OpenRaiser/Intern-Atlas huggingface dataset:
Learning to Align Molecules and Proteins: A Geometry-Aware Approach to Binding Affinity
Venue: arXiv cs.LG 2025
Year: 2025

Accurate prediction of drug-target binding affinity can accelerate drug discovery by prioritizing promising compounds before costly wet-lab screening. While deep learning has advanced this task, most models fuse ligand and protein representations via simple concatenation and lack explicit geometric regularization, resulting in poor generalization across chemical space and time. We introduce FIRM-DTI, a lightweight framework that conditions molecular embeddings on protein embeddings through a feature-wise linear modulation (FiLM) layer and enforces metric structure with a triplet loss. An RBF regression head operating on embedding distances yields smooth, interpretable affinity predictions. Despite its modest size, FIRM-DTI achieves state-of-the-art performance on the Therapeutics Data Commons DTI-DG benchmark, as demonstrated by an extensive ablation study and out-of-domain evaluation. Our results underscore the value of conditioning and metric learning for robust drug-target affinity prediction.
Joint Flow Trajectory Optimization For Feasible Robot Motion Generation from Video Demonstrations
Venue: arXiv cs.RO 2025
Year: 2025

Learning from human video demonstrations offers a scalable alternative to teleoperation or kinesthetic teaching, but poses challenges for robot manipulators due to embodiment differences and joint feasibility constraints. We address this problem by proposing the Joint Flow Trajectory Optimization (JFTO) framework for grasp pose generation and object trajectory imitation under the video-based Learning-from-Demonstration (LfD) paradigm. Rather than directly imitating human hand motions, our method treats demonstrations as object-centric guides, balancing three objectives: (i) selecting a feasible grasp pose, (ii) generating object trajectories consistent with demonstrated motions, and (iii) ensuring collision-free execution within robot kinematics. To capture the multimodal nature of demonstrations, we extend flow matching to $\SE(3)$ for probabilistic modeling of object trajectories, enabling density-aware imitation that avoids mode collapse. The resulting optimization integrates grasp similarity, trajectory likelihood, and collision penalties into a unified differentiable objective. We validate our approach in both simulation and real-world experiments across diverse real-world manipulation tasks.
RobotDancing: Residual-Action Reinforcement Learning Enables Robust Long-Horizon Humanoid Motion Tracking
Venue: arXiv cs.RO 2025
Year: 2025

Long-horizon, high-dynamic motion tracking on humanoids remains brittle because absolute joint commands cannot compensate model-plant mismatch, leading to error accumulation. We propose RobotDancing, a simple, scalable framework that predicts residual joint targets to explicitly correct dynamics discrepancies. The pipeline is end-to-end--training, sim-to-sim validation, and zero-shot sim-to-real--and uses a single-stage reinforcement learning (RL) setup with a unified observation, reward, and hyperparameter configuration. We evaluate primarily on Unitree G1 with retargeted LAFAN1 dance sequences and validate transfer on H1/H1-2. RobotDancing can track multi-minute, high-energy behaviors (jumps, spins, cartwheels) and deploys zero-shot to hardware with high motion tracking quality.
Meta-Memory: Retrieving and Integrating Semantic-Spatial Memories for Robot Spatial Reasoning
Venue: arXiv cs.AI 2025
Year: 2025

Navigating complex environments requires robots to effectively store observations as memories and leverage them to answer human queries about spatial locations, which is a critical yet underexplored research challenge. While prior work has made progress in constructing robotic memory, few have addressed the principled mechanisms needed for efficient memory retrieval and integration. To bridge this gap, we propose Meta-Memory, a large language model (LLM)-driven agent that constructs a high-density memory representation of the environment. The key innovation of Meta-Memory lies in its capacity to retrieve and integrate relevant memories through joint reasoning over semantic and spatial modalities in response to natural language location queries, thereby empowering robots with robust and accurate spatial reasoning capabilities. To evaluate its performance, we introduce SpaceLocQA, a large-scale dataset encompassing diverse real-world spatial question-answering scenarios. Experimental results show that Meta-Memory significantly outperforms state-of-the-art methods on both the SpaceLocQA and the public NaVQA benchmarks. Furthermore, we successfully deployed Meta-Memory on real-world robotic platforms, demonstrating its practical utility in complex environments. Project page: https://itsbaymax.github.io/meta-memory.github.io/ .
ExpIDS: A Drift-adaptable Network Intrusion Detection System With Improved Explainability
Venue: arXiv cs.CR 2025
Year: 2025

Despite all the advantages associated with Network Intrusion Detection Systems (NIDSs) that utilize machine learning (ML) models, there is a significant reluctance among cyber security experts to implement these models in real-world production settings. This is primarily because of their opaque nature, meaning it is unclear how and why the models make their decisions. In this work, we design a deep learning-based NIDS, ExpIDS to have high decision tree explanation fidelity, i.e., the predictions of decision tree explanation corresponding to ExpIDS should be as close to ExpIDS's predictions as possible. ExpIDS can also adapt to changes in network traffic distribution (drift). With the help of extensive experiments, we verify that ExpIDS achieves higher decision tree explanation fidelity and a malicious traffic detection performance comparable to state-of-the-art NIDSs for common attacks with varying levels of real-world drift.
Performance Consistency of Learning Methods for Information Retrieval Tasks
Venue: arXiv cs.IR 2025
Year: 2025

A range of approaches have been proposed for estimating the accuracy or robustness of the measured performance of IR methods. One is to use bootstrapping of test sets, which, as we confirm, provides an estimate of variation in performance. For IR methods that rely on a seed, such as those that involve machine learning, another approach is to use a random set of seeds to examine performance variation. Using three different IR tasks we have used such randomness to examine a range of traditional statistical learning models and transformer-based learning models. While the statistical models are stable, the transformer models show huge variation as seeds are changed. In 9 of 11 cases the F1-scores (in the range 0.0--1.0) had a standard deviation of over 0.075; while 7 of 11 precision values (also in the range 0.0--1.0) had a standard deviation of over 0.125. This is in a context where differences of less than 0.02 have been used as evidence of method improvement. Our findings highlight the vulnerability of transformer models to training instabilities and moreover raise questions about the reliability of previous results, thus underscoring the need for rigorous evaluation practices.
Verification Limits Code LLM Training
Venue: arXiv cs.SE 2025
Year: 2025

Large language models for code generation increasingly rely on synthetic data, where both problem solutions and verification tests are generated by models. While this enables scalable data creation, it introduces a previously unexplored bottleneck: the verification ceiling, in which the quality and diversity of training data are fundamentally constrained by the capabilities of synthetic verifiers. In this work, we systematically study how verification design and strategies influence model performance. We investigate (i) what we verify by analyzing the impact of test complexity and quantity: richer test suites improve code generation capabilities (on average +3 pass@1), while quantity alone yields diminishing returns, (ii) how we verify by exploring relaxed pass thresholds: rigid 100% pass criteria can be overly restrictive. By allowing for relaxed thresholds or incorporating LLM-based soft verification, we can recover valuable training data, leading to a 2-4 point improvement in pass@1 performance. However, this benefit is contingent upon the strength and diversity of the test cases used, and (iii) why verification remains necessary through controlled comparisons of formally correct versus incorrect solutions and human evaluation: retaining diverse correct solutions per problem yields consistent generalization gains. Our results show that Verification as currently practiced is too rigid, filtering out valuable diversity. But it cannot be discarded, only recalibrated. By combining calibrated verification with diverse, challenging problem-solution pairs, we outline a path to break the verification ceiling and unlock stronger code generation models.
Plant identification based on noisy web data: the amazing performance of deep learning (LifeCLEF 2017)
Venue: arXiv cs.CV 2025
Year: 2025

The 2017-th edition of the LifeCLEF plant identification challenge is an important milestone towards automated plant identification systems working at the scale of continental floras with 10.000 plant species living mainly in Europe and North America illustrated by a total of 1.1M images. Nowadays, such ambitious systems are enabled thanks to the conjunction of the dazzling recent progress in image classification with deep learning and several outstanding international initiatives, such as the Encyclopedia of Life (EOL), aggregating the visual knowledge on plant species coming from the main national botany institutes. However, despite all these efforts the majority of the plant species still remain without pictures or are poorly illustrated. Outside the institutional channels, a much larger number of plant pictures are available and spread on the web through botanist blogs, plant lovers web-pages, image hosting websites and on-line plant retailers. The LifeCLEF 2017 plant challenge presented in this paper aimed at evaluating to what extent a large noisy training dataset collected through the web and containing a lot of labelling errors can compete with a smaller but trusted training dataset checked by experts. To fairly compare both training strategies, the test dataset was created from a third data source, i.e. the Pl@ntNet mobile application that collects millions of plant image queries all over the world. This paper presents more precisely the resources and assessments of the challenge, summarizes the approaches and systems employed by the participating research groups, and provides an analysis of the main outcomes.
Model-Based Reinforcement Learning under Random Observation Delays
Venue: arXiv cs.LG 2025
Year: 2025

Delays frequently occur in real-world environments, yet standard reinforcement learning (RL) algorithms often assume instantaneous perception of the environment. We study random sensor delays in POMDPs, where observations may arrive out-of-sequence, a setting that has not been previously addressed in RL. We analyze the structure of such delays and demonstrate that naive approaches, such as stacking past observations, are insufficient for reliable performance. To address this, we propose a model-based filtering process that sequentially updates the belief state based on an incoming stream of observations. We then introduce a simple delay-aware framework that incorporates this idea into model-based RL, enabling agents to effectively handle random delays. Applying this framework to Dreamer, we compare our approach to delay-aware baselines developed for MDPs. Our method consistently outperforms these baselines and demonstrates robustness to delay distribution shifts during deployment. Additionally, we present experiments on simulated robotic tasks, comparing our method to common practical heuristics and emphasizing the importance of explicitly modeling observation delays.
Plant identification in an open-world (LifeCLEF 2016)
Venue: arXiv cs.CV 2025
Year: 2025

The LifeCLEF plant identification challenge aims at evaluating plant identification methods and systems at a very large scale, close to the conditions of a real-world biodiversity monitoring scenario. The 2016-th edition was actually conducted on a set of more than 110K images illustrating 1000 plant species living in West Europe, built through a large-scale participatory sensing platform initiated in 2011 and which now involves tens of thousands of contributors. The main novelty over the previous years is that the identification task was evaluated as an open-set recognition problem, i.e. a problem in which the recognition system has to be robust to unknown and never seen categories. Beyond the brute-force classification across the known classes of the training set, the big challenge was thus to automatically reject the false positive classification hits that are caused by the unknown classes. This overview presents more precisely the resources and assessments of the challenge, summarizes the approaches and systems employed by the participating research groups, and provides an analysis of the main outcomes.
Further Results on Rendering Geometric Intersection Graphs Sparse by Dispersion
Venue: arXiv cs.CG 2025
Year: 2025

Removing overlaps is a central task in domains such as scheduling, visibility, and map labelling. This can be modelled using graphs, where overlap removals correspond to enforcing a certain sparsity constraint on the graph structure. We continue the study of the problem Geometric Graph Edit Distance (GGED), where the aim is to minimise the total cost of editing a geometric intersection graph to obtain a graph contained in a specific graph class. For us, the edit operation is the movement of objects, and the cost is the movement distance. We present an algorithm for rendering the intersection graph of a set of unit circular arcs (i)~edgeless, (ii)~acyclic, and (iii) $k$-clique-free in $O(n\log n)$ time, where $n$ is the number of arcs. We also show that GGED remains strongly NP-hard on unweighted interval graphs, solving an open problem of Honorato-Droguett et al. [WADS 2025]. We complement this result by showing that GGED is strongly NP-hard on sets of $d$-balls and $d$-cubes, for any $d\ge 2$. Finally, we present an XP algorithm (parameterised by the number of maximal cliques) that removes all edges from the intersection graph of a set of weighted unit intervals.
GALAX: Graph-Augmented Language Model for Explainable Reinforcement-Guided Subgraph Reasoning in Precision Medicine
Venue: arXiv cs.AI 2025
Year: 2025

In precision medicine, quantitative multi-omic features, topological context, and textual biological knowledge play vital roles in identifying disease-critical signaling pathways and targets. Existing pipelines capture only part of these-numerical omics ignore topological context, text-centric LLMs lack quantitative grounded reasoning, and graph-only models underuse node semantics and the generalization of LLMs-limiting mechanistic interpretability. Although Process Reward Models (PRMs) aim to guide reasoning in LLMs, they remain limited by unreliable intermediate evaluation, and vulnerability to reward hacking with computational cost. These gaps motivate integrating quantitative multi-omic signals, topological structure with node annotations, and literature-scale text via LLMs, using subgraph reasoning as the principle bridge linking numeric evidence, topological knowledge and language context. Therefore, we propose GALAX (Graph Augmented LAnguage model with eXplainability), an innovative framework that integrates pretrained Graph Neural Networks (GNNs) into Large Language Models (LLMs) via reinforcement learning guided by a Graph Process Reward Model (GPRM), which generates disease-relevant subgraphs in a step-wise manner initiated by an LLM and iteratively evaluated by a pretrained GNN and schema-based rule check, enabling process-level supervision without explicit labels. As an application, we also introduced Target-QA, a benchmark combining CRISPR-identified targets, multi-omic profiles, and biomedical graph knowledge across diverse cancer cell lines, which enables GNN pretraining for supervising step-wise graph construction and supports long-context reasoning over text-numeric graphs (TNGs), providing a scalable and biologically grounded framework for explainable, reinforcement-guided subgraph reasoning toward reliable and interpretable target discovery in precision medicine.
Decoupled-Value Attention for Prior-Data Fitted Networks: GP Inference for Physical Equations
Venue: arXiv cs.LG 2025
Year: 2025

Prior-data fitted networks (PFNs) are a promising alternative to time-consuming Gaussian process (GP) inference for creating fast surrogates of physical systems. PFN reduces the computational burden of GP-training by replacing Bayesian inference in GP with a single forward pass of a learned prediction model. However, with standard Transformer attention, PFNs show limited effectiveness on high-dimensional regression tasks. We introduce Decoupled-Value Attention (DVA)-- motivated by the GP property that the function space is fully characterized by the kernel over inputs and the predictive mean is a weighted sum of training targets. DVA computes similarities from inputs only and propagates labels solely through values. Thus, the proposed DVA mirrors the GP update while remaining kernel-free. We demonstrate that PFNs are backbone architecture invariant and the crucial factor for scaling PFNs is the attention rule rather than the architecture itself. Specifically, our results demonstrate that (a) localized attention consistently reduces out-of-sample validation loss in PFNs across different dimensional settings, with validation loss reduced by more than 50% in five- and ten-dimensional cases, and (b) the role of attention is more decisive than the choice of backbone architecture, showing that CNN, RNN and LSTM-based PFNs can perform at par with their Transformer-based counterparts. The proposed PFNs provide 64-dimensional power flow equation approximations with a mean absolute error of the order of E-03, while being over 80x faster than exact GP inference.
Unlocking Financial Insights: An advanced Multimodal Summarization with Multimodal Output Framework for Financial Advisory Videos
Venue: arXiv cs.CV 2025
Year: 2025

The dynamic propagation of social media has broadened the reach of financial advisory content through podcast videos, yet extracting insights from lengthy, multimodal segments (30-40 minutes) remains challenging. We introduce FASTER (Financial Advisory Summariser with Textual Embedded Relevant images), a modular framework that tackles three key challenges: (1) extracting modality-specific features, (2) producing optimized, concise summaries, and (3) aligning visual keyframes with associated textual points. FASTER employs BLIP for semantic visual descriptions, OCR for textual patterns, and Whisper-based transcription with Speaker diarization as BOS features. A modified Direct Preference Optimization (DPO)-based loss function, equipped with BOS-specific fact-checking, ensures precision, relevance, and factual consistency against the human-aligned summary. A ranker-based retrieval mechanism further aligns keyframes with summarized content, enhancing interpretability and cross-modal coherence. To acknowledge data resource scarcity, we introduce Fin-APT, a dataset comprising 470 publicly accessible financial advisory pep-talk videos for robust multimodal research. Comprehensive cross-domain experiments confirm FASTER's strong performance, robustness, and generalizability when compared to Large Language Models (LLMs) and Vision-Language Models (VLMs). By establishing a new standard for multimodal summarization, FASTER makes financial advisory content more accessible and actionable, thereby opening new avenues for research. The dataset and code are available at: https://github.com/sarmistha-D/FASTER
RL Grokking Recipe: How Does RL Unlock and Transfer New Algorithms in LLMs?
Venue: arXiv cs.LG 2025
Year: 2025

It remains an open question whether LLMs can acquire or generalize genuinely new reasoning strategies, beyond the sharpened skills encoded in their parameters during pre-training or post-training. To attempt to answer this debate, we introduce DELTA-Code -- Distributional Evaluation of Learnability and Transferrability in Algorithmic Coding -- a controlled benchmark of synthetic coding problem families designed to probe two fundamental aspects: learnability -- can LLMs, through reinforcement learning (RL), solve problem families where pretrained models exhibit failure with large enough attempts (pass@K=0)? -- and transferrability -- if learnability happens, can such skills transfer systematically to out-of-distribution (OOD) test sets? Unlike prior public coding datasets, DELTA isolates reasoning skills through templated problem generators and introduces fully OOD problem families that demand novel strategies rather than tool invocation or memorized patterns. Our experiments reveal a striking grokking phase transition: after an extended period with near-zero reward, RL-trained models abruptly climb to near-perfect accuracy. To enable learnability on previously unsolvable problem families, we explore key training ingredients such as staged warm-up with dense rewards, experience replay, curriculum training, and verification-in-the-loop. Beyond learnability, we use DELTA to evaluate transferability or generalization along exploratory, compositional, and transformative axes, as well as cross-family transfer. Results show solid gains within families and for recomposed skills, but persistent weaknesses in transformative cases. DELTA thus offers a clean testbed for probing the limits of RL-driven reasoning and for understanding how models can move beyond existing priors to acquire new algorithmic skills.
A Novel Integrated Architecture for Intent Based Approach and Zero Touch Networks
Venue: arXiv cs.NI 2025
Year: 2025

The transition to Sixth Generation (6G) networks presents challenges in managing quality of service (QoS) of diverse applications and achieving Service Level Agreements (SLAs) under varying network conditions. Hence, network management must be automated with the help of Machine Learning (ML) and Artificial Intelligence (AI) to achieve real-time requirements. Zero touch network (ZTN) is one of the frameworks to automate network management with mechanisms such as closed loop control to ensure that the goals are met perpetually. Intent- Based Networking (IBN) specifies the user intents with diverse network requirements or goals which are then translated into specific network configurations and actions. This paper presents a novel architecture for integrating IBN and ZTN to serve the intent goals. Users provides the intent in the form of natural language, e.g., English, which is then translated using natural language processing (NLP) techniques (e.g., retrieval augmented generation (RAG)) into Network Intent LanguagE (Nile). The Nile intent is then passed on to the BiLSTM and Q-learning based ZTN closed loop framework as a goal which maintains the intent under varying network conditions. Thus, the proposed architecture can work autonomously to ensure the network performance goal is met by just specifying the user intent in English. The integrated architecture is also implemented on a testbed using OpenAirInterface (OAI). Additionally, to evaluate the architecture, an optimization problem is formulated which evaluated with Monte Carlo simulations. Results demonstrate how ZTN can help achieve the bandwidth goals autonomously set by user intent. The simulation and the testbed results are compared and they show similar trend. Mean Opinion Score (MOS) for Quality of Experience (QoE) is also measured to indicate the user satisfaction of the intent.