standOff, and the article is at its publisher via the link below. When we have changed our mind. Some entries in the table begin with a word in capitals and the reason for it. EVIDENCE CORRECTED — the finding still stands, but we had quoted the wrong sentence from the paper, and the quotation has been replaced with the right one. RETRACTED — the entry itself was wrong; it stays on the page, marked, with the reason, rather than being deleted. WITHDRAWN AND REPLACED — the entry was wrong, and a corrected version of it appears in the entries below. Each mark carries its own reason, in brackets, because the reasons differ from one entry to the next. An entry we have WITHDRAWN is removed from this page and kept in the record, with its reason. A line reading Audit and a date is a later re-reading of the entry against its whole sentence: DOUBTFUL means it was kept, and the reason says what is loose about it. Quotation marks inside the tagger's sentence. Where a tag is the tagger's own sentence, a phrase in quotation marks inside it is borrowed from the paper — the tagger's wording around it is not. The paper's own sentence is the evidence quote for that row; on this page it is withheld with the article, and the article is at its publisher. Nothing inside quotation marks anywhere on this page is ours: if it is quoted, it is the paper's. Whose words a concept carries. A concept entry records a term the paper itself uses, so the term, the sense given for it, and its evidence are the paper's own words, quoted where the paper fixes them. This is the opposite of a sense entry in the tag table, which is the tagger's sentence about how the paper uses a term. Where a concept entry could not be grounded in the paper's words, the entry says so on its own row.| relation to other work | claim_relations | how this paper stands to another: agrees, contradicts, extends, qualifies |
| claim type | claim_type | the shape of the claim: existence, mechanism, method, critique, prediction, null |
| concept edge | concept_edges | an asserted relation between two concepts, with the sentence asserting it |
| concept | concepts | an idea the paper works with, quoted where the paper uses it |
| content tag | content_tags | a finding, definition, quantity, statistic or variable named in the paper |
| contribution | contribution | what the paper claims to add |
| control | controls | an experiment run to eliminate a rival explanation |
| limitation | limitations | what the paper says its evidence cannot support |
| mechanism | mechanisms | how the reported effect is said to come about |
| method | method | how the paper produced its evidence |
| object of study | object_of_study | what the paper is about — the thing it investigates |
| phenomenon | phenomenon | the effect or regularity under study |
| research question | research_question | the question the paper sets itself |
| sense | senses | a distinct use of a term, quoted where the paper fixes it |
| unrecordable relation | unhoused_relations | a relation the paper asserts that this vocabulary cannot express, with the reason |
Relations on this page carry a quotation for the claim. Where a relation was separately evidenced — and so tested against the vocabulary for its type — the row says so; none of 2 relations here carry that mark. The rest are the tagger’s reading of the sentence quoted beside them.
| facet | tag | field | conf. | whose words |
|---|---|---|---|---|
| object_of_study | cells measured two ways at once - transcriptome plus surface protein, or plus chromatin accessibility - and the problem of deciding which measurement to believe Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | object_of_study | the paper's words | |
| research_question | how to combine several simultaneous measurements of one cell into a single definition of its state, without being told in advance which measurement matters Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | research_question | the paper's words | |
| contribution | weighted-nearest-neighbor analysis: a per-cell, unsupervised weight for each modality, plus a 211,000-cell multimodal reference atlas and a way to map new datasets onto it Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | contribution | the paper's words | |
| claim_type | method Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | claim_type | the paper's words | |
| phenomenon | cell states that one measurement type cannot separate and another can - CD4 and CD8 T cells blend in the transcriptome and separate in protein; dendritic cells do the reverse Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | phenomenon | the paper's words | |
| method | system-or-tool-building Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: system-or-tool-building | method | the paper's words | |
| mechanisms | the core move: if a cell's neighbours in one modality predict its measured profile well, that modality is capturing its state; if they predict badly, it is not. The weight is the ratio of those two accuracies Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | mechanisms[0] | 0.95 | the tagger's words |
| mechanisms | why rare cells are not penalised: a fixed neighbour count for the kernel bandwidth would hold common and rare states to the same scale, so the bandwidth is set from the 20 cells with the LOWEST non-zero Jaccard similarity - similar enough to matter, unlikely to be the same state Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: adaptive kernel bandwidth | mechanisms[1] | 0.95 | the tagger's words |
| mechanisms | how a spurious edge is told from a real one - the Jaccard metric counts shared nearest neighbours, so local density separates well-supported links from coincidental similarity Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: shared-neighbour filtering | mechanisms[2] | 0.95 | the tagger's words |
| mechanisms | what the weighting buys: one data type is allowed to make up for another's weakness, cell by cell, so the combined analysis is not limited by whichever measurement happens to be poor for that cell Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: compensation between modalities | mechanisms[3] | 0.9 | the tagger's words |
| limitations | WNN needs a dimensional reduction to describe neighbourhood structure, so it does not work on categorical or low-dimensional data Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | limitations[0] | 0.95 | the tagger's words |
| limitations | IT ASSUMES THE MODALITIES DO NOT DEFINE CONFLICTING SETS OF CELL STATES - and the authors say the assumption may be problematic when integrating morphological, functional and molecular data. An integration method whose premise is that its inputs agree Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | limitations[1] | 0.95 | the tagger's words |
| limitations | the atlas is built from peripheral blood mononuclear cells, so it contains almost no erythrocytes or granulocytes - and any query containing them will have nowhere to map them Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | limitations[2] | 0.95 | the tagger's words |
| limitations | demonstrated on exactly that: neutrophil populations present in a COVID-19 query and absent from the reference could not be mapped Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | limitations[3] | 0.95 | the tagger's words |
| limitations | the enrichment panels achieve high fold-enrichment and still cannot sort a truly homogeneous population - the precision and recall figures are published alongside the enrichment ones Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | limitations[4] | 0.95 | the tagger's words |
| limitations | heterogeneity in monocyte inflammatory genes was left undivided BECAUSE it varied across volunteers - a cluster the authors declined to call a cell state Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | limitations[5] | 0.95 | the tagger's words |
| controls | adding increasing amounts of random Gaussian noise to the protein data, to mimic nonspecific antibody binding, and watching what the learned weights do Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: the modality weights being an artefact of the method rather than a measurement of information content - THE WEIGHTS FELL DOSE-DEPENDENTLY AND REACHED ZERO, which is the behaviour the method claims and could have failed to show · outcome: held | controls[0] | 0.95 | the tagger's words |
| controls | calculating the modality weights with no knowledge of cell-type labels, then checking whether they line up with known biology Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: the weights being read off the answer - CD8 T cells got high protein weights and dendritic cells high RNA weights, and the labels were not available to the calculation · outcome: held | controls[1] | 0.95 | the tagger's words |
| controls | counting incorrect CD8/CD4 edges in each graph as a hard number rather than judging the UMAP pictures Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: a visual impression of better separation standing in for a measurement - 944 wrong edges in RNA, 12 in protein, 20 in the combined graph · outcome: held | controls[2] | 0.95 | the tagger's words |
| controls | varying k from 10 to 50 and re-running the whole procedure Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: the result depending on the neighbourhood size, which is the one free parameter a reader would suspect first · outcome: held | controls[3] | 0.95 | the tagger's words |
| controls | benchmarking against two named alternative methods, totalVI and MOFA+, on a stated metric - how well each integrated space reconstructs a cell's molecular state from its neighbours Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: 'our method is better' resting on the authors' own preferred view of the output; the metric is declared before the comparison and applies equally to all three · outcome: held | controls[4] | 0.95 | the tagger's words |
| controls | HOLDING THE QUERY DATASET'S PROTEIN MEASUREMENTS OUT of the reference mapping, then using them to check the annotations the transcriptome alone produced Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: the mapping being scored on the data it was given - the protein data is a true held-out test, and the predicted cell types carried the protein markers they should · outcome: held | controls[5] | 0.95 | the tagger's words |
| controls | validating a computational prediction on a different instrument - CyTOF on the original samples plus 16 more, against the scRNA-seq-predicted MAIT abundance Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: a depletion that exists only in the pipeline; the correlation between the two methods was 0.911 and the CyTOF cohort reproduced the depletion independently · outcome: held | controls[6] | 0.95 | the tagger's words |
| controls | sorting cells by the predicted marker panels and sequencing them in bulk, using THE EXACT ANTIBODY CLONES from the CITE-seq panel Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. eliminates: a discrepancy between the two assays caused by different antibodies binding different epitopes - the authors name this as the reason for using the same clones · outcome: held | controls[7] | 0.95 | the tagger's words |
| concepts | modality weights Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: modality weights | concepts[0] | 0.95 | the paper's words |
| concepts | modalities Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: modalities | concepts[1] | 0.95 | the paper's words |
| concepts | spurious edges Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: spurious edges | concepts[2] | 0.95 | the paper's words |
| concepts | Jaccard metric Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: Jaccard metric | concepts[3] | 0.95 | the paper's words |
| concepts | cell states Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: cell states | concepts[4] | 0.95 | the paper's words |
| concepts | transcriptome Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: transcriptome | concepts[5] | 0.95 | the paper's words |
| concepts | scRNA-seq Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: scRNA-seq | concepts[6] | 0.95 | the paper's words |
| concepts | CITE-seq Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: CITE-seq | concepts[7] | 0.95 | the paper's words |
| concepts | CyTOF Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: CyTOF | concepts[8] | 0.95 | the paper's words |
| concepts | totalVI Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: totalVI | concepts[9] | 0.95 | the paper's words |
| concepts | sPCA Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: sPCA | concepts[10] | 0.95 | the paper's words |
| concepts | neutrophils Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: neutrophils | concepts[11] | 0.95 | the paper's words |
| unhoused_relations | modality weights → cell states Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. A NUMBER WHOSE MEANING IS UNDECIDED, AND THE PAPER SAYS SO. The weight is a proxy for the technical quality of a measurement AND may reflect the biological importance of that modality to the cell's identity. Those are different claims about different things and the same float carries both. There is no relation type for 'this measure has two candidate interpretations and we cannot separate them' - the nearest available, 'operationalised-as', would pick one and hide the other | unhoused_relations[0] | the tagger's words | |
| unhoused_relations | modalities → cell states Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. AN ASSUMPTION OF NON-CONFLICT, WHICH IS THE METHOD'S PREMISE AND ITS SECOND STATED LIMITATION. 'WNN assumes that…', and the authors flag that the assumption may fail for morphological and functional data. Every one of the eight relation types asserts something HOLDS between two concepts; none can say 'these two are assumed not to disagree, and the method has no behaviour if they do' | unhoused_relations[1] | the tagger's words | |
| senses | modality weight - A PER-CELL NUMBER, NOT A PER-DATASET ONE, AND THE PAPER SAYS IT HAS TWO POSSIBLE MEANINGS. It is a proxy for the TECHNICAL QUALITY of a measurement in that cell, and it `may also reflect the biological importance of each modality in determining cellular identity` - progenitors and differentiated cells came out with divergent weights. The same figure can mean `this instrument worked here` or `this axis is what this cell is`, and nothing in the number distinguishes them Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | senses[0] | 0.95 | the tagger's words |
| senses | weight, as computed here - EARNED BY A PREDICTION TEST, not assigned. Each cell is predicted from its neighbours within each modality and across them, the predictions are compared with the cell's actual measurements, and the RATIO of those accuracies becomes the weight after a softmax. Non-negative, unique to each cell, summing to 1 Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | senses[1] | 0.95 | the tagger's words |
| senses | unsupervised, of this procedure - MEANS UNAWARE OF CELL-TYPE LABELS, AND THAT IS WHAT MAKES THE AGREEMENT EVIDENCE. CD8 T cells got high protein weights and dendritic cells high RNA weights, `despite the fact that the calculation of modality weights was unsupervised and unaware of cell-type labels`. The recapitulation of a known biology is the check, and it only counts because the labels were withheld Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | senses[2] | 0.95 | the tagger's words |
| senses | spurious edge - A LINK BETWEEN CELLS THAT RESEMBLE EACH OTHER WITHOUT BEING IN THE SAME STATE, and the paper counts them rather than describing them: 944 wrong CD8/CD4 edges in the RNA graph, 12 in the protein graph, 20 in the combined one. A quality claim with an integer behind it Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | senses[3] | 0.95 | the tagger's words |
| senses | annotation, in this atlas - THREE NESTED TIERS AND A CELL CARRIES ALL THREE. Level 1 has 8 categories, level 2 has 30, level 3 has 57. A result reported at one tier is not comparable with a result reported at another, and the granularity is a choice the reader has to make rather than one the data settles Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | senses[4] | 0.95 | the tagger's words |
| senses | supervised, in `supervised principal component analysis` - SUPERVISED BY THE WNN GRAPH, NOT BY A HUMAN. sPCA finds the transcriptomic projection that best captures the structure the multimodal analysis already found, so the supervision comes from the other modality rather than from labels. `Supervised` and `unsupervised` are both used in this paper about the same pipeline, meaning different things Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | senses[5] | 0.95 | the tagger's words |
| claim_relations | distinguishes-from → totalVI and MOFA+, two recently introduced multimodal integration methods based on deep neural networks with a hierarchical Bayesian model and on factor analysis respectively Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | claim_relations[0] | 0.95 | the tagger's words |
| claim_relations | distinguishes-from → scArches, a method for mapping single-cell RNA-seq queries onto reference datasets Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | claim_relations[1] | 0.95 | the tagger's words |
| claim_relations | critiques → the practice of defining cell states from the transcriptome alone, which cannot separate functionally distinct T cell populations however sensitive the technology Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | claim_relations[2] | 0.95 | the tagger's words |
| claim_relations | extends → the unsupervised clustering analysis of Wilk et al.'s COVID-19 PBMC dataset, which found six T cell clusters where reference mapping resolved twelve Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. note: and the extension is not one-directional - the same comparison shows what the reference CANNOT do: neutrophils that the original unsupervised analysis found, because they were absent from the reference, could not be mapped at all | claim_relations[3] | 0.9 | the tagger's words |
| claim_relations | builds-on → Barshan et al.'s supervised principal component analysis, applied here with the WNN graph as the supervising structure Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | claim_relations[4] | 0.95 | the tagger's words |
| concept_edges | transcriptome —contrasted-with→ modalities Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. strength of the relation: 0.8 · note: the paper's whole framing: the transcriptome is one modality among several and has been treated as the definition of cell state
Audit 2026-09-28: DOUBTFUL - read against its span and kept, but the span questions defining cell states from the transcriptome alone; contrasted-with 'modalities' is loose. also in: transcriptome · modalities | concept_edges[2] | the tagger's words | |
| concept_edges | CITE-seq —distinct-from→ CyTOF Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. strength of the relation: 0.9 · note: and the distinctness is what makes the agreement worth something - the MAIT depletion was found in one and confirmed in the other at R = 0.911
Audit 2026-09-28: DOUBTFUL - read against its full span and kept, but CITE-seq provides a 'unique opportunity' beside flow cytometry and CyTOF; distinct-from is loose. | concept_edges[3] | the tagger's words | |
| content_tags | per-cell modality weights, learned unsupervised, recover known biology: CD8 T cells weight protein highly, dendritic cells weight RNA highly Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.findings[0] | 0.95 | the tagger's words |
| content_tags | The RNA KNN graph had 944 incorrect CD8+/CD4+ edges, the protein graph 12. Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.findings[1] | 0.95 | the tagger's words |
| content_tags | adding Gaussian noise to the protein data drove protein weights down dose-dependently and to zero, correctly redirecting the analysis to RNA alone Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.findings[2] | 0.95 | the tagger's words |
| content_tags | The final multimodal dataset has 210,911 cells covering resting and post-vaccination immune states. Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.findings[3] | 0.95 | the tagger's words |
| content_tags | MAIT-cell fractions predicted by scRNA-seq agreed with CyTOF measurements at R = 0.911. Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.findings[4] | 0.95 | the tagger's words |
| content_tags | WNN matched or beat alternative approaches in reconstructing each of 25 proteins. Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.findings[5] | 0.95 | the tagger's words |
| content_tags | modality weights = per-cell values reflecting the relative information content of each data type in that cell; non-negative, unique per cell, summing to 1 Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: modality weights | content_tags.definitions[0] | 0.95 | the tagger's words |
| content_tags | the four steps: build a KNN graph per modality, predict within and across modalities, compute per-cell weights, build the WNN graph Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: weighted nearest neighbor analysis | content_tags.definitions[1] | 0.95 | the tagger's words |
| content_tags | spurious edge = a link between cells that share some molecular similarity but are not in a matched molecular state Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: spurious edges | content_tags.definitions[2] | 0.95 | the tagger's words |
| content_tags | sPCA = the transcriptomic projection that maximally captures the structure defined in the WNN graph, rather than the one maximising total variance Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. also in: sPCA | content_tags.definitions[3] | 0.95 | the tagger's words |
| content_tags | the weights come from a softmax over the ratio of within-modality to cross-modality prediction affinities Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.statistics[0] | 0.95 | the tagger's words |
| content_tags | the kernel bandwidth is set from the 20 cells with the LOWEST non-zero Jaccard similarity - similar enough to matter, unlikely to be the same state Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.statistics[1] | 0.95 | the tagger's words |
| content_tags | results held across k from 10 to 50, and the protein information did not cost transcriptomic neighbourhood coherence Quotation withheld — this record is not cleared for redistribution. The sentence is in the paper at the link above. | content_tags.statistics[2] | 0.95 | the tagger's words |
Tags that could not be placed in the text:
What was deliberately not tagged, and why, is recorded per paper by the tagger. Where a paper has no such record, this page says so rather than implying that nothing was declined.