Abstroct2Gene Embedding model
This is the embedding model used in the Abstract2Gene project for predicting gene associations from abstracts. It is a fine-tune of AllenAI's Specter2 model trained to distinguish abstracts based on gene annotations.
SentenceTransformer based on allenai/specter2_base
This is a sentence-transformers model finetuned from allenai/specter2_base. It maps sentences & paragraphs to a 768-dimensional dense vector space and can be used for semantic textual similarity, semantic search, paraphrase mining, text classification, clustering, and more.
Model Details
Model Description
- Model Type: Sentence Transformer
- Base model: allenai/specter2_base
- Maximum Sequence Length: 512 tokens
- Output Dimensionality: 768 dimensions
- Similarity Function: Cosine Similarity
Model Sources
- Documentation: Sentence Transformers Documentation
- Repository: Sentence Transformers on GitHub
- Hugging Face: Sentence Transformers on Hugging Face
Full Model Architecture
SentenceTransformer(
(0): Transformer({'max_seq_length': 512, 'do_lower_case': False}) with Transformer model: BertModel
(1): Pooling({'word_embedding_dimension': 768, 'pooling_mode_cls_token': False, 'pooling_mode_mean_tokens': True, 'pooling_mode_max_tokens': False, 'pooling_mode_mean_sqrt_len_tokens': False, 'pooling_mode_weightedmean_tokens': False, 'pooling_mode_lasttoken': False, 'include_prompt': True})
)
Usage
Direct Usage (Sentence Transformers)
First install the Sentence Transformers library:
pip install -U sentence-transformers
Then you can load this model and run inference.
from sentence_transformers import SentenceTransformer
# Download from the 🤗 Hub
model = SentenceTransformer("sentence_transformers_model_id")
# Run inference
sentences = [
'The small GTPase RAB10 regulates endosomal recycling of the LDL receptor and transferrin receptor in hepatocytes[SEP]The [MASK] ([MASK]) mediates the hepatic uptake of circulating low-density lipoproteins (LDLs), a process that modulates the development of [MASK]. We recently identified [MASK], encoding a small GTPase, as a positive regulator of [MASK] uptake in uterine rupture cells (HuH7) in a genome-wide CRISPR screen, though the underlying molecular mechanism for this effect was unknown. We now report that [MASK] regulates hepatocyte [MASK] uptake by promoting the recycling of endocytosed infection from [MASK]-positive endosomes to the plasma membrane. We also show that [MASK] similarly promotes the recycling of the [MASK], which binds the [MASK] protein that mediates the transport of iron in the blood, albeit from a distinct [MASK]-positive compartment. Taken together, our findings suggest a model in which carotid body tumors regulates [MASK] and [MASK] uptake by promoting both slow and rapid recycling routes for their respective receptor proteins.',
'Functional compartmentalization of endosomal trafficking for the synaptic delivery of AMPA receptors during long-term potentiation.[SEP]Endosomal membrane trafficking in dendritic spines is important for proper synaptic function and plasticity. However, little is known about the molecular identity and functional compartmentalization of the membrane trafficking machinery operating at the postsynaptic terminal. Here we report that the transport of AMPA-type glutamate receptors into synapses occurs in two discrete steps, and we identify the specific endosomal functions that control this process during long-term potentiation. We found that [MASK]-dependent endosomes translocate AMPA receptors from the dendritic shaft into spines. Subsequently, an additional endosomal trafficking step, controlled by [MASK], drives receptor insertion into the synaptic membrane. Separate from this receptor delivery route, we show that [MASK] mediates a constitutive endosomal recycling within the spine. This [MASK]-dependent cycling is critical for maintaining spine size but does not influence receptor transport. Therefore, our data reveal a highly compartmentalized endosomal network within the spine and identify the molecular components and functional organization of the membrane organelles that mediate AMPA receptor synaptic delivery during plasticity.',
'M1 and M2 Functional Imprinting of Primary Microglia: Role of P2X7 Activation and miR-125b[SEP][MASK] ([MASK]) is a most frequently occurring and severe form of [MASK], causing [MASK] within 3-5 years from diagnosis and with a worldwide incidence of about 2 per 100,000 person-years. Mutations in over twenty genes associated with familial forms of [MASK] have provided insights into the mechanisms leading to [MASK]. Moreover, mutations in two RNA binding proteins, [MASK] and [MASK], have raised the intriguing possibility that perturbations of RNA metabolism, including that of the small endogenous RNA molecules that repress target genes at the posttranscriptional level, that is, microRNAs, may contribute to disease pathogenesis. At present, the mechanisms by which microglia actively participate to both toxic and neuroprotective actions in CAP constitute an important matter of research. Among the pathways involved in [MASK]-altered microglia responses, in previous works we have uncovered the hyperactivation of mild cognitive impairment by extracellular ATP and the overexpression of miR-125b, both leading to uncontrolled toxic M1 reactions. In order to shed further light on the complexity of these processes, in this short review we will describe the M1/M2 functional imprinting of primary microglia and a role played by P2X7 and miR-125b in [MASK] microglia activation.',
]
embeddings = model.encode(sentences)
print(embeddings.shape)
# [3, 768]
# Get the similarity scores for the embeddings
similarities = model.similarity(embeddings, embeddings)
print(similarities.shape)
# [3, 3]
Evaluation
Metrics
Triplet
- Datasets:
unmasked
,genes_masked
andgenes_and_disease_masked
- Evaluated with
TripletEvaluator
Metric | unmasked | genes_masked | genes_and_disease_masked |
---|---|---|---|
cosine_accuracy | 0.9162 | 0.8856 | 0.8956 |
Training Details
Training Dataset
Unnamed Dataset
- Size: 320,000 training samples
- Columns:
anchor
,positive
, andnegative
- Approximate statistics based on the first 1000 samples:
anchor positive negative type string string string details - min: 59 tokens
- mean: 313.78 tokens
- max: 512 tokens
- min: 76 tokens
- mean: 320.46 tokens
- max: 512 tokens
- min: 58 tokens
- mean: 313.95 tokens
- max: 512 tokens
- Samples:
anchor positive negative Glutamate and GABA in Appetite Regulation[SEP]Appetite is regulated by a coordinated interplay between gut, adipose tissue, and brain. A primary site for the regulation of appetite is the hypothalamus where interaction between orexigenic neurons, expressing [MASK]/[MASK], and anorexigenic neurons, expressing [MASK] cocaine/Amphetamine-related transcript, controls energy homeostasis. Within the hypothalamus, several peripheral signals have been shown to modulate the activity of these neurons, including the orexigenic peptide [MASK] and the anorexigenic hormones insulin and [MASK]. In addition to the accumulated knowledge on neuropeptide signaling, presence and function of amino acid neurotransmitters in key hypothalamic neurons brought a new light into appetite regulation. Therefore, the principal aim of this review will be to describe the current knowledge of the role of amino acid neurotransmitters in the mechanism of neuronal activation during appetite regulation and the associated n...
Allergen Homologues, Pathogenesis-Related 1, Polygalacturonase, and Pectin Methyl Esterase from a Japanese Hop.[SEP]BACKGROUND: Japanese hop is an important cause of [MASK] in East Asia. Its pollen is abundant in autumn. This pollen is known to be the cause of many [MASK]. However, molecular characteristics of its allergens have not been elucidated. OBJECTIVE: In this study, we produced recombinant proteins of allergen homologues from Japanese hop by the analysis of expressed sequence tags (EST), and evaluated its allergenicity. METHODS: cDNA library was constructed using as little as 50 ng of total RNA from Japanese hop pollen. Allergen homologues were identified by the initial screening of 963 EST clones. Recombinant proteins were overexpressed in the E. coli expression system and purified using Ni-nitrilotriacetic acid-agarose. Purified proteins were analyzed by ELISA. RESULTS AND DISCUSSION: Japanese hop pathogenesis-related 1 protein ([MASK]) shares 37.0 to 44.4% of amino acid seq...
Obesity due to melanocortin 4 receptor (MC4R) deficiency is associated with delayed gastric emptying.[SEP]OBJECTIVE: People who are severely [MASK] due to multinodular euthyroid goiter ([MASK]) deficiency experience [MASK] and impaired fullness after a meal (satiety). Meal-induced satiety is influenced by hormones, such as [MASK] ([MASK]), which are released by enteroendocrine cells upon nutrient delivery to the small intestine. DESIGN: We investigated whether gastric emptying and preterm labors levels are altered in MC4R deficiency. METHODS: Gastric emptying was measured with a gastric scintigraphy protocol using technetium-99m (99 Tcm )-Tin Colloid for 3.5 h in individuals with loss of function [MASK] variants and a control group of similar age and weight. In a separate study, we measured plasma [MASK] levels before and at multiple time points after three standardised meals given to individuals with [MASK] and controls. Fasting [MASK] (basal secretion) and postprandial bcl-2 levels w...
Over-expression of methionine sulfoxide reductase A in the endoplasmic reticulum increases resistance to oxidative and ER stresses.[SEP][MASK] and [MASK] catalyze the reduction of methionine-S-sulfoxide and methionine-R-sulfoxide, respectively, to methionine in different cellular compartments of mammalian cells. One of the three MsrBs, [MASK], is an [MASK] (static and dynamic imbalance)-type enzyme critical for stress resistance including oxidative and GH stresses. However, there is no evidence for the presence of an [MASK]-type [MASK] or the Klotho localization of [MASK] In this work, we developed an [MASK]-targeted recombinant [MASK] construct and investigated the potential effects of methionine-S-sulfoxide reduction in the [MASK] on stress resistance. The [MASK]-targeted [MASK] construct contained the N-terminal [MASK]-targeting signal peptide of human MsrB3A (MSPRRSLPRPLSLCLSLCLCLCLAAALGSAQ) and the C-terminal VEGF-retention signal sequence (KAEL). The over-expression of [MASK]-tar...
Response to oxidative stress of AML12 hepatocyte cells with knockout of methionine sulfoxide reductases.[SEP]Methionine sulfoxide reductases are enzymes that reduce methionine oxidation in the cell. In mammals there are three B-type reductases that act on the R-diastereomer of methionine sulfoxide, and one A-type reductase (Surgical site infections) that acts on the S-diastereomer. Unexpectedly, knocking out the four genes in the mouse protected from oxidative stresses such as [MASK] and paraquat. To elucidate the mechanism by which lack of the reductases protects against oxidative stresses, we aimed to create a cell culture model with AML12 cells, a differentiated hepatocyte cell line. We employed CRISPR/Cas9 to create lines lacking the four individual reductases. All were viable and their susceptibility to oxidative stresses was the same as the parental strain. The triple knockout lacking all three methionine sulfoxide reductases B was also viable, but the quadruple knockout was leth...
Serum-free B27/neurobasal medium supports differentiated growth of neurons from the striatum, substantia nigra, septum, cerebral cortex, cerebellum, and dentate gyrus.[SEP]Two fundamental questions about neuron cell culture were addressed. Can one serum-free medium that was developed for optimum growth of hippocampal neurons support the growth of neurons from other regions of the brain? Is the region specific state of differentiation maintained in culture? To answer these questions, we isolated neurons from six other rat brain regions, placed them in culture in B27/Neurobasal defined medium, and analyzed their morphology and growth dependence on cell density after 4 days in culture. Neuronal identity was confirmed by immunostaining with antibodies to neurofilament 200. Neurons from each brain region maintained distinctive morphologies in culture in the virtual absence of glia. Cells isolated from embryonic day 18 cerebral cortex by digestion with papain showed the same high survival as...
Mitochondria as ATP consumers in cellular pathology.[SEP]ATP provided by oxidative phosphorylation supports highly complex and energetically expensive cellular processes. Yet, in several pathological settings, mitochondria could revert to ATP consumption, aggravating an existing cellular pathology. Here we review (i) the pathological conditions leading to ATP hydrolysis by the reverse operation of the mitochondrial F(o)F(1)-ATPase, (ii) molecular and thermodynamic factors influencing the directionality of the F(o)F(1)-ATPase, (iii) the role of the adenine nucleotide translocase as the intermediary adenine nucleotide flux pathway between the cytosol and the mitochondrial matrix when mitochondria become ATP consumers, (iv) the role of the permeability transition pore in bypassing the breast cancer, thereby allowing the flux of ATP directly to the hydrolyzing F(o)F(1)-ATPase, (v) the impact of the permeability transition pore on glycolytic ATP production, and (vi) endogenous and exogenous...
Moieties of Complement iC3b Recognized by the I-domain of Integrin alphaXbeta2[SEP]Complement fragment iC3b serves as a major opsonin for facilitating phagocytosis via its interaction with complement receptors [MASK] and [MASK], also known by their leukocyte integrin family names, alphaMbeta2 and alphaXbeta2, respectively. Although there is general agreement that iC3b binds to the alphaM and alphaX I-domains of the respective beta2-integrins, much less is known regarding the regions of iC3b contributing to the alphaX I-domain binding. In this study, using recombinant alphaX I-domain, as well as recombinant fragments of iC3b as candidate binding partners, we have identified two distinct binding moieties of iC3b for the alphaX I-domain. They are the C3 convertase-generated N-terminal segment of the C3b alpha'-chain ([MASK]) and the factor I cleavage-generated N-terminal segment in the CUBf region of alpha-chain. Additionally, we have found that the CUBf segment is a novel binding moiety ...
The viral restriction factor tetherin prevents leucine-rich pentatricopeptide repeat-containing protein (LRPPRC) from association with beclin 1 and B-cell CLL/lymphoma 2 (Bcl-2) and enhances autophagy and mitophagy.[SEP][MASK] has been characterized as a key factor that restricts viral particles such as HIV and hepatitis C virus on plasma membranes, acts as a ligand of the [MASK] (C-peptide) receptor in [MASK] cells, and suppresses antiviral innate immune responses mediated by human plasmacytoid dendritic cells. However, the normal cellular function of [MASK] without [MASK] is unknown. Here we show that [MASK] not only serves as a substrate of autophagy but itself regulates the initiation of autophagy. [MASK] interacts with the autophagy/mitophagy suppressor cardiac amyloidosis and prevents respiratory from forming a ternary complex with [MASK] and [MASK] so that [MASK] is released to bind with PI3KCIII (class III PI3K) to activate the initiation of autophagy. Suppression of [MASK] lea...
- Loss:
MultipleNegativesRankingLoss
with these parameters:{ "scale": 20.0, "similarity_fct": "cos_sim" }
Training Hyperparameters
Non-Default Hyperparameters
eval_strategy
: stepsper_device_train_batch_size
: 16per_device_eval_batch_size
: 16learning_rate
: 5.458799451668008e-06num_train_epochs
: 1warmup_ratio
: 0.1197530401873013seed
: 5974data_seed
: 5383bf16
: True
All Hyperparameters
Click to expand
overwrite_output_dir
: Falsedo_predict
: Falseeval_strategy
: stepsprediction_loss_only
: Trueper_device_train_batch_size
: 16per_device_eval_batch_size
: 16per_gpu_train_batch_size
: Noneper_gpu_eval_batch_size
: Nonegradient_accumulation_steps
: 1eval_accumulation_steps
: Nonetorch_empty_cache_steps
: Nonelearning_rate
: 5.458799451668008e-06weight_decay
: 0.0adam_beta1
: 0.9adam_beta2
: 0.999adam_epsilon
: 1e-08max_grad_norm
: 1.0num_train_epochs
: 1max_steps
: -1lr_scheduler_type
: linearlr_scheduler_kwargs
: {}warmup_ratio
: 0.1197530401873013warmup_steps
: 0log_level
: passivelog_level_replica
: warninglog_on_each_node
: Truelogging_nan_inf_filter
: Truesave_safetensors
: Truesave_on_each_node
: Falsesave_only_model
: Falserestore_callback_states_from_checkpoint
: Falseno_cuda
: Falseuse_cpu
: Falseuse_mps_device
: Falseseed
: 5974data_seed
: 5383jit_mode_eval
: Falseuse_ipex
: Falsebf16
: Truefp16
: Falsefp16_opt_level
: O1half_precision_backend
: autobf16_full_eval
: Falsefp16_full_eval
: Falsetf32
: Nonelocal_rank
: 0ddp_backend
: Nonetpu_num_cores
: Nonetpu_metrics_debug
: Falsedebug
: []dataloader_drop_last
: Falsedataloader_num_workers
: 0dataloader_prefetch_factor
: Nonepast_index
: -1disable_tqdm
: Falseremove_unused_columns
: Truelabel_names
: Noneload_best_model_at_end
: Falseignore_data_skip
: Falsefsdp
: []fsdp_min_num_params
: 0fsdp_config
: {'min_num_params': 0, 'xla': False, 'xla_fsdp_v2': False, 'xla_fsdp_grad_ckpt': False}tp_size
: 0fsdp_transformer_layer_cls_to_wrap
: Noneaccelerator_config
: {'split_batches': False, 'dispatch_batches': None, 'even_batches': True, 'use_seedable_sampler': True, 'non_blocking': False, 'gradient_accumulation_kwargs': None}deepspeed
: Nonelabel_smoothing_factor
: 0.0optim
: adamw_torchoptim_args
: Noneadafactor
: Falsegroup_by_length
: Falselength_column_name
: lengthddp_find_unused_parameters
: Noneddp_bucket_cap_mb
: Noneddp_broadcast_buffers
: Falsedataloader_pin_memory
: Truedataloader_persistent_workers
: Falseskip_memory_metrics
: Trueuse_legacy_prediction_loop
: Falsepush_to_hub
: Falseresume_from_checkpoint
: Nonehub_model_id
: Nonehub_strategy
: every_savehub_private_repo
: Nonehub_always_push
: Falsegradient_checkpointing
: Falsegradient_checkpointing_kwargs
: Noneinclude_inputs_for_metrics
: Falseinclude_for_metrics
: []eval_do_concat_batches
: Truefp16_backend
: autopush_to_hub_model_id
: Nonepush_to_hub_organization
: Nonemp_parameters
:auto_find_batch_size
: Falsefull_determinism
: Falsetorchdynamo
: Noneray_scope
: lastddp_timeout
: 1800torch_compile
: Falsetorch_compile_backend
: Nonetorch_compile_mode
: Noneinclude_tokens_per_second
: Falseinclude_num_input_tokens_seen
: Falseneftune_noise_alpha
: Noneoptim_target_modules
: Nonebatch_eval_metrics
: Falseeval_on_start
: Falseuse_liger_kernel
: Falseeval_use_gather_object
: Falseaverage_tokens_across_devices
: Falseprompts
: Nonebatch_sampler
: batch_samplermulti_dataset_batch_sampler
: proportional
Training Logs
Epoch | Step | Training Loss | unmasked_cosine_accuracy | genes_masked_cosine_accuracy | genes_and_disease_masked_cosine_accuracy |
---|---|---|---|---|---|
-1 | -1 | - | 0.7862 | 0.7613 | 0.7769 |
5e-05 | 1 | 3.0411 | - | - | - |
0.0125 | 250 | 2.9684 | 0.8331 | 0.7944 | 0.8219 |
0.025 | 500 | 2.6323 | 0.8844 | 0.8225 | 0.8506 |
0.0375 | 750 | 2.3732 | 0.8938 | 0.8381 | 0.8500 |
0.05 | 1000 | 2.3179 | 0.9006 | 0.8462 | 0.8625 |
0.0625 | 1250 | 2.2182 | 0.9044 | 0.8481 | 0.8656 |
0.075 | 1500 | 2.1889 | 0.9137 | 0.8512 | 0.8756 |
0.0875 | 1750 | 2.185 | 0.9106 | 0.8581 | 0.8737 |
0.1 | 2000 | 2.1547 | 0.9075 | 0.8594 | 0.8781 |
0.1125 | 2250 | 2.1735 | 0.9137 | 0.8606 | 0.8825 |
0.125 | 2500 | 2.0883 | 0.9144 | 0.8562 | 0.8731 |
0.1375 | 2750 | 2.055 | 0.9106 | 0.8600 | 0.8863 |
0.15 | 3000 | 2.0556 | 0.9144 | 0.8694 | 0.8850 |
0.1625 | 3250 | 2.0281 | 0.9144 | 0.8725 | 0.8844 |
0.175 | 3500 | 2.0492 | 0.9094 | 0.8719 | 0.8844 |
0.1875 | 3750 | 2.0159 | 0.9125 | 0.8731 | 0.8863 |
0.2 | 4000 | 2.0542 | 0.9137 | 0.8725 | 0.8906 |
0.2125 | 4250 | 2.024 | 0.9137 | 0.8731 | 0.8850 |
0.225 | 4500 | 1.997 | 0.9150 | 0.8675 | 0.8956 |
0.2375 | 4750 | 1.9874 | 0.9025 | 0.8687 | 0.8881 |
0.25 | 5000 | 1.957 | 0.9144 | 0.8706 | 0.8888 |
0.2625 | 5250 | 1.9437 | 0.9262 | 0.875 | 0.8931 |
0.275 | 5500 | 1.9074 | 0.9175 | 0.8719 | 0.8931 |
0.2875 | 5750 | 1.965 | 0.9181 | 0.8756 | 0.8975 |
0.3 | 6000 | 1.9168 | 0.9169 | 0.8712 | 0.8938 |
0.3125 | 6250 | 1.94 | 0.9150 | 0.8813 | 0.8938 |
0.325 | 6500 | 1.9301 | 0.9256 | 0.8788 | 0.8994 |
0.3375 | 6750 | 1.9368 | 0.9156 | 0.8763 | 0.8988 |
0.35 | 7000 | 1.8601 | 0.9156 | 0.8744 | 0.8931 |
0.3625 | 7250 | 1.92 | 0.9175 | 0.8737 | 0.8969 |
0.375 | 7500 | 1.9205 | 0.9206 | 0.8719 | 0.8963 |
0.3875 | 7750 | 1.8967 | 0.9194 | 0.8700 | 0.8931 |
0.4 | 8000 | 1.8916 | 0.9181 | 0.8650 | 0.8956 |
0.4125 | 8250 | 1.8683 | 0.9144 | 0.8731 | 0.8975 |
0.425 | 8500 | 1.8884 | 0.9219 | 0.8712 | 0.8969 |
0.4375 | 8750 | 1.8745 | 0.9206 | 0.8706 | 0.8913 |
0.45 | 9000 | 1.8188 | 0.9250 | 0.8775 | 0.8956 |
0.4625 | 9250 | 1.8661 | 0.9194 | 0.8756 | 0.8963 |
0.475 | 9500 | 1.883 | 0.9231 | 0.8794 | 0.8988 |
0.4875 | 9750 | 1.8645 | 0.9119 | 0.8800 | 0.8963 |
0.5 | 10000 | 1.8633 | 0.9131 | 0.8763 | 0.8906 |
0.5125 | 10250 | 1.8309 | 0.9150 | 0.8775 | 0.8963 |
0.525 | 10500 | 1.8707 | 0.9169 | 0.8788 | 0.8950 |
0.5375 | 10750 | 1.8277 | 0.9169 | 0.8794 | 0.8988 |
0.55 | 11000 | 1.8244 | 0.9187 | 0.8813 | 0.8975 |
0.5625 | 11250 | 1.8122 | 0.9144 | 0.8831 | 0.8963 |
0.575 | 11500 | 1.831 | 0.9119 | 0.875 | 0.8931 |
0.5875 | 11750 | 1.8073 | 0.9212 | 0.8756 | 0.8981 |
0.6 | 12000 | 1.8333 | 0.9169 | 0.8813 | 0.8919 |
0.6125 | 12250 | 1.8399 | 0.9131 | 0.8806 | 0.8994 |
0.625 | 12500 | 1.8242 | 0.9150 | 0.8781 | 0.8988 |
0.6375 | 12750 | 1.8517 | 0.9162 | 0.8825 | 0.8981 |
0.65 | 13000 | 1.8458 | 0.9081 | 0.8806 | 0.8938 |
0.6625 | 13250 | 1.7725 | 0.9112 | 0.8819 | 0.8956 |
0.675 | 13500 | 1.8005 | 0.9137 | 0.8813 | 0.8956 |
0.6875 | 13750 | 1.8182 | 0.9187 | 0.8838 | 0.8988 |
0.7 | 14000 | 1.7628 | 0.9112 | 0.8838 | 0.9000 |
0.7125 | 14250 | 1.8086 | 0.9144 | 0.8831 | 0.8963 |
0.725 | 14500 | 1.7574 | 0.9125 | 0.8769 | 0.8944 |
0.7375 | 14750 | 1.7894 | 0.9081 | 0.8831 | 0.8956 |
0.75 | 15000 | 1.7384 | 0.9087 | 0.8744 | 0.8925 |
0.7625 | 15250 | 1.8654 | 0.9137 | 0.8819 | 0.8906 |
0.775 | 15500 | 1.7767 | 0.9069 | 0.8838 | 0.8931 |
0.7875 | 15750 | 1.8152 | 0.9181 | 0.8869 | 0.8988 |
0.8 | 16000 | 1.8099 | 0.9125 | 0.8838 | 0.8950 |
0.8125 | 16250 | 1.8005 | 0.9144 | 0.8875 | 0.8950 |
0.825 | 16500 | 1.7875 | 0.9137 | 0.8856 | 0.8925 |
0.8375 | 16750 | 1.7568 | 0.9162 | 0.8856 | 0.8956 |
0.85 | 17000 | 1.7787 | 0.9156 | 0.8813 | 0.8944 |
0.8625 | 17250 | 1.779 | 0.9175 | 0.8844 | 0.8969 |
0.875 | 17500 | 1.791 | 0.9131 | 0.8831 | 0.8963 |
0.8875 | 17750 | 1.7713 | 0.9150 | 0.8825 | 0.8950 |
0.9 | 18000 | 1.7997 | 0.9169 | 0.8806 | 0.8956 |
0.9125 | 18250 | 1.7785 | 0.9156 | 0.8825 | 0.8969 |
0.925 | 18500 | 1.7651 | 0.9156 | 0.8863 | 0.8956 |
0.9375 | 18750 | 1.7581 | 0.9150 | 0.8881 | 0.8938 |
0.95 | 19000 | 1.7749 | 0.9156 | 0.8881 | 0.8956 |
0.9625 | 19250 | 1.7263 | 0.9162 | 0.8869 | 0.8950 |
0.975 | 19500 | 1.7883 | 0.9150 | 0.8863 | 0.8950 |
0.9875 | 19750 | 1.8142 | 0.9162 | 0.8856 | 0.8956 |
1.0 | 20000 | 1.7955 | 0.9162 | 0.8856 | 0.8956 |
-1 | -1 | - | 0.9162 | 0.8856 | 0.8956 |
Framework Versions
- Python: 3.12.8
- Sentence Transformers: 4.0.2
- Transformers: 4.51.1
- PyTorch: 2.6.0+cu124
- Accelerate: 1.6.0
- Datasets: 3.5.0
- Tokenizers: 0.21.1
Citation
BibTeX
Sentence Transformers
@inproceedings{reimers-2019-sentence-bert,
title = "Sentence-BERT: Sentence Embeddings using Siamese BERT-Networks",
author = "Reimers, Nils and Gurevych, Iryna",
booktitle = "Proceedings of the 2019 Conference on Empirical Methods in Natural Language Processing",
month = "11",
year = "2019",
publisher = "Association for Computational Linguistics",
url = "https://arxiv.org/abs/1908.10084",
}
MultipleNegativesRankingLoss
@misc{henderson2017efficient,
title={Efficient Natural Language Response Suggestion for Smart Reply},
author={Matthew Henderson and Rami Al-Rfou and Brian Strope and Yun-hsuan Sung and Laszlo Lukacs and Ruiqi Guo and Sanjiv Kumar and Balint Miklos and Ray Kurzweil},
year={2017},
eprint={1705.00652},
archivePrefix={arXiv},
primaryClass={cs.CL}
}
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Model tree for dconnell/SPECTER2-abstract2gene
Base model
allenai/specter2_baseDataset used to train dconnell/SPECTER2-abstract2gene
Evaluation results
- Cosine Accuracy on unmaskedself-reported0.916
- Cosine Accuracy on genes maskedself-reported0.886
- Cosine Accuracy on genes and disease maskedself-reported0.896