arXiv subjects

Morteza Ziyadi

Publications and source records attributed to Morteza Ziyadi.

18 recordsLinked to original sources

arXiv2026

RAGPPI: RAG Benchmark for Protein-Protein Interactions in Drug Discovery

Retrieving the biological impacts of protein-protein interactions (PPIs) is essential for target identification (Target ID) in drug development. Given the vast number of proteins involved, this process remains time-consuming and challenging. Large Language Models (LLMs) and Retrieval-Augmented Generation (RAG) frameworks have supported Target ID; however, no benchmark currently exists for identifying the biological impacts of PPIs. To bridge this gap, we introduce the RAG Benchmark for PPIs (RAGPPI), a factual question-answer benchmark of 4,420 question-answer pairs that focus on the potential biological impacts of PPIs. Through interviews with experts, we identified criteria for a benchmark dataset, such as a type of QA and source. We built a gold-standard dataset (500 QA pairs) through expert-driven data annotation. We developed an ensemble auto-evaluation LLM that incorporates expert labeling characteristics, average fact-abstract similarity (F1), and low-similarity fact counts (F2), enabling the construction of a silver-standard dataset (3,720 QA pairs). We are committed to maintaining RAGPPI as a resource to support the research community in advancing RAG systems for drug discovery QA solutions.

cs.CL↗

arXiv2026

C-MORAL: Controllable Multi-Objective Molecular Optimization with Reinforcement Alignment for LLMs

Large language models (LLMs) show promise for molecular optimization, but aligning them with selective and competing drug-design constraints remains challenging. We propose C-Moral, a reinforcement learning post-training framework for controllable multi-objective molecular optimization. C-Moral combines group-based relative optimization, property score alignment for heterogeneous objectives, and bottleneck-sensitive non-linear reward aggregation to improve stability across competing molecular properties. Experiments on C-MuMOInstruct and S$^2$-Bench MolOpt show that C-Moral achieves the best performance among compared methods on both benchmarks. On C-MuMOInstruct, C-Moral achieves the best Success Optimized Rate (SOR) of 48.9\% on in-domain tasks and 39.5\% on out-of-domain tasks while preserving scaffold similarity. On S$^2$-Bench MolOpt, it also achieves the strongest results across LogP, MR, and QED optimization tasks. These results suggest that C-Moral is an effective way to align molecular LLMs with continuous and constrained molecular design objectives. Our code and models are publicly available at https://github.com/Rwigie/C-MORAL.

cs.LG↗

arXiv2026

BeyondBench: Contamination-Resistant Evaluation of Reasoning in Language Models

Evaluating language models fairly is increasingly difficult as static benchmarks risk contamination by training data, obscuring whether models truly reason or recall. We introduce BeyondBench, an evaluation framework using algorithmic problem generation to create mathematically grounded problems on the fly, ensuring each test remains uncontaminated. Our framework covers 44 algorithmic tasks with 117 variations across three difficulty levels: the Easy Suite (29 tasks) for arithmetic and statistics, the Medium Suite (5 tasks, 49 variations) for sequence patterns and reasoning, and the Hard Suite (10 tasks, 68 variations) for NP-complete and constraint satisfaction problems. Each task draws from a space exceeding 10^15 unique instances, with deterministically verified solutions. We evaluated 101 language models (85 open-source, 16 closed-source), spanning 0.5B to 141B parameters and multiple quantization schemes, using three-fold evaluation for robustness. Results reveal consistent reasoning deficiencies, with performance degrading sharply as complexity increases. In Hard Suite evaluations, Gemini-2.5-pro, Llama-3.3-70B, and Qwen2.5-72B achieved accuracies of 56.21%, 27.16%, and 33.37% respectively. Performance drops significantly without tool usage, with GPT-5, GPT-5-mini, and GPT-5-nano showing declines of 16.81%, 15.86%, and 43.95% in overall accuracy. Contamination resistance rests on three guarantees: (i) the problem space vastly exceeds any static dataset, (ii) every instance has a deterministically verifiable solution, and (iii) isomorphic transformations yield semantically equivalent but syntactically novel problems. BeyondBench redefines reasoning evaluation via genuine algorithmic problem-solving. Our leaderboard is at https://ctrl-gaurav.github.io/BeyondBench/, Python package at https://pypi.org/project/beyondbench/, and codebase at https://github.com/ctrl-gaurav/BeyondBench.

cs.CL↗

arXiv2026

InterPrior: Scaling Generative Control for Physics-Based Human-Object Interactions

Humans rarely plan whole-body interactions with objects at the level of explicit whole-body movements. High-level intentions, such as affordance, define the goal, while coordinated balance, contact, and manipulation can emerge naturally from underlying physical and motor priors. Scaling such priors is key to enabling humanoids to compose and generalize loco-manipulation skills across diverse contexts while maintaining physically coherent whole-body coordination. To this end, we introduce InterPrior, a scalable framework that learns a unified generative controller through large-scale imitation pretraining and post-training by reinforcement learning. InterPrior first distills a full-reference imitation expert into a versatile, goal-conditioned variational policy that reconstructs motion from multimodal observations and high-level intent. While the distilled policy reconstructs training behaviors, it does not generalize reliably due to the vast configuration space of large-scale human-object interactions. To address this, we apply data augmentation with physical perturbations, and then perform reinforcement learning finetuning to improve competence on unseen goals and initializations. Together, these steps consolidate the reconstructed latent skills into a valid manifold, yielding a motion prior that generalizes beyond the training data, e.g., it can incorporate new behaviors such as interactions with unseen objects. We further demonstrate its effectiveness for user-interactive control and its potential for real robot deployment.

cs.CV↗

arXiv2025

Deep Research Comparator: A Platform For Fine-grained Human Annotations of Deep Research Agents

Effectively evaluating deep research agents that autonomously search the web, analyze information, and generate reports remains a major challenge, particularly when it comes to assessing long reports and giving detailed feedback on their intermediate steps. To address these gaps, we introduce Deep Research Comparator, a platform that offers a holistic framework for deep research agent hosting, side-by-side comparison, fine-grained human feedback collection, and ranking calculation. Given a user query, our platform displays the final reports from two different agents along with their intermediate steps during generation. Annotators can evaluate the overall quality of final reports based on side-by-side comparison, and also provide detailed feedback separately by assessing intermediate steps or specific text spans within the final report. Furthermore, we develop Simple Deepresearch, an end-to-end agent scaffold. This scaffold serves as a baseline that facilitates the easy integration of various large language models to transform them into deep research agents for evaluation. To demonstrate the platform's utility for deep research agent development, we have collected real user preference data from 17 annotators on three deep research agents. A demo video of our platform can be found at https://www.youtube.com/watch?v=g4d2dnbdseg.

cs.AI↗

arXiv2025

MAVERIX: Multimodal Audio-Visual Evaluation and Recognition IndeX

We introduce MAVERIX (Multimodal audiovisual Evaluation and Recognition IndeX), a unified benchmark to probe the video understanding in multimodal LLMs, encompassing video, audio, text inputs with human performance baselines. Although recent advancements in models with vision and audio understanding capabilities have shown substantial progress, the field lacks a standardized evaluation framework to thoroughly assess their cross-modality comprehension performance. MAVERIX curates 2,556 questions from 700 videos, in the form of both multiple-choice and open-ended formats, explicitly designed to evaluate multimodal models through questions that necessitate tight integration of video and audio information, spanning a broad spectrum of agentic scenarios. MAVERIX uniquely provides models with audiovisual questions, closely mimicking the multimodal perceptual experiences available to humans during inference and decision-making processes. To our knowledge, MAVERIX is the first benchmark aimed explicitly at assessing comprehensive audiovisual integration in such granularity. Experiments with state-of-the-art models, including Qwen 2.5 Omni and Gemini 2.5 Flash-Lite, show performance around 64% accuracy, while human experts reach near-ceiling performance of 92.8%, exposing a substantial gap to human-level comprehension. With standardized evaluation protocols, a rigorously annotated pipeline, and a public toolkit, MAVERIX establishes a challenging testbed for advancing audiovisual multimodal intelligence.

cs.MM↗

arXiv2025

JudgeBoard: Benchmarking and Enhancing Small Language Models for Reasoning Evaluation

While small language models (SLMs) have shown promise on various reasoning tasks, their ability to judge the correctness of answers remains unclear compared to large language models (LLMs). Prior work on LLM-as-a-judge frameworks typically relies on comparing candidate answers against ground-truth labels or other candidate answers using predefined metrics like entailment. However, this approach is inherently indirect and difficult to fully automate, offering limited support for fine-grained and scalable evaluation of reasoning outputs. In this work, we propose JudgeBoard, a novel evaluation pipeline that directly queries models to assess the correctness of candidate answers without requiring extra answer comparisons. We focus on two core reasoning domains: mathematical reasoning and science/commonsense reasoning, and construct task-specific evaluation leaderboards using both accuracy-based ranking and an Elo-based rating system across five benchmark datasets, enabling consistent model comparison as judges rather than comparators. To improve judgment performance in lightweight models, we propose MAJ (Multi-Agent Judging), a novel multi-agent evaluation framework that leverages multiple interacting SLMs with distinct reasoning profiles to approximate LLM-level judgment accuracy through collaborative deliberation. Experimental results reveal a significant performance gap between SLMs and LLMs in isolated judging tasks. However, our MAJ framework substantially improves the reliability and consistency of SLMs. On the MATH dataset, MAJ using smaller-sized models as backbones performs comparatively well or even better than their larger-sized counterparts. Our findings highlight that multi-agent SLM systems can potentially match or exceed LLM performance in judgment tasks, with implications for scalable and efficient assessment.

cs.AI↗

arXiv2025

VMDT: Decoding the Trustworthiness of Video Foundation Models

As foundation models become more sophisticated, ensuring their trustworthiness becomes increasingly critical; yet, unlike text and image, the video modality still lacks comprehensive trustworthiness benchmarks. We introduce VMDT (Video-Modal DecodingTrust), the first unified platform for evaluating text-to-video (T2V) and video-to-text (V2T) models across five key trustworthiness dimensions: safety, hallucination, fairness, privacy, and adversarial robustness. Through our extensive evaluation of 7 T2V models and 19 V2T models using VMDT, we uncover several significant insights. For instance, all open-source T2V models evaluated fail to recognize harmful queries and often generate harmful videos, while exhibiting higher levels of unfairness compared to image modality models. In V2T models, unfairness and privacy risks rise with scale, whereas hallucination and adversarial robustness improve -- though overall performance remains low. Uniquely, safety shows no correlation with model size, implying that factors other than scale govern current safety levels. Our findings highlight the urgent need for developing more robust and trustworthy video foundation models, and VMDT provides a systematic framework for measuring and tracking progress toward this goal. The code is available at https://sunblaze-ucb.github.io/VMDT-page/.

cs.CV↗

arXiv2025

RARE: Retrieval-Aware Robustness Evaluation for Retrieval-Augmented Generation Systems

Retrieval-Augmented Generation (RAG) enhances recency and factuality in answers. However, existing evaluations rarely test how well these systems cope with real-world noise, conflicting between internal and external retrieved contexts, or fast-changing facts. We introduce Retrieval-Aware Robustness Evaluation (RARE), a unified framework and large-scale benchmark that jointly stress-tests query and document perturbations over dynamic, time-sensitive corpora. One of the central features of RARE is a knowledge-graph-driven synthesis pipeline (RARE-Get) that automatically extracts single and multi-hop relations from the customized corpus and generates multi-level question sets without manual intervention. Leveraging this pipeline, we construct a dataset (RARE-Set) spanning 527 expert-level time-sensitive finance, economics, and policy documents and 48295 questions whose distribution evolves as the underlying sources change. To quantify resilience, we formalize retrieval-conditioned robustness metrics (RARE-Met) that capture a model's ability to remain correct or recover when queries, documents, or real-world retrieval results are systematically altered. Our findings reveal that RAG systems are unexpectedly sensitive to perturbations. Moreover, they consistently demonstrate lower robustness on multi-hop queries compared to single-hop queries across all domains.

cs.CL↗

arXiv2025

OPTAGENT: Optimizing Multi-Agent LLM Interactions Through Verbal Reinforcement Learning for Enhanced Reasoning

Large Language Models (LLMs) have shown remarkable reasoning capabilities in mathematical and scientific tasks. To enhance complex reasoning, multi-agent systems have been proposed to harness the collective intelligence of LLM agents. However, existing collaboration structures are either predefined or rely on majority voting or round-table debates, which can suppress correct but less dominant agent contributions. Recent approaches model multi-agent systems as graph networks but optimize purely for agent performance, neglecting the quality of interactions. We hypothesize that effective agent communication is crucial for multi-agent reasoning and that debating quality plays a significant role. To address this, we propose $\ours$, a multi-agent verbal reinforcement learning algorithm that dynamically constructs and refines multi-agent collaboration structures. Our method defines action spaces and a feedback mechanism that evaluates communication robustness and coherence throughout the debate. The final decision is achieved through a majority vote over all the agents. We assess $\ours$ on various reasoning tasks, including mathematical reasoning, creative writing, scientific reasoning, and numerical sorting. Results demonstrate that our approach significantly outperforms single-agent prompting methods and state-of-the-art multi-agent frameworks on diverse tasks.

cs.AI↗

arXiv2025

Mind2Web 2: Evaluating Agentic Search with Agent-as-a-Judge

Agentic search such as Deep Research systems-where agents autonomously browse the web, synthesize information, and return comprehensive citation-backed answers-represents a major shift in how users interact with web-scale information. While promising greater efficiency and cognitive offloading, the growing complexity and open-endedness of agentic search have outpaced existing evaluation benchmarks and methodologies, which largely assume short search horizons and static answers. In this paper, we introduce Mind2Web 2, a benchmark of 130 realistic, high-quality, and long-horizon tasks that require real-time web browsing and extensive information synthesis, constructed with over 1000 hours of human labor. To address the challenge of evaluating time-varying and complex answers, we propose a novel Agent-as-a-Judge framework. Our method constructs task-specific judge agents based on a tree-structured rubric design to automatically assess both answer correctness and source attribution. We conduct a comprehensive evaluation of ten frontier agentic search systems and human performance, along with a detailed error analysis to draw insights for future development. The best-performing system, OpenAI Deep Research, can already achieve 50-70% of human performance while spending half the time, highlighting its great potential. Altogether, Mind2Web 2 provides a rigorous foundation for developing and benchmarking the next generation of agentic search systems.

cs.AI↗

arXiv2025

Certifying Counterfactual Bias in LLMs

Large Language Models (LLMs) can produce biased responses that can cause representational harms. However, conventional studies are insufficient to thoroughly evaluate biases across LLM responses for different demographic groups (a.k.a. counterfactual bias), as they do not scale to large number of inputs and do not provide guarantees. Therefore, we propose the first framework, LLMCert-B that certifies LLMs for counterfactual bias on distributions of prompts. A certificate consists of high-confidence bounds on the probability of unbiased LLM responses for any set of counterfactual prompts - prompts differing by demographic groups, sampled from a distribution. We illustrate counterfactual bias certification for distributions of counterfactual prompts created by applying prefixes sampled from prefix distributions, to a given set of prompts. We consider prefix distributions consisting random token sequences, mixtures of manual jailbreaks, and perturbations of jailbreaks in LLM's embedding space. We generate non-trivial certificates for SOTA LLMs, exposing their vulnerabilities over distributions of prompts generated from computationally inexpensive prefix distributions.

cs.AI↗

arXiv2024

Partial Federated Learning

Federated Learning (FL) is a popular algorithm to train machine learning models on user data constrained to edge devices (for example, mobile phones) due to privacy concerns. Typically, FL is trained with the assumption that no part of the user data can be egressed from the edge. However, in many production settings, specific data-modalities/meta-data are limited to be on device while others are not. For example, in commercial SLU systems, it is typically desired to prevent transmission of biometric signals (such as audio recordings of the input prompt) to the cloud, but egress of locally (i.e. on the edge device) transcribed text to the cloud may be possible. In this work, we propose a new algorithm called Partial Federated Learning (PartialFL), where a machine learning model is trained using data where a subset of data modalities or their intermediate representations can be made available to the server. We further restrict our model training by preventing the egress of data labels to the cloud for better privacy, and instead use a contrastive learning based model objective. We evaluate our approach on two different multi-modal datasets and show promising results with our proposed approach.

cs.LG↗

arXiv2022

Reasoning Like Program Executors

Reasoning over natural language is a long-standing goal for the research community. However, studies have shown that existing language models are inadequate in reasoning. To address the issue, we present POET, a novel reasoning pre-training paradigm. Through pre-training language models with programs and their execution results, POET empowers language models to harvest the reasoning knowledge possessed by program executors via a data-driven approach. POET is conceptually simple and can be instantiated by different kinds of program executors. In this paper, we showcase two simple instances POET-Math and POET-Logic, in addition to a complex instance, POET-SQL. Experimental results on six benchmarks demonstrate that POET can significantly boost model performance in natural language reasoning, such as numerical reasoning, logical reasoning, and multi-hop reasoning. POET opens a new gate on reasoning-enhancement pre-training, and we hope our analysis would shed light on the future research of reasoning like program executors.

cs.CL↗

arXiv2022

TAPEX: Table Pre-training via Learning a Neural SQL Executor

Recent progress in language model pre-training has achieved a great success via leveraging large-scale unstructured textual data. However, it is still a challenge to apply pre-training on structured tabular data due to the absence of large-scale high-quality tabular data. In this paper, we propose TAPEX to show that table pre-training can be achieved by learning a neural SQL executor over a synthetic corpus, which is obtained by automatically synthesizing executable SQL queries and their execution outputs. TAPEX addresses the data scarcity challenge via guiding the language model to mimic a SQL executor on the diverse, large-scale and high-quality synthetic corpus. We evaluate TAPEX on four benchmark datasets. Experimental results demonstrate that TAPEX outperforms previous table pre-training approaches by a large margin and achieves new state-of-the-art results on all of them. This includes the improvements on the weakly-supervised WikiSQL denotation accuracy to 89.5% (+2.3%), the WikiTableQuestions denotation accuracy to 57.5% (+4.8%), the SQA denotation accuracy to 74.5% (+3.5%), and the TabFact accuracy to 84.2% (+3.2%). To our knowledge, this is the first work to exploit table pre-training via synthetic executable programs and to achieve new state-of-the-art results on various downstream tasks. Our code can be found at https://github.com/microsoft/Table-Pretraining.

cs.CL↗

arXiv2020

Example-Based Named Entity Recognition

We present a novel approach to named entity recognition (NER) in the presence of scarce data that we call example-based NER. Our train-free few-shot learning approach takes inspiration from question-answering to identify entity spans in a new and unseen domain. In comparison with the current state-of-the-art, the proposed method performs significantly better, especially when using a low number of support examples.

cs.CL↗

arXiv2020

MT-BioNER: Multi-task Learning for Biomedical Named Entity Recognition using Deep Bidirectional Transformers

Conversational agents such as Cortana, Alexa and Siri are continuously working on increasing their capabilities by adding new domains. The support of a new domain includes the design and development of a number of NLU components for domain classification, intents classification and slots tagging (including named entity recognition). Each component only performs well when trained on a large amount of labeled data. Second, these components are deployed on limited-memory devices which requires some model compression. Third, for some domains such as the health domain, it is hard to find a single training data set that covers all the required slot types. To overcome these mentioned problems, we present a multi-task transformer-based neural architecture for slot tagging. We consider the training of a slot tagger using multiple data sets covering different slot types as a multi-task learning problem. The experimental results on the biomedical domain have shown that the proposed approach outperforms the previous state-of-the-art systems for slot tagging on the different benchmark biomedical datasets in terms of (time and memory) efficiency and effectiveness. The output slot tagger can be used by the conversational agent to better identify entities in the input utterances.

cs.CL↗

arXiv2016

Spatial Phase and Amplitude Structuring of Beams Using a Combination of Multiple Orthogonal Spatial Functions with Complex Coefficients

Analogous to time signals that can be composed of multiple frequency functions, we use uniquely structured orthogonal spatial modes to create different beam shapes. We tailor the spatial structure by judiciously choosing a weighted combination of multiple modal states within an orthogonal basis set, and we can tunably create beam phase and intensity "shapes" that are not otherwise readily achievable. As an example shape, we use a series of orbital-angular-momentum (OAM) functions with adjustable complex weights to create a reconfigurable spatial region of higher localized power as compared to traditional beam combining. We simulate a structured beam created by coherently combining several orthogonal OAM beams with different complex weights, and we achieve a >10X localized power density enhancement with 19 beams. Additionally, we can create unique shapes by passing a single beam through a specially designed phase and intensity mask that contains the combination of multiple OAM functions each with complex weights. Using this approach, we experimentally demonstrate a ~2.5X localized power density increase when utilizing 9 functions.

physics.optics↗