers with cipher embeddings, our experiments illustrate the notable efficiency of cipher in accelerating the training process and attaining better optima compared to conventional training paradigms. Experiments on the integration of bit-cipher embedding layers with Roberta, T5, and OPT, prior to or as a substitute for fine-tuning, showcase a promising enhancement to transfer learning, allowing rapid model convergence while preserving competitive performance.

  • 2 authors
·
Nov 18, 2023

MapFormer: Boosting Change Detection by Using Pre-change Information

Change detection in remote sensing imagery is essential for a variety of applications such as urban planning, disaster management, and climate research. However, existing methods for identifying semantically changed areas overlook the availability of semantic information in the form of existing maps describing features of the earth's surface. In this paper, we leverage this information for change detection in bi-temporal images. We show that the simple integration of the additional information via concatenation of latent representations suffices to significantly outperform state-of-the-art change detection methods. Motivated by this observation, we propose the new task of *Conditional Change Detection*, where pre-change semantic information is used as input next to bi-temporal images. To fully exploit the extra information, we propose *MapFormer*, a novel architecture based on a multi-modal feature fusion module that allows for feature processing conditioned on the available semantic information. We further employ a supervised, cross-modal contrastive loss to guide the learning of visual representations. Our approach outperforms existing change detection methods by an absolute 11.7\% and 18.4\% in terms of binary change IoU on DynamicEarthNet and HRSCD, respectively. Furthermore, we demonstrate the robustness of our approach to the quality of the pre-change semantic information and the absence pre-change imagery. The code is available at https://github.com/mxbh/mapformer.

  • 3 authors
·
Mar 31, 2023

Improving Image-to-Image Translation via a Rectified Flow Reformulation

In this work, we propose Image-to-Image Rectified Flow Reformulation (I2I-RFR), a practical plug-in reformulation that recasts standard I2I regression networks as continuous-time transport models. While pixel-wise I2I regression is simple, stable, and easy to adapt across tasks, it often over-smooths ill-posed and multimodal targets, whereas generative alternatives often require additional components, task-specific tuning, and more complex training and inference pipelines. Our method augments the backbone input by channel-wise concatenation with a noise-corrupted version of the ground-truth target and optimizes a simple t-reweighted pixel loss. This objective admits a rectified-flow interpretation via an induced velocity field, enabling ODE-based progressive refinement at inference time while largely preserving the standard supervised training pipeline. In most cases, adopting I2I-RFR requires only expanding the input channels, and inference can be performed with a few explicit solver steps (e.g., 3 steps) without distillation. Extensive experiments across multiple image-to-image translation and video restoration tasks show that I2I-RFR generally improves performance across a wide range of tasks and backbones, with particularly clear gains in perceptual quality and detail preservation. Overall, I2I-RFR provides a lightweight way to incorporate continuous-time refinement into conventional I2I models without requiring a heavy generative pipeline.

  • 3 authors
·
Mar 20

ReSee: Responding through Seeing Fine-grained Visual Knowledge in Open-domain Dialogue

Incorporating visual knowledge into text-only dialogue systems has become a potential direction to imitate the way humans think, imagine, and communicate. However, existing multimodal dialogue systems are either confined by the scale and quality of available datasets or the coarse concept of visual knowledge. To address these issues, we provide a new paradigm of constructing multimodal dialogues as well as two datasets extended from text-only dialogues under such paradigm (ReSee-WoW, ReSee-DD). We propose to explicitly split the visual knowledge into finer granularity (``turn-level'' and ``entity-level''). To further boost the accuracy and diversity of augmented visual information, we retrieve them from the Internet or a large image dataset. To demonstrate the superiority and universality of the provided visual knowledge, we propose a simple but effective framework ReSee to add visual representation into vanilla dialogue models by modality concatenations. We also conduct extensive experiments and ablations w.r.t. different model configurations and visual knowledge settings. Empirical, encouraging results not only demonstrate the effectiveness of introducing visual knowledge at both entity and turn level but also verify the proposed model ReSee outperforms several state-of-the-art methods on automatic and human evaluations. By leveraging text and vision knowledge, ReSee can produce informative responses with real-world visual concepts. Our code is available at https://github.com/ImKeTT/ReSee.

  • 4 authors
·
May 22, 2023

VIOLET : End-to-End Video-Language Transformers with Masked Visual-token Modeling

A great challenge in video-language (VidL) modeling lies in the disconnection between fixed video representations extracted from image/video understanding models and downstream VidL data. Recent studies try to mitigate this disconnection via end-to-end training. To make it computationally feasible, prior works tend to "imagify" video inputs, i.e., a handful of sparsely sampled frames are fed into a 2D CNN, followed by a simple mean-pooling or concatenation to obtain the overall video representations. Although achieving promising results, such simple approaches may lose temporal information that is essential for performing downstream VidL tasks. In this work, we present VIOLET, a fully end-to-end VIdeO-LanguagE Transformer, which adopts a video transformer to explicitly model the temporal dynamics of video inputs. Further, unlike previous studies that found pre-training tasks on video inputs (e.g., masked frame modeling) not very effective, we design a new pre-training task, Masked Visual-token Modeling (MVM), for better video modeling. Specifically, the original video frame patches are "tokenized" into discrete visual tokens, and the goal is to recover the original visual tokens based on the masked patches. Comprehensive analysis demonstrates the effectiveness of both explicit temporal modeling via video transformer and MVM. As a result, VIOLET achieves new state-of-the-art performance on 5 video question answering tasks and 4 text-to-video retrieval tasks.

  • 7 authors
·
Nov 24, 2021

Dataset Decomposition: Faster LLM Training with Variable Sequence Length Curriculum

Large language models (LLMs) are commonly trained on datasets consisting of fixed-length token sequences. These datasets are created by randomly concatenating documents of various lengths and then chunking them into sequences of a predetermined target length. However, this method of concatenation can lead to cross-document attention within a sequence, which is neither a desirable learning signal nor computationally efficient. Additionally, training on long sequences becomes computationally prohibitive due to the quadratic cost of attention. In this study, we introduce dataset decomposition, a novel variable sequence length training technique, to tackle these challenges. We decompose a dataset into a union of buckets, each containing sequences of the same size extracted from a unique document. During training, we use variable sequence length and batch size, sampling simultaneously from all buckets with a curriculum. In contrast to the concat-and-chunk baseline, which incurs a fixed attention cost at every step of training, our proposed method incurs a penalty proportional to the actual document lengths at each step, resulting in significant savings in training time. We train an 8k context-length 1B model at the same cost as a 2k context-length model trained with the baseline approach. Experiments on a web-scale corpus demonstrate that our approach significantly enhances performance on standard language evaluations and long-context benchmarks, reaching target accuracy 3x faster compared to the baseline. Our method not only enables efficient pretraining on long sequences but also scales effectively with dataset size. Lastly, we shed light on a critical yet less studied aspect of training large language models: the distribution and curriculum of sequence lengths, which results in a non-negligible difference in performance.

  • 7 authors
·
May 21, 2024

The Base Dependent Behavior of Kaprekar's Routine: A Theoretical and Computational Study Revealing New Regularities

Consider the following process: Take any four-digit number which has at least two distinct digits. Then, rearrange the digits of the original number in ascending and descending order, take these two numbers, and find the difference between the two. Finally, repeat this routine using the difference as the new four-digit number. In 1949, D. R. Kaprekar became the first to discover that this process, known as the Kaprekar Routine, would always yield 6174 within 7 iterations. Since this number remains unchanged after an application of the Kaprekar Routine, it became known as Kaprekar's Constant. Previous works have shown that the only base 10 Kaprekar's Constants are 495 and 6174, the 3-digit and 4-digit case. However, little attention has been given to other bases or determining which digit cases and which bases have a Kaprekar's Constant. This paper analyzes the behavior of the Kaprekar Routine in the 3-digit case, deriving an expression for all 3-digit Kaprekar Constants. In addition, the author developed a series of C++ programs to analyze the paths integers followed to their respective Kaprekar's Constant. Surprisingly, it was determined from this program that the most commonly required number of iterations required to reach Kaprekar's Constant for 3-digit integers was consistently 3, regardless of base. When loaded as a matrix, the iteration requirement data demonstrates a precise recurring relationship reminiscent of Pascal's Triangle.

  • 1 authors
·
Oct 16, 2017

A Triadic Suffix Tokenization Scheme for Numerical Reasoning

Standard subword tokenization methods fragment numbers inconsistently, causing large language models (LLMs) to lose positional and decimal structure - a primary driver of errors in arithmetic and scientific reasoning. We introduce Triadic Suffix Tokenization (TST), a deterministic scheme that partitions digits into three-digit triads and annotates each triad with an explicit magnitude marker. Critically, the scheme defines a fixed, one-to-one mapping between suffixes and orders of magnitude for the integer part (thousands, millions, billions, etc.) and a parallel system of replicated markers for fractional depth (tenths, thousandths, millionths, etc.). Unlike approaches that rely on positional inference, this method provides a consistent gradient signal, which should ensure stable convergence. Two implementation variants are proposed: (1) a vocabulary-based approach that adds at most 10,000 fixed tokens to an existing vocabulary, covering 33 orders of magnitude (10^{-15} to 10^{18}); and (2) a suffix-marker approach that uses a small set of special tokens to denote magnitude dynamically. Both variants preserve exact digits while making order-of-magnitude relationships transparent at the token level. The framework is inherently scalable, allowing for linear vocabulary expansion to accommodate arbitrary precision and range. TST is architecture-agnostic and can be integrated as a drop-in preprocessing step. Experimental validation is deferred to future work.

  • 1 authors
·
Apr 12 1