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Sadamori Kojaku

Publications and source records attributed to Sadamori Kojaku.

At least 19 recordsLinked to original sources

Multi-agent discussion gains less when dissent is withheld

Multi-agent systems of LLMs add discussion to majority voting and are therefore expected to be more capable. However, empirical reports conflict on whether discussion improves accuracy or leads to an incorrect consensus. Here, we introduce a parsimonious model that explains when discussion improves accuracy and when it ends in an incorrect consensus, built from four behaviors repeatedly observed in LLM agents: (1) withholding dissent, (2) internalizing a stated answer, (3) reconsidering after seeing dissent, and (4) correcting toward the correct answer. The model shows that discussion can overturn an incorrect initial majority only when the withholding rate $c$ is below a critical rate $c^* = γ/(γ+ a)$, set by the net correction rate $γ$ and the internalization rate $a$. We estimate these rates from conversation logs with a Bayesian method and place LLM teams relative to $c^*$. As the model predicts, the gain from discussion shrinks as withholding rises, across LLMs and on a hidden profile benchmark, HiddenBench, and MedEInst. Instructing agents not to withhold dissent increases this gain. Turning reasoning off also increases the gain, because reasoning raises the internalization rate $a$ and keeps agents from reconsidering a minority answer. These findings reconcile the conflicting reports and identify when discussion outperforms majority voting.

physics.soc-ph↗

Doc2LoRA Provides Decodable Representations of Scientific Ideas

Representing scientific papers as points in a space lets us search for similar papers and inquire about how fields relate to one another and drive innovation. Beyond search, the vector space of papers invites generation: mixing papers through simple vector operations creates new points, mirroring combinatorial novelty, the recombination of existing ideas into new ones. However, a mixed point often represents an idea no paper has yet realized, with no papers nearby to identify the idea. We propose representing each paper by a LoRA adapter generated by the Doc-to-LoRA hypernetwork. Every point in the space, including mixtures, thus represents a large language model (LLM) open to questions and instructions in natural language. On papers from the American Physical Society (APS), we instruct the LLM at the average of each subfield to name the field in a few words and obtain labels closer to the official names than the labels of five baselines, as judged by word overlap and a panel of five LLM judges. We also ask the LLMs at points between two APS papers to write an abstract and obtain descriptions shifting from one paper to the other in step with the mixing weight. While Doc-to-LoRA is trained for generation, a small invertible transform makes the embeddings competitive for search, on par with SPECTER2 and EmbeddingGemma and close to SBERT. Because the transform is invertible, every point in the transformed space still maps back to an LLM. The embeddings thus serve both search and generation, enabling researchers to question the idea at any point in the space as a starting point for generating new ideas.

cs.CL↗

Detectability threshold in weighted modular networks

We study the necessary condition to detect, by means of spectral modularity optimization, the ground-truth partition in networks generated according to the weighted planted-partition model with two equally sized communities. We analytically derive a general expression for the maximum level of mixing tolerated by the algorithm to retrieve community structure, showing that the value of this detectability threshold depends on the first two moments of the distributions of node degree and edge weight. We focus on the standard case of Poisson-distributed node degrees and compare the detectability thresholds of five edge-weight distributions: Dirac, Poisson, exponential, geometric, and signed Bernoulli. We show that Dirac distributed weights yield the smallest detectability threshold, while exponentially distributed weights increase the threshold by a factor $\sqrt{2}$, with other distributions exhibiting distinct behaviors that depend, either or both, on the average values of the degree and weight distributions. Our results indicate that larger variability in edge weights can make communities less detectable. In cases where edge weights carry no information about community structure, incorporating weights in community detection is detrimental.

physics.soc-ph↗

Scale invariance and statistical significance in complex weighted networks

Most networks encountered in nature, society, and technology have weighted edges, representing the strength of the interaction/association between their vertices. Randomizing the structure of a network is a classic procedure used to estimate the statistical significance of properties of the network, such as transitivity, centrality and community structure. Randomization of weighted networks has traditionally been done via the weighted configuration model (WCM), a simple extension of the configuration model, where weights are interpreted as bundles of edges. It has previously been shown that the ensemble of randomizations provided by the WCM is affected by the specific scale used to compute the weights, but the consequences for statistical significance were unclear. Here we find that statistical significance based on the WCM is scale-dependent, whereas in most cases results should be independent of the choice of the scale. More generally, we find that designing a null model that does not violate scale invariance is challenging. A two-step approach, originally introduced for network reconstruction, in which one first randomizes the structure, then the weights, with a suitable distribution, restores scale invariance, and allows us to conduct unbiased assessments of significance on weighted networks.

physics.soc-ph↗

Measuring Research Interest Similarity with Transition Probabilities

We introduce a family of paper and author similarity measures based on the concept that papers are more similar if they are more likely to be retrieved during a literature search following backward and forward citations. Since this browsing process resembles a walk in a citation network, we operationalize the concept using the transition probability (TP) of random walkers. The proposed measures are continuous, symmetric, and can be implemented on any citation network. We conduct validation tests of the TP concept and other extant alternatives to gauge which metric can classify papers and predict future co-authors most consistently across different scales of analysis (co-authorships, journals, and disciplines). Our results show that the proposed basic TP measure outperforms alternative metrics such as personalized PageRank and the Node2vec machine-learning technique in classification tasks at various scales. Additionally, we discuss how publication-level data can be leveraged to approximate the research interest similarity of individual scientists. This paper is accompanied by a Python package that implements all the tested metrics.

cs.DL↗

Fast Unbiased Sampling of Networks with Given Expected Degrees and Strengths

The configuration model is a cornerstone of statistical assessment of network structure. While the Chung-Lu model is among the most widely used configuration models, it systematically oversamples edges between large-degree nodes, leading to inaccurate statistical conclusions. Although the maximum entropy principle offers unbiased configuration models, its high computational cost has hindered widespread adoption, making the Chung-Lu model an inaccurate yet persistently practical choice. Here, we propose fast and efficient sampling algorithms for the max-entropy-based models by adapting the Miller-Hagberg algorithm. Evaluation on 103 empirical networks demonstrates 10-1000 times speedup, making theoretically rigorous configuration models practical and contributing to a more accurate understanding of network structure.

cs.SI↗

VizTrust: A Visual Analytics Tool for Capturing User Trust Dynamics in Human-AI Communication

Trust plays a fundamental role in shaping the willingness of users to engage and collaborate with artificial intelligence (AI) systems. Yet, measuring user trust remains challenging due to its complex and dynamic nature. While traditional survey methods provide trust levels for long conversations, they fail to capture its dynamic evolution during ongoing interactions. Here, we present VizTrust, which addresses this challenge by introducing a real-time visual analytics tool that leverages a multi-agent collaboration system to capture and analyze user trust dynamics in human-agent communication. Built on established human-computer trust scales-competence, integrity, benevolence, and predictability-, VizTrust enables stakeholders to observe trust formation as it happens, identify patterns in trust development, and pinpoint specific interaction elements that influence trust. Our tool offers actionable insights into human-agent trust formation and evolution in real time through a dashboard, supporting the design of adaptive conversational agents that responds effectively to user trust signals.

cs.HC↗

Uncovering simultaneous breakthroughs with a robust measure of disruptiveness

Progress in science and technology is punctuated by disruptive innovation and breakthroughs. Researchers have characterized these disruptions to explore the factors that spark such innovations and to assess their long-term trends. However, although understanding disruptive breakthroughs and their drivers hinges upon accurately quantifying disruptiveness, the core metric used in previous studies -- the disruption index -- remains insufficiently understood and tested. Here, after demonstrating the critical shortcomings of the disruption index, including its conflicting evaluations for simultaneous discoveries, we propose a new, continuous measure of disruptiveness based on a neural embedding framework that addresses these limitations. Our measure not only better distinguishes disruptive works, such as Nobel Prize-winning papers, from others, but also reveals simultaneous disruptions by allowing us to identify the "twins" that have the most similar future context. By offering a more robust and precise lens for identifying disruptive innovations and simultaneous discoveries, our study provides a foundation for deepening insights into the mechanisms driving scientific breakthroughs while establishing a more equitable basis for evaluating transformative contributions.

cs.SI↗

Representing the Disciplinary Structure of Physics: A Comparative Evaluation of Graph and Text Embedding Methods

Recent advances in machine learning offer new ways to represent and study scholarly works and the space of knowledge. Graph and text embeddings provide a convenient vector representation of scholarly works based on citations and text. Yet, it is unclear whether their representations are consistent or provide different views of the structure of science. Here, we compare graph and text embedding by testing their ability to capture the hierarchical structure of the Physics and Astronomy Classification Scheme (PACS) of papers published by the American Physical Society (APS). We also provide a qualitative comparison of the overall structure of the graph and text embeddings for reference. We find that neural network-based methods outperform traditional methods and graph embedding methods such as node2vec are better than other methods at capturing the PACS structure. Our results call for further investigations into how different contexts of scientific papers are captured by different methods, and how we can combine and leverage such information in an interpretable manner.

cs.SI↗

Community-centric modeling of citation dynamics explains collective citation patterns in science, law, and patents

Many human knowledge systems, such as science, law, and invention, are built on documents and the citations that link them. Citations, while serving multiple purposes, primarily function as a way to explicitly document the use of prior work and thus have become central to the study of knowledge systems. Analyzing citation dynamics has revealed statistical patterns that shed light on knowledge production, recognition, and formalization, and has helped identify key mechanisms driving these patterns. However, most quantitative findings are confined to scientific citations, raising the question of universality of these findings. Moreover, existing models of individual citation trajectories fail to explain phenomena such as delayed recognition, calling for a unifying framework. Here, we analyze a newly available corpus of U.S. case law, in addition to scientific and patent citation networks, to show that they share remarkably similar citation patterns, including a heavy-tailed distribution of sleeping beauties. We propose a holistic model that captures the three core mechanisms driving collective dynamics and replicates the elusive phenomenon of delayed recognition. We demonstrate that the model not only replicates observed citation patterns, but also better predicts future successes by considering the whole system. Our work offers insights into key mechanisms that govern large-scale patterns of collective human knowledge systems and may provide generalizable perspectives on discovery and innovation across domains.

physics.soc-ph↗

Network community detection via neural embeddings

Recent advances in machine learning research have produced powerful neural graph embedding methods, which learn useful, low-dimensional vector representations of network data. These neural methods for graph embedding excel in graph machine learning tasks and are now widely adopted. However, how and why these methods work -- particularly how network structure gets encoded in the embedding -- remain largely unexplained. Here, we show that node2vec -- shallow, linear neural network -- encodes communities into separable clusters better than random partitioning down to the information-theoretic detectability limit for the stochastic block models. We show that this is due to the equivalence between the embedding learned by node2vec and the spectral embedding via the eigenvectors of the symmetric normalized Laplacian matrix. Numerical simulations demonstrate that node2vec is capable of learning communities on sparse graphs generated by the stochastic blockmodel, as well as on sparse degree-heterogeneous networks. Our results highlight the features of graph neural networks that enable them to separate communities in embedding space.

physics.soc-ph↗

Matrix-weighted networks for modeling multidimensional dynamics

Networks are powerful tools for modeling interactions in complex systems. While traditional networks use scalar edge weights, many real-world systems involve multidimensional interactions. For example, in social networks, individuals often have multiple interconnected opinions that can affect different opinions of other individuals, which can be better characterized by matrices. We propose a novel, general framework for modeling such multidimensional interacting dynamics: matrix-weighted networks (MWNs). We present the mathematical foundations of MWNs and examine consensus dynamics and random walks within this context. Our results reveal that the coherence of MWNs gives rise to non-trivial steady states that generalize the notions of communities and structural balance in traditional networks.

cs.SI↗

Implicit degree bias in the link prediction task

Link prediction -- a task of distinguishing actual hidden edges from random unconnected node pairs -- is one of the quintessential tasks in graph machine learning. Despite being widely accepted as a universal benchmark and a downstream task for representation learning, the validity of the link prediction benchmark itself has been rarely questioned. Here, we show that the common edge sampling procedure in the link prediction task has an implicit bias toward high-degree nodes and produces a highly skewed evaluation that favors methods overly dependent on node degree, to the extent that a ``null'' link prediction method based solely on node degree can yield nearly optimal performance. We propose a degree-corrected link prediction task that offers a more reasonable assessment that aligns better with the performance in the recommendation task. Finally, we demonstrate that the degree-corrected benchmark can more effectively train graph machine-learning models by reducing overfitting to node degrees and facilitating the learning of relevant structures in graphs.

cs.SI↗

Iterative embedding and reweighting of complex networks reveals community structure

Graph embeddings learn the structure of networks and represent it in low-dimensional vector spaces. Community structure is one of the features that are recognized and reproduced by embeddings. We show that an iterative procedure, in which a graph is repeatedly embedded and its links are reweighted based on the geometric proximity between the nodes, reinforces intra-community links and weakens inter-community links, making the clusters of the initial network more visible and more easily detectable. The geometric separation between the communities can become so strong that even a very simple parsing of the links may recover the communities as isolated components with surprisingly high precision. Furthermore, when used as a pre-processing step, our embedding and reweighting procedure can improve the performance of traditional community detection algorithms.

physics.soc-ph↗

Unsupervised embedding of trajectories captures the latent structure of scientific migration

Human migration and mobility drives major societal phenomena including epidemics, economies, innovation, and the diffusion of ideas. Although human mobility and migration have been heavily constrained by geographic distance throughout the history, advances and globalization are making other factors such as language and culture increasingly more important. Advances in neural embedding models, originally designed for natural language, provide an opportunity to tame this complexity and open new avenues for the study of migration. Here, we demonstrate the ability of the model word2vec to encode nuanced relationships between discrete locations from migration trajectories, producing an accurate, dense, continuous, and meaningful vector-space representation. The resulting representation provides a functional distance between locations, as well as a digital double that can be distributed, re-used, and itself interrogated to understand the many dimensions of migration. We show that the unique power of word2vec to encode migration patterns stems from its mathematical equivalence with the gravity model of mobility. Focusing on the case of scientific migration, we apply word2vec to a database of three million migration trajectories of scientists derived from the affiliations listed on their publication records. Using techniques that leverage its semantic structure, we demonstrate that embeddings can learn the rich structure that underpins scientific migration, such as cultural, linguistic, and prestige relationships at multiple levels of granularity. Our results provide a theoretical foundation and methodological framework for using neural embeddings to represent and understand migration both within and beyond science.

cs.LG↗

Residual2Vec: Debiasing graph embedding with random graphs

Graph embedding maps a graph into a convenient vector-space representation for graph analysis and machine learning applications. Many graph embedding methods hinge on a sampling of context nodes based on random walks. However, random walks can be a biased sampler due to the structural properties of graphs. Most notably, random walks are biased by the degree of each node, where a node is sampled proportionally to its degree. The implication of such biases has not been clear, particularly in the context of graph representation learning. Here, we investigate the impact of the random walks' bias on graph embedding and propose residual2vec, a general graph embedding method that can debias various structural biases in graphs by using random graphs. We demonstrate that this debiasing not only improves link prediction and clustering performance but also allows us to explicitly model salient structural properties in graph embedding.

cs.LG↗

Detecting anomalous citation groups in journal networks

The ever-increasing competitiveness in the academic publishing market incentivizes journal editors to pursue higher impact factors. This translates into journals becoming more selective, and, ultimately, into higher publication standards. However, the fixation on higher impact factors leads some journals to artificially boost impact factors through the coordinated effort of a "citation cartel" of journals. "Citation cartel" behavior has become increasingly common in recent years, with several instances being reported. Here, we propose an algorithm -- named CIDRE -- to detect anomalous groups of journals that exchange citations at excessively high rates when compared against a null model that accounts for scientific communities and journal size. CIDRE detects more than half of the journals suspended from Journal Citation Reports due to anomalous citation behavior in the year of suspension or in advance. Furthermore, CIDRE detects many new anomalous groups, where the impact factors of the member journals are lifted substantially higher by the citations from other member journals. We describe a number of such examples in detail and discuss the implications of our findings with regard to the current academic climate.

physics.soc-ph↗

The effectiveness of backward contact tracing in networks

Discovering and isolating infected individuals is a cornerstone of epidemic control. Because many infectious diseases spread through close contacts, contact tracing is a key tool for case discovery and control. However, although contact tracing has been performed widely, the mathematical understanding of contact tracing has not been fully established and it has not been clearly understood what determines the efficacy of contact tracing. Here, we reveal that, compared with "forward" tracing---tracing to whom disease spreads, "backward" tracing---tracing from whom disease spreads---is profoundly more effective. The effectiveness of backward tracing is due to simple but overlooked biases arising from the heterogeneity in contacts. Using simulations on both synthetic and high-resolution empirical contact datasets, we show that even at a small probability of detecting infected individuals, strategically executed contact tracing can prevent a significant fraction of further transmissions. We also show that---in terms of the number of prevented transmissions per isolation---case isolation combined with a small amount of contact tracing is more efficient than case isolation alone. By demonstrating that backward contact tracing is highly effective at discovering super-spreading events, we argue that the potential effectiveness of contact tracing has been underestimated. Therefore, there is a critical need for revisiting current contact tracing strategies so that they leverage all forms of biases. Our results also have important consequences for digital contact tracing because it will be crucial to incorporate the capability for backward and deep tracing while adhering to the privacy-preserving requirements of these new platforms.

q-bio.PE↗